diff --git a/articles/a01_building_base_cohorts.html b/articles/a01_building_base_cohorts.html index 8c059e7a..3b231329 100644 --- a/articles/a01_building_base_cohorts.html +++ b/articles/a01_building_base_cohorts.html @@ -117,7 +117,7 @@

Demographic based cohort creation median_start_age = median(age), max_start_age = max(age)) #> # Source: SQL [1 x 3] -#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1//tmp/RtmpZ6xMJp/file1adf377ea2ce.duckdb] +#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1//tmp/RtmpIHhO79/file1a5632d75182.duckdb] #> min_start_age median_start_age max_start_age #> <int> <dbl> <int> #> 1 17 18 18 @@ -128,7 +128,7 @@

Demographic based cohort creation median_start_age = median(age), max_start_age = max(age)) #> # Source: SQL [1 x 3] -#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1//tmp/RtmpZ6xMJp/file1adf377ea2ce.duckdb] +#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1//tmp/RtmpIHhO79/file1a5632d75182.duckdb] #> min_start_age median_start_age max_start_age #> <int> <dbl> <int> #> 1 31 57 65 diff --git a/index.html b/index.html index 8ce39960..5e4e6a21 100644 --- a/index.html +++ b/index.html @@ -60,48 +60,71 @@

CohortConstructor

-
-

This package is currently experimental. Please use with care and report any issues you might come across.

-
-

The goal of CohortConstructor is to support the creation and manipulation of cohorts in the OMOP Common Data Model.

+

The goal of CohortConstructor is to support the creation and manipulation of study cohorts in data mapped to the OMOP CDM.

Installation

-

You can install the development version of CohortConstructor from GitHub with:

+

The package can be installed from CRAN:

+install.packages("CohortConstructor")
+

Or you can install the development version of CohortConstructor from GitHub:

+
 # install.packages("devtools")
 devtools::install_github("ohdsi/CohortConstructor")

Creating and manipulating cohorts

-

To illustrate how the functionality let’s create a CDM reference for the Eunomia dataset Using the CDMConnector package.

-
-library(CDMConnector)
+
To illustrate how the functionality let’s create a set of fracture cohorts using the Eunomia dataset. We’ll first load required packages and create a cdm reference for the data.

+
+
+con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir())
 cdm <- cdm_from_con(con, cdm_schema = "main", 
                     write_schema = c(prefix = "my_study_", schema = "main"))
-print(cdm)

+cdm
+#> 
+#> ── # OMOP CDM reference (duckdb) of Synthea synthetic health database ──────────
+#> • omop tables: person, observation_period, visit_occurrence, visit_detail,
+#> condition_occurrence, drug_exposure, procedure_occurrence, device_exposure,
+#> measurement, observation, death, note, note_nlp, specimen, fact_relationship,
+#> location, care_site, provider, payer_plan_period, cost, drug_era, dose_era,
+#> condition_era, metadata, cdm_source, concept, vocabulary, domain,
+#> concept_class, concept_relationship, relationship, concept_synonym,
+#> concept_ancestor, source_to_concept_map, drug_strength
+#> • cohort tables: -
+#> • achilles tables: -
+#> • other tables: -
-

Generating concept based cohorts +

Generating concept-based fracture cohorts

-

We start by making a concept based cohort. For this we only need to provide concept sets and we will get a cohort back, with cohort end date the event date associated with the records, overlapping records collapsed, and only records in observation kept.

-
+
We will start by making a simple concept-based cohort for each of our fracture of interest. First we create a codelist for each ankle, forearm and hip fractures (note, we just use one code for each because we are using synthetic data).

+
+fracture_codes <- newCodelist(list("ankle_fracture" = 4059173L,
+                                   "forearm_fracture" = 4278672L,
+                                   "hip_fracture" = 4230399L))
+fracture_codes
+#> 
+#> ── 3 codelists ─────────────────────────────────────────────────────────────────
+#> 
+#> - ankle_fracture (1 codes)
+#> - forearm_fracture (1 codes)
+#> - hip_fracture (1 codes)

+
Now we can quickly create a set of cohorts for each fracture type. For this we only need to provide the codes we have defined and we will get a cohort back, with cohort end date set as the event date associated with the records, overlapping records collapsed, and only records in observation kept.

+
 cdm$fractures <- cdm |> 
-  conceptCohort(conceptSet = list(
-    "ankle_fracture" = 4059173,
-    "forearm_fracture" = 4278672,
-    "hip_fracture" = 4230399),
+  conceptCohort(conceptSet = fracture_codes,
   name = "fractures")

 
We can see that our starting cohorts, before we add any additional restrictions, have the following associated settings, counts, and attrition.

-
+
 settings(cdm$fractures) %>% glimpse()
 #> Rows: 3
 #> Columns: 2
@@ -125,20 +148,64 @@ 
Generating concept based cohorts#> $ excluded_subjects    <int> 0, 0, 0

 

 

+
Create an overall fracture cohort
+

+
So far we have created three separate fracture cohorts. Let’s say we also want a cohort of people with any of the fractures. We could union our three cohorts to create this overall cohort like so:

+
+cdm$any_fracture <- cdm$fractures |> 
+  CohortConstructor::unionCohorts(cohortName = "any_fracture", name = "any_fracture")
+#> Warning: ! 1 casted column in any_fracture (cohort_set) as do not match expected column
+#>   type:
+#> • `cohort_definition_id` from numeric to integer
+#> Warning: ! 6 casted column in any_fracture (cohort_attrition) as do not match expected
+#>   column type:
+#> • `cohort_definition_id` from numeric to integer
+#> • `number_records` from numeric to integer
+#> • `number_subjects` from numeric to integer
+#> • `reason_id` from numeric to integer
+#> • `excluded_records` from numeric to integer
+#> • `excluded_subjects` from numeric to integer
+#> Warning: ! 1 casted column in any_fracture (cohort_codelist) as do not match expected
+#>   column type:
+#> • `cohort_definition_id` from numeric to integer
+#> Warning: ! 1 column in any_fracture do not match expected column type:
+#> • `cohort_definition_id` is numeric but expected integer
+cdm <- bind(cdm$fractures,
+            cdm$any_fracture, 
+            name = "fractures")

+
+settings(cdm$fractures)
+#> # A tibble: 4 × 3
+#>   cohort_definition_id cohort_name        gap
+#>                  <int> <chr>            <dbl>
+#> 1                    1 ankle_fracture      NA
+#> 2                    2 forearm_fracture    NA
+#> 3                    3 hip_fracture        NA
+#> 4                    4 any_fracture         0
+cohortCount(cdm$fractures)
+#> # A tibble: 4 × 3
+#>   cohort_definition_id number_records number_subjects
+#>                  <int>          <int>           <int>
+#> 1                    1            464             427
+#> 2                    2            569             510
+#> 3                    3            138             132
+#> 4                    4           1171             924

+

+

 
Require in date range
 

-
Once we have created our base cohort, we can then start applying additional cohort requirements. For example, first we can require that individuals’ cohort start date fall within a certain date range.

-
+
Once we have created our base fracture cohort, we can then start applying additional cohort requirements. For example, first we can require that individuals’ cohort start date fall within a certain date range.

+
 cdm$fractures <- cdm$fractures %>% 
   requireInDateRange(dateRange = as.Date(c("2000-01-01", "2020-01-01")))

 
Now that we’ve applied this date restriction, we can see that our cohort attributes have been updated

-
+
 cohort_count(cdm$fractures) %>% glimpse()
-#> Rows: 3
+#> Rows: 4
 #> Columns: 3
-#> $ cohort_definition_id <int> 1, 2, 3
-#> $ number_records       <int> 108, 152, 62
-#> $ number_subjects      <int> 104, 143, 60
+#> $ cohort_definition_id <int> 1, 2, 3, 4
+#> $ number_records       <int> 108, 152, 62, 322
+#> $ number_subjects      <int> 104, 143, 60, 287
 attrition(cdm$fractures) %>% 
   filter(reason == "cohort_start_date between 2000-01-01 & 2020-01-01") %>% 
   glimpse()
@@ -156,85 +223,71 @@ 
Require in date rangeApplying demographic requirements
 

 
We can also add restrictions on patient characteristics such as age (on cohort start date by default) and sex.

-
+
 cdm$fractures <- cdm$fractures %>% 
   requireDemographics(ageRange = list(c(40, 65)),
                       sex = "Female")

 
Again we can see how many individuals we’ve lost after applying these criteria.

-
+
 attrition(cdm$fractures) %>% 
   filter(reason == "Age requirement: 40 to 65") %>% 
   glimpse()
-#> Rows: 3
+#> Rows: 4
 #> Columns: 7
-#> $ cohort_definition_id <int> 1, 2, 3
-#> $ number_records       <int> 43, 64, 22
-#> $ number_subjects      <int> 43, 62, 22
-#> $ reason_id            <int> 4, 4, 4
+#> $ cohort_definition_id <int> 1, 2, 3, 4
+#> $ number_records       <int> 43, 64, 22, 129
+#> $ number_subjects      <int> 43, 62, 22, 122
+#> $ reason_id            <int> 4, 4, 4, 4
 #> $ reason               <chr> "Age requirement: 40 to 65", "Age requirement: 40…
-#> $ excluded_records     <int> 65, 88, 40
-#> $ excluded_subjects    <int> 61, 81, 38
+#> $ excluded_records     <int> 65, 88, 40, 193
+#> $ excluded_subjects    <int> 61, 81, 38, 165
 
 attrition(cdm$fractures) %>% 
   filter(reason == "Sex requirement: Female") %>% 
   glimpse()
-#> Rows: 3
+#> Rows: 4
 #> Columns: 7
-#> $ cohort_definition_id <int> 1, 2, 3
-#> $ number_records       <int> 19, 37, 12
-#> $ number_subjects      <int> 19, 36, 12
-#> $ reason_id            <int> 5, 5, 5
+#> $ cohort_definition_id <int> 1, 2, 3, 4
+#> $ number_records       <int> 19, 37, 12, 68
+#> $ number_subjects      <int> 19, 36, 12, 65
+#> $ reason_id            <int> 5, 5, 5, 5
 #> $ reason               <chr> "Sex requirement: Female", "Sex requirement: Fema…
-#> $ excluded_records     <int> 24, 27, 10
-#> $ excluded_subjects    <int> 24, 26, 10

+#> $ excluded_records     <int> 24, 27, 10, 61
+#> $ excluded_subjects    <int> 24, 26, 10, 57

 

 

 
Require presence in another cohort
 

-
We can also require that individuals are in another cohort over some window. Here for example we require that study participants are in a GI bleed cohort any time prior up to their entry in the fractures cohort.

-
+
We can also require that individuals are (or are not) in another cohort over some window. Here for example we require that study participants are in a GI bleed cohort any time prior up to their entry in the fractures cohort.

+
 cdm$gibleed <- cdm |> 
-  conceptCohort(conceptSet = list("gibleed" = 192671),
+  conceptCohort(conceptSet = list("gibleed" = 192671L),
   name = "gibleed")
 
 cdm$fractures <- cdm$fractures %>% 
   requireCohortIntersect(targetCohortTable = "gibleed",
-                             window = c(-Inf, 0))

-
+                         intersections = 0,
+                         window = c(-Inf, 0))

+
 attrition(cdm$fractures) %>% 
-  filter(reason == "In cohort gibleed between -Inf & 0 days relative to cohort_start_date") %>% 
+  filter(reason == "Not in cohort gibleed between -Inf & 0 days relative to cohort_start_date") %>% 
   glimpse()
-#> Rows: 3
+#> Rows: 4
 #> Columns: 7
-#> $ cohort_definition_id <int> 1, 2, 3
-#> $ number_records       <int> 5, 7, 2
-#> $ number_subjects      <int> 5, 6, 2
-#> $ reason_id            <int> 8, 8, 8
-#> $ reason               <chr> "In cohort gibleed between -Inf & 0 days relative…
-#> $ excluded_records     <int> 14, 30, 10
-#> $ excluded_subjects    <int> 14, 30, 10

+#> $ cohort_definition_id <int> 1, 2, 3, 4
+#> $ number_records       <int> 14, 30, 10, 54
+#> $ number_subjects      <int> 14, 30, 10, 52
+#> $ reason_id            <int> 8, 8, 8, 8
+#> $ reason               <chr> "Not in cohort gibleed between -Inf & 0 days rela…
+#> $ excluded_records     <int> 5, 7, 2, 14
+#> $ excluded_subjects    <int> 5, 6, 2, 13

+
 

 

-
Combining cohorts
+
More information
 

-
Currently we have separate fracture cohorts.

-
Let’s say we want to create a cohort of people with any of the fractures. We could create this cohort like so:

-
-cdm$fractures <- cdm$fractures |> 
-  CohortConstructor::unionCohorts()
-
-settings(cdm$fractures)
-#> # A tibble: 1 × 3
-#>   cohort_definition_id cohort_name                                    gap
-#>                  <dbl> <chr>                                        <dbl>
-#> 1                    1 ankle_fracture_forearm_fracture_hip_fracture     0
-cohortCount(cdm$fractures)
-#> # A tibble: 1 × 3
-#>   cohort_definition_id number_records number_subjects
-#>                  <int>          <int>           <int>
-#> 1                    1             14              13

-
+
CohortConstructor provides much more functionality for creating and manipulating cohorts. See the package website for more details.

 

 

 

diff --git a/pkgdown.yml b/pkgdown.yml
index 6fccd7e5..0bb425fd 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -7,7 +7,7 @@ articles:
   a02_applying_cohort_restrictions: a02_applying_cohort_restrictions.html
   a03_age_sex_matching: a03_age_sex_matching.html
   a04_cohort_manipulations: a04_cohort_manipulations.html
-last_built: 2024-08-27T09:07Z
+last_built: 2024-08-27T12:15Z
 urls:
   reference: https://ohdsi.github.io/CohortConstructor/reference
   article: https://ohdsi.github.io/CohortConstructor/articles
diff --git a/reference/conceptCohort.html b/reference/conceptCohort.html
index 48ccd041..7ffae571 100644
--- a/reference/conceptCohort.html
+++ b/reference/conceptCohort.html
@@ -146,6 +146,7 @@ 
Examples#> Note: method with signature ‘DBIConnection#Id’ chosen for function ‘dbExistsTable’,
 #>  target signature ‘duckdb_connection#Id’.
 #>  "duckdb_connection#ANY" would also be valid
+#> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■      90% | ETA:  0s
 
 cohort <- conceptCohort(cdm = cdm, conceptSet = list(a = 1), name = "cohort")
 #> Warning: ! `codelist` contains numeric values, they are casted to integers.
diff --git a/reference/entryAtFirstDate.html b/reference/entryAtFirstDate.html
index d7c4ab54..2fab3b05 100644
--- a/reference/entryAtFirstDate.html
+++ b/reference/entryAtFirstDate.html
@@ -172,9 +172,9 @@ 
Examples#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:]
 #>   cohort_definition_id subject_id cohort_start_date cohort_end_date entry_reason
 #>                  <dbl>      <dbl> <date>            <date>          <chr>       
-#> 1                    1          1 2001-08-01        2001-09-01      date_1; dat…
+#> 1                    1          2 2001-01-01        2001-01-12      date_1      
 #> 2                    1          3 2015-02-14        2015-02-15      date_2      
-#> 3                    1          2 2001-01-01        2001-01-12      date_1      
+#> 3                    1          1 2001-08-01        2001-09-01      date_1; dat…
 #> 4                    1          4 2002-12-09        2002-12-09      date_1; dat…
 # }
 

diff --git a/reference/entryAtLastDate.html b/reference/entryAtLastDate.html
index eb934109..505b9165 100644
--- a/reference/entryAtLastDate.html
+++ b/reference/entryAtLastDate.html
@@ -169,10 +169,10 @@ 
Examples#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:]
 #>   cohort_definition_id subject_id cohort_start_date cohort_end_date entry_reason
 #>                  <dbl>      <dbl> <date>            <date>          <chr>       
-#> 1                    1          1 2001-08-01        2001-09-01      date_2; dat…
-#> 2                    1          3 2015-02-14        2015-02-15      date_2      
-#> 3                    1          4 2002-12-09        2002-12-09      date_2; dat…
-#> 4                    1          2 2001-01-01        2001-01-12      date_1      
+#> 1                    1          2 2001-01-01        2001-01-12      date_1      
+#> 2                    1          4 2002-12-09        2002-12-09      date_2; dat…
+#> 3                    1          3 2015-02-14        2015-02-15      date_2      
+#> 4                    1          1 2001-08-01        2001-09-01      date_2; dat…
 # }
diff --git a/reference/exitAtDeath.html b/reference/exitAtDeath.html index 1927eaeb..8a425764 100644 --- a/reference/exitAtDeath.html +++ b/reference/exitAtDeath.html @@ -102,15 +102,15 @@

Examples#> cohort_definition_id subject_id cohort_start_date cohort_end_date #> <int> <int> <date> <date> #> 1 2 2 1998-11-05 2008-01-27 -#> 2 1 6 2006-12-25 2022-11-01 -#> 3 2 1 1951-11-28 2019-01-16 +#> 2 2 1 1951-11-28 2019-01-16 +#> 3 1 6 2006-12-25 2022-11-01 #> 4 2 5 2113-08-18 2144-11-05 #> 5 2 8 1954-07-05 1955-07-17 #> 6 3 7 2029-01-30 2050-08-27 #> 7 3 10 2003-01-05 2060-02-27 -#> 8 2 3 1993-12-06 1997-05-26 -#> 9 2 9 2109-11-07 2115-08-03 -#> 10 1 4 2017-04-18 2077-11-07 +#> 8 1 4 2017-04-18 2077-11-07 +#> 9 2 3 1993-12-06 1997-05-26 +#> 10 2 9 2109-11-07 2115-08-03 # }

diff --git a/reference/exitAtFirstDate.html b/reference/exitAtFirstDate.html index ddf9ba02..ab27fe69 100644 --- a/reference/exitAtFirstDate.html +++ b/reference/exitAtFirstDate.html @@ -173,9 +173,9 @@

Examples#> cohort_definition_id subject_id cohort_start_date cohort_end_date exit_reason #> <dbl> <dbl> <date> <date> <chr> #> 1 1 3 2015-01-15 2015-01-15 date_1 -#> 2 1 4 2000-12-09 2002-12-09 date_2; dat… +#> 2 1 1 2000-06-03 2001-08-01 date_1; dat… #> 3 1 2 2000-01-01 2001-01-01 date_1 -#> 4 1 1 2000-06-03 2001-08-01 date_2; dat… +#> 4 1 4 2000-12-09 2002-12-09 date_1; dat… # } diff --git a/reference/exitAtLastDate.html b/reference/exitAtLastDate.html index 4e0dcf41..518a378b 100644 --- a/reference/exitAtLastDate.html +++ b/reference/exitAtLastDate.html @@ -173,9 +173,9 @@

Examples#> cohort_definition_id subject_id cohort_start_date cohort_end_date exit_reason #> <dbl> <dbl> <date> <date> <chr> #> 1 1 2 2000-01-01 2001-01-01 date_1 -#> 2 1 4 2000-12-09 2002-12-09 date_2; dat… +#> 2 1 1 2000-06-03 2001-08-01 date_1; dat… #> 3 1 3 2015-01-15 2015-04-15 date_2 -#> 4 1 1 2000-06-03 2001-08-01 date_2; dat… +#> 4 1 4 2000-12-09 2002-12-09 date_1; dat… # } diff --git a/reference/exitAtObservationEnd.html b/reference/exitAtObservationEnd.html index d92cb577..4a36a023 100644 --- a/reference/exitAtObservationEnd.html +++ b/reference/exitAtObservationEnd.html @@ -96,9 +96,9 @@

Examples#> 1 1 4 1996-06-30 2013-12-31 #> 2 1 2 2000-05-04 2003-06-15 #> 3 1 7 2014-03-07 2014-04-09 -#> 4 1 1 2001-05-30 2013-06-29 -#> 5 1 5 2012-03-20 2013-02-10 -#> 6 1 3 2015-01-27 2015-10-11 +#> 4 1 5 2012-03-20 2013-02-10 +#> 5 1 3 2015-01-27 2015-10-11 +#> 6 1 1 2001-05-30 2013-06-29 # } diff --git a/reference/matchCohorts.html b/reference/matchCohorts.html index 5c420858..a7f62231 100644 --- a/reference/matchCohorts.html +++ b/reference/matchCohorts.html @@ -121,7 +121,7 @@

Examples#> ℹ Creating copy of target cohort. #> • 1 cohort to be matched. #> ℹ Creating controls cohorts. -#> Warning: ! 2 casted column in tmp_004_og_039_1724749686 (cohort_attrition) as do not +#> Warning: ! 2 casted column in tmp_004_og_039_1724761022 (cohort_attrition) as do not #> match expected column type: #> • `number_records` from numeric to integer #> • `number_subjects` from numeric to integer @@ -139,16 +139,16 @@

Examples#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date cluster_id #> <int> <int> <date> <date> <dbl> -#> 1 1 118 1975-11-28 1981-05-30 6 -#> 2 1 56 2007-09-28 2008-07-15 18 -#> 3 1 63 2008-08-23 2008-09-02 19 -#> 4 1 20 1985-08-15 1990-06-06 26 -#> 5 1 19 2003-06-22 2005-07-21 36 -#> 6 1 84 2000-04-13 2006-06-11 42 -#> 7 1 121 2007-10-25 2010-01-05 47 -#> 8 1 113 2015-09-05 2016-01-10 50 -#> 9 1 24 2016-12-17 2016-12-29 59 -#> 10 1 62 2017-01-18 2017-04-26 74 +#> 1 1 19 2003-06-22 2005-07-21 36 +#> 2 1 84 1995-08-28 1999-04-05 42 +#> 3 1 113 2015-09-05 2016-01-10 50 +#> 4 1 94 2017-11-01 2018-07-05 59 +#> 5 1 118 1975-11-28 1981-05-30 6 +#> 6 1 56 2007-09-28 2008-07-15 18 +#> 7 1 63 2008-08-23 2008-09-02 19 +#> 8 1 20 1990-06-07 1993-11-05 26 +#> 9 1 83 2011-01-15 2011-02-06 94 +#> 10 1 7 2014-03-06 2014-03-08 98 #> # ℹ more rows # } diff --git a/reference/measurementCohort.html b/reference/measurementCohort.html index fbaebd6f..12cb9cea 100644 --- a/reference/measurementCohort.html +++ b/reference/measurementCohort.html @@ -180,8 +180,8 @@

Examples#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> <int> <dbl> <date> <date> -#> 1 1 1 2000-07-01 2000-07-01 -#> 2 1 3 2015-02-19 2015-02-19 +#> 1 1 3 2015-02-19 2015-02-19 +#> 2 1 1 2000-07-01 2000-07-01 # } diff --git a/reference/requireDeathFlag.html b/reference/requireDeathFlag.html index c403a061..b35c2b47 100644 --- a/reference/requireDeathFlag.html +++ b/reference/requireDeathFlag.html @@ -115,6 +115,7 @@

Examples#> intersectCohorts, unionCohorts library(CohortConstructor) cdm <- mockCohortConstructor(death = TRUE) +#> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 90% | ETA: 0s cdm$cohort1 <- cdm$cohort1 |> requireDeathFlag(window = list(c(0, Inf))) attrition(cdm$cohort1) #> # A tibble: 2 × 7 diff --git a/reference/requireTableIntersect.html b/reference/requireTableIntersect.html index ec9b28cf..7ededead 100644 --- a/reference/requireTableIntersect.html +++ b/reference/requireTableIntersect.html @@ -127,7 +127,6 @@

Examples
# \donttest{
 library(CohortConstructor)
 cdm <- mockCohortConstructor(drugExposure = TRUE)
-#> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■      90% | ETA:  0s
 cdm$cohort1 |>
   requireTableIntersect(tableName = "drug_exposure",
                             indexDate = "cohort_start_date",
diff --git a/reference/sampleCohorts.html b/reference/sampleCohorts.html
index 490ff854..43f6cbf7 100644
--- a/reference/sampleCohorts.html
+++ b/reference/sampleCohorts.html
@@ -90,16 +90,16 @@ 
Examples#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:]
 #>    cohort_definition_id subject_id cohort_start_date cohort_end_date
 #>                   <int>      <int> <date>            <date>         
-#>  1                    1          1 2001-02-15        2001-10-28     
-#>  2                    1          1 2001-10-29        2003-03-15     
-#>  3                    1          1 2003-03-16        2005-02-08     
-#>  4                    1          2 1999-11-11        2002-04-09     
-#>  5                    1         28 2005-04-01        2005-04-03     
-#>  6                    1         28 2005-04-04        2005-08-23     
-#>  7                    1         48 1964-01-15        1966-03-08     
-#>  8                    1         48 1966-03-09        1966-08-01     
-#>  9                    1         48 1966-08-02        1967-04-16     
-#> 10                    1         48 1967-04-17        1974-01-28     
+#>  1                    1          6 2011-03-07        2014-01-24     
+#>  2                    1          7 2014-03-08        2014-03-19     
+#>  3                    1         14 1986-11-29        1987-12-14     
+#>  4                    1         14 1987-12-15        1988-03-19     
+#>  5                    1         15 1978-07-09        2000-06-12     
+#>  6                    1         22 1993-09-22        1994-04-10     
+#>  7                    1         22 1994-04-11        1996-04-26     
+#>  8                    1         22 1996-04-27        1999-08-31     
+#>  9                    1         59 2014-08-29        2015-04-10     
+#> 10                    1         59 2015-04-11        2016-01-05     
 #> # ℹ more rows
 # }
diff --git a/reference/trimDemographics.html b/reference/trimDemographics.html index fd323bf0..03453dda 100644 --- a/reference/trimDemographics.html +++ b/reference/trimDemographics.html @@ -120,16 +120,16 @@

Examples#> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> <int> <int> <date> <date> -#> 1 1 14 1987-12-15 1988-03-19 -#> 2 1 20 1990-10-19 1997-01-08 -#> 3 1 28 2005-04-04 2005-08-23 -#> 4 1 60 1974-02-12 1979-10-10 -#> 5 1 79 1991-10-01 1996-02-15 -#> 6 1 81 2009-08-24 2010-07-01 -#> 7 1 14 1987-03-20 1987-12-14 -#> 8 1 20 1990-03-24 1990-10-18 -#> 9 1 28 2005-04-01 2005-04-03 -#> 10 1 79 1991-02-24 1991-09-30 +#> 1 1 43 2014-10-05 2015-09-27 +#> 2 1 48 1970-07-29 1974-01-28 +#> 3 1 64 1993-05-18 2001-05-18 +#> 4 1 75 1974-01-17 1974-10-19 +#> 5 1 43 2014-07-21 2014-10-04 +#> 6 1 29 2006-11-24 2008-03-21 +#> 7 1 43 2014-07-06 2014-07-20 +#> 8 1 29 2006-10-02 2006-11-23 +#> 9 1 29 2006-07-07 2006-10-01 +#> 10 1 14 1987-12-15 1988-03-19 #> # ℹ more rows # } diff --git a/search.json b/search.json index a43e83ff..7a0b2b4b 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004 ","code":""},{"path":[]},{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":"id_1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. Definitions","title":"Apache License","text":"“License” shall mean terms conditions use, reproduction, distribution defined Sections 1 9 document. “Licensor” shall mean copyright owner entity authorized copyright owner granting License. “Legal Entity” shall mean union acting entity entities control, controlled , common control entity. purposes definition, “control” means () power, direct indirect, cause direction management entity, whether contract otherwise, (ii) ownership fifty percent (50%) outstanding shares, (iii) beneficial ownership entity. “” (“”) shall mean individual Legal Entity exercising permissions granted License. “Source” form shall mean preferred form making modifications, including limited software source code, documentation source, configuration files. “Object” form shall mean form resulting mechanical transformation translation Source form, including limited compiled object code, generated documentation, conversions media types. “Work” shall mean work authorship, whether Source Object form, made available License, indicated copyright notice included attached work (example provided Appendix ). “Derivative Works” shall mean work, whether Source Object form, based (derived ) Work editorial revisions, annotations, elaborations, modifications represent, whole, original work authorship. purposes License, Derivative Works shall include works remain separable , merely link (bind name) interfaces , Work Derivative Works thereof. “Contribution” shall mean work authorship, including original version Work modifications additions Work Derivative Works thereof, intentionally submitted Licensor inclusion Work copyright owner individual Legal Entity authorized submit behalf copyright owner. purposes definition, “submitted” means form electronic, verbal, written communication sent Licensor representatives, including limited communication electronic mailing lists, source code control systems, issue tracking systems managed , behalf , Licensor purpose discussing improving Work, excluding communication conspicuously marked otherwise designated writing copyright owner “Contribution.” “Contributor” shall mean Licensor individual Legal Entity behalf Contribution received Licensor subsequently incorporated within Work.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":"id_2-grant-of-copyright-license","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"2. 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Redistribution","title":"Apache License","text":"may reproduce distribute copies Work Derivative Works thereof medium, without modifications, Source Object form, provided meet following conditions: () must give recipients Work Derivative Works copy License; (b) must cause modified files carry prominent notices stating changed files; (c) must retain, Source form Derivative Works distribute, copyright, patent, trademark, attribution notices Source form Work, excluding notices pertain part Derivative Works; (d) Work includes “NOTICE” text file part distribution, Derivative Works distribute must include readable copy attribution notices contained within NOTICE file, excluding notices pertain part Derivative Works, least one following places: within NOTICE text file distributed part Derivative Works; within Source form documentation, provided along Derivative Works; , within display generated Derivative Works, wherever third-party notices normally appear. contents NOTICE file informational purposes modify License. may add attribution notices within Derivative Works distribute, alongside addendum NOTICE text Work, provided additional attribution notices construed modifying License. may add copyright statement modifications may provide additional different license terms conditions use, reproduction, distribution modifications, Derivative Works whole, provided use, reproduction, distribution Work otherwise complies conditions stated License.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":"id_5-submission-of-contributions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"5. 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Disclaimer of Warranty","title":"Apache License","text":"Unless required applicable law agreed writing, Licensor provides Work (Contributor provides Contributions) “” BASIS, WITHOUT WARRANTIES CONDITIONS KIND, either express implied, including, without limitation, warranties conditions TITLE, NON-INFRINGEMENT, MERCHANTABILITY, FITNESS PARTICULAR PURPOSE. solely responsible determining appropriateness using redistributing Work assume risks associated exercise permissions License.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":"id_8-limitation-of-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"8. Limitation of Liability","title":"Apache License","text":"event legal theory, whether tort (including negligence), contract, otherwise, unless required applicable law (deliberate grossly negligent acts) agreed writing, shall Contributor liable damages, including direct, indirect, special, incidental, consequential damages character arising result License use inability use Work (including limited damages loss goodwill, work stoppage, computer failure malfunction, commercial damages losses), even Contributor advised possibility damages.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":"id_9-accepting-warranty-or-additional-liability","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"9. Accepting Warranty or Additional Liability","title":"Apache License","text":"redistributing Work Derivative Works thereof, may choose offer, charge fee , acceptance support, warranty, indemnity, liability obligations /rights consistent License. However, accepting obligations, may act behalf sole responsibility, behalf Contributor, agree indemnify, defend, hold Contributor harmless liability incurred , claims asserted , Contributor reason accepting warranty additional liability. END TERMS CONDITIONS","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":"appendix-how-to-apply-the-apache-license-to-your-work","dir":"","previous_headings":"","what":"APPENDIX: How to apply the Apache License to your work","title":"Apache License","text":"apply Apache License work, attach following boilerplate notice, fields enclosed brackets [] replaced identifying information. (Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a00_introduction.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Introduction","text":"CohortConstructor package designed support cohort building pipelines. using package general workflow first build set base cohorts subsequently apply inclusion criteria derive final study cohorts interest. Base cohorts built domain (rather cohort definition) one base cohort many study cohorts can derived.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a00_introduction.html","id":"building-a-cohort-set-by-domain","dir":"Articles","previous_headings":"","what":"Building a cohort set by domain","title":"Introduction","text":"Let´s say want build 5 cohorts 3 (asthma, copd, diabetes) defined based concepts seen condition occurrence table 2 (acetaminophen warfarin) based concepts recorded drug exposure table. can build cohorts independently, one . However, approach mean repeating 3 joins condition occurrence tables 2 joins drug exposure table (concepts concept sets). make less computationally expensive, instead create cohorts domain. case instead make one join condition occurrence table one drug exposure (using concept sets together).","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a00_introduction.html","id":"deriving-study-cohorts-from-base-cohorts","dir":"Articles","previous_headings":"","what":"Deriving study cohorts from base cohorts","title":"Introduction","text":"making study cohorts often concept sets define clinical event along various study-specific inclusion criteria, example criteria around amount prior observation age. Often may sensitivity analysis concept set remains inclusion criteria change. situations can make cohorts one--one. However, can lead duplication can see example identify asthma records multiple times. alternative approach build base cohort, case based asthma records, derive multiple cohorts different inclusion criteria applied.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a00_introduction.html","id":"considerations-when-building-cohorts","dir":"Articles","previous_headings":"","what":"Considerations when building cohorts","title":"Introduction","text":"CohortConstructor provides means building cohorts via pipeline, cohorts created application sequence functions. important note order sequence often important implications. example just one individual three recorded diagnoses asthma. One diagnosis 2008 two 2009, last coming individual´s 18th birthday. three cohort pipelines shown restrictions around calendar dates, age, record first. cohort pipeline , however, individual included final cohort, third diagnosis used cohort start. pipeline B C individual excluded.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a01_building_base_cohorts.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Building base cohorts","text":"Let’s first create cdm reference Eunomia synthetic data.","code":"library(CDMConnector) library(CodelistGenerator) library(PatientProfiles) library(CohortConstructor) library(dplyr) con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) cdm <- cdm_from_con(con, cdm_schema = \"main\", write_schema = c(prefix = \"my_study_\", schema = \"main\"))"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a01_building_base_cohorts.html","id":"demographic-based-cohort-creation","dir":"Articles","previous_headings":"","what":"Demographic based cohort creation","title":"Building base cohorts","text":"One base cohort can create based around patient demographics. example create cohort people enter 18th birthday leave age 65 ","code":"cdm$working_age_cohort <- demographicsCohort(cdm = cdm, ageRange = c(18, 65), name = \"working_age_cohort\") settings(cdm$working_age_cohort) #> # A tibble: 1 × 3 #> cohort_definition_id cohort_name age_range #> #> 1 1 demographics 18_65 cohortCount(cdm$working_age_cohort) #> # A tibble: 1 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 2694 2694 attrition(cdm$working_age_cohort) #> # A tibble: 2 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 2694 2694 1 Initial qualify… #> 2 1 2694 2694 2 Age requirement… #> # ℹ 2 more variables: excluded_records , excluded_subjects cdm$working_age_cohort |> addAge(indexDate = \"cohort_start_date\") |> summarise(min_start_age = min(age), median_start_age = median(age), max_start_age = max(age)) #> # Source: SQL [1 x 3] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1//tmp/RtmpZ6xMJp/file1adf377ea2ce.duckdb] #> min_start_age median_start_age max_start_age #> #> 1 17 18 18 cdm$working_age_cohort |> addAge(indexDate = \"cohort_end_date\") |> summarise(min_start_age = min(age), median_start_age = median(age), max_start_age = max(age)) #> # Source: SQL [1 x 3] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1//tmp/RtmpZ6xMJp/file1adf377ea2ce.duckdb] #> min_start_age median_start_age max_start_age #> #> 1 31 57 65"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a01_building_base_cohorts.html","id":"concept-based-cohort-creation","dir":"Articles","previous_headings":"","what":"Concept based cohort creation","title":"Building base cohorts","text":"","code":"drug_codes <- getDrugIngredientCodes(cdm, name = c(\"diclofenac\", \"acetaminophen\")) drug_codes #> #> - 161_acetaminophen (7 codes) #> - 3355_diclofenac (1 codes) cdm$medications <- conceptCohort(cdm = cdm, conceptSet = drug_codes, name = \"medications\") settings(cdm$medications) #> # A tibble: 2 × 4 #> cohort_definition_id cohort_name cdm_version vocabulary_version #> #> 1 1 161_acetaminophen 5.3 v5.0 18-JAN-19 #> 2 2 3355_diclofenac 5.3 v5.0 18-JAN-19 cohortCount(cdm$medications) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 13908 2679 #> 2 2 830 830"},{"path":[]},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a02_applying_cohort_restrictions.html","id":"keep-only-the-first-record-per-person","dir":"Articles","previous_headings":"","what":"Keep only the first record per person","title":"Applying cohort restrictions","text":"Individuals can contribute multiple records per cohort. However now ’ll keep earliest cohort entry remaining records using requireIsFirstEntry() CohortConstructor. can see one record per person cohort. Note, applying criteria later applying criteria result different result. ’re requiring individuals meet inclusion criteria time first use diclofenac acetaminophen.","code":"cdm$medications <- cdm$medications %>% requireIsFirstEntry(indexDate = \"cohort_start_date\") cohortCount(cdm$medications) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 2580 2580 #> 2 2 830 830"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a02_applying_cohort_restrictions.html","id":"applying-restrictions-on-patient-demographics","dir":"Articles","previous_headings":"","what":"Applying restrictions on patient demographics","title":"Applying cohort restrictions","text":"Using requireDemographics() ’ll require individuals medications cohort female , relative cohort start date, 18 85 least 30 days prior observation time database. can see many people people excluded based demographic requirements.","code":"cdm$medications <- cdm$medications %>% requireDemographics(indexDate = \"cohort_start_date\", ageRange = list(c(18, 85)), sex = \"Female\", minPriorObservation = 30) cohort_attrition(cdm$medications) %>% dplyr::filter(reason == \"Demographic requirements\") %>% dplyr::glimpse() #> Rows: 0 #> Columns: 7 #> $ cohort_definition_id #> $ number_records #> $ number_subjects #> $ reason_id #> $ reason #> $ excluded_records #> $ excluded_subjects "},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a02_applying_cohort_restrictions.html","id":"restrictions-on-calendar-dates","dir":"Articles","previous_headings":"","what":"Restrictions on calendar dates","title":"Applying cohort restrictions","text":"Next can use requireInDateRange() keep records cohort entry particular date range. , can track cohort attrition","code":"cdm$medications <- cdm$medications %>% requireInDateRange(indexDate = \"cohort_start_date\", dateRange = as.Date(c(\"2000-01-01\", \"2015-01-01\"))) cohort_attrition(cdm$medications) %>% dplyr::filter(reason == \"cohort_start_date between 2000-01-01 and 2015-01-01\") %>% dplyr::glimpse() #> Rows: 0 #> Columns: 7 #> $ cohort_definition_id #> $ number_records #> $ number_subjects #> $ reason_id #> $ reason #> $ excluded_records #> $ excluded_subjects "},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a02_applying_cohort_restrictions.html","id":"restrictions-on-cohort-presence","dir":"Articles","previous_headings":"","what":"Restrictions on cohort presence","title":"Applying cohort restrictions","text":"require individuals medication cohorts history GI bleed. can use requireCohortIntersect() function, requiring individuals one intersections GI bleed cohort. Instead requiring individuals history GI bleed, instead require don’t history . case can use requireCohortIntersect() function, time set intersections argument 0 require individuals’ absence cohort rather presence .","code":"cdm$medications_gi_bleed <- cdm$medications %>% requireCohortIntersect(intersections = c(1,Inf), targetCohortTable = \"gi_bleed\", targetCohortId = 1, indexDate = \"cohort_start_date\", window = c(-Inf, 0), name = \"medications_gi_bleed\") cohort_count(cdm$medications_gi_bleed) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 0 0 #> 2 2 0 0 cdm$medications_no_gi_bleed <- cdm$medications %>% requireCohortIntersect(intersections = 0, targetCohortTable = \"gi_bleed\", targetCohortId = 1, indexDate = \"cohort_start_date\", window = c(-Inf, 0), name = \"medications_no_gi_bleed\") cohort_count(cdm$medications_no_gi_bleed) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 101 101 #> 2 2 179 179"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Generate a matched age and sex cohort","text":"CohortConstructor packages includes function obtain age sex matched cohort, generateMatchedCohortSet() function. vignette, explore usage function.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"create-mock-data","dir":"Articles","previous_headings":"Introduction","what":"Create mock data","title":"Generate a matched age and sex cohort","text":"first use mockDrugUtilisation() function DrugUtilisation package create mock data. use cohort1 explore generateMatchedCohortSet(), let us first use cohort_attrition() CDMConnector package explore cohort:","code":"library(CohortConstructor) library(dplyr) cdm <- mockCohortConstructor(nPerson = 1000) CDMConnector::cohort_set(cdm$cohort1)"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"use-generatematchedcohortset-to-create-an-age-sex-matched-cohort","dir":"Articles","previous_headings":"","what":"Use generateMatchedCohortSet() to create an age-sex matched cohort","title":"Generate a matched age and sex cohort","text":"Let us first see example function works. usage, need provide cdm object, targetCohortName, name table containing cohort interest, name new generated tibble containing cohort matched cohort. also use argument targetCohortId specify want matched cohort cohort_definition_id = 1. Notice generated tibble, two cohorts: cohort_definition_id = 1 (original cohort), cohort_definition_id = 4 (matched cohort). target_cohort_name column indicates original cohort. match_sex match_year_of_birth adopt boolean values (TRUE/FALSE) indicating matched sex age, . match_status indicate original cohort (target) matched cohort (matched). target_cohort_id indicates cohort_id original cohort. Check exclusion criteria applied generate new cohorts using cohort_attrition() CDMConnector package: Briefly, original cohort, exclude first individuals match, individuals matching pair observation assigned cohort_start_date. matched cohort, start whole database first exclude individuals original cohort. Afterwards, exclude individuals match, individuals observation assigned cohort_start_date, finally remove many individuals required fulfill ratio. Notice matching pairs randomly assigned, probable every time execute function, generated cohorts change. Use set.seed() avoid .","code":"cdm$matched_cohort1 <- matchCohorts( cohort = cdm$cohort1, cohortId = 1, name = \"matched_cohort1\") CDMConnector::cohort_set(cdm$matched_cohort1) # Original cohort CDMConnector::cohort_attrition(cdm$matched_cohort1) %>% filter(cohort_definition_id == 1) # Matched cohort CDMConnector::cohort_attrition(cdm$matched_cohort1) %>% filter(cohort_definition_id == 4)"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"matchsex-parameter","dir":"Articles","previous_headings":"Use generateMatchedCohortSet() to create an age-sex matched cohort","what":"matchSex parameter","title":"Generate a matched age and sex cohort","text":"matchSex boolean parameter (TRUE/FALSE) indicating want match sex (TRUE) want (FALSE).","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"matchyear-parameter","dir":"Articles","previous_headings":"Use generateMatchedCohortSet() to create an age-sex matched cohort","what":"matchYear parameter","title":"Generate a matched age and sex cohort","text":"matchYear another boolean parameter (TRUE/FALSE) indicating want match age (TRUE) want (FALSE). Notice matchSex = FALSE matchYear = FALSE, obtain unmatched comparator cohort.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"ratio-parameter","dir":"Articles","previous_headings":"Use generateMatchedCohortSet() to create an age-sex matched cohort","what":"ratio parameter","title":"Generate a matched age and sex cohort","text":"default matching ratio 1:1 (ratio = 1). Use cohort_counts() CDMConnector check matching done desired. can modify ratio parameter tailor matched cohort. ratio can adopt values 1 Inf.","code":"CDMConnector::cohort_count(cdm$matched_cohort1) cdm$matched_cohort2 <- matchCohorts( cohort = cdm$cohort1, cohortId = 1, name = \"matched_cohort2\", ratio = Inf) CDMConnector::cohort_count(cdm$matched_cohort2)"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"generate-matched-cohorts-simultaneously-across-multiple-cohorts","dir":"Articles","previous_headings":"Use generateMatchedCohortSet() to create an age-sex matched cohort","what":"Generate matched cohorts simultaneously across multiple cohorts","title":"Generate a matched age and sex cohort","text":"functionalities can implemented across multiple cohorts simultaneously. Specify targetCohortId parameter cohorts interest. set NULL, cohorts present targetCohortName matched. Notice cohort (independent cohorts) matched cohort.","code":"cdm$matched_cohort3 <- matchCohorts( cohort = cdm$cohort1, cohortId = c(1,3), name = \"matched_cohort3\", ratio = 2) CDMConnector::cohort_set(cdm$matched_cohort3) %>% arrange(cohort_definition_id) CDMConnector::cohort_count(cdm$matched_cohort3) %>% arrange(cohort_definition_id)"},{"path":"https://ohdsi.github.io/CohortConstructor/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edward Burn. Author, maintainer. Marti Catala. Author. Nuria Mercade-Besora. Author. Marta Alcalde-Herraiz. Author. Mike Du. Author. Yuchen Guo. Author. Xihang Chen. Author. Kim Lopez. Author.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Burn E, Catala M, Mercade-Besora N, Alcalde-Herraiz M, Du M, Guo Y, Chen X, Lopez K (2024). CohortConstructor: Build Manipulate Study Cohorts Using Common Data Model. R package version 0.2.2, https://ohdsi.github.io/CohortConstructor/.","code":"@Manual{, title = {CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model}, author = {Edward Burn and Marti Catala and Nuria Mercade-Besora and Marta Alcalde-Herraiz and Mike Du and Yuchen Guo and Xihang Chen and Kim Lopez}, year = {2024}, note = {R package version 0.2.2}, url = {https://ohdsi.github.io/CohortConstructor/}, }"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"cohortconstructor-","dir":"","previous_headings":"","what":"Build and Manipulate Study Cohorts Using a Common Data Model","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"package currently experimental. Please use care report issues might come across. goal CohortConstructor support creation manipulation cohorts OMOP Common Data Model.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"can install development version CohortConstructor GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"ohdsi/CohortConstructor\")"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"creating-and-manipulating-cohorts","dir":"","previous_headings":"","what":"Creating and manipulating cohorts","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"illustrate functionality let’s create CDM reference Eunomia dataset Using CDMConnector package.","code":"library(CDMConnector) library(PatientProfiles) library(dplyr) library(CohortConstructor) con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) cdm <- cdm_from_con(con, cdm_schema = \"main\", write_schema = c(prefix = \"my_study_\", schema = \"main\")) print(cdm)"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"generating-concept-based-cohorts","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Generating concept based cohorts","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"start making concept based cohort. need provide concept sets get cohort back, cohort end date event date associated records, overlapping records collapsed, records observation kept. can see starting cohorts, add additional restrictions, following associated settings, counts, attrition.","code":"cdm$fractures <- cdm |> conceptCohort(conceptSet = list( \"ankle_fracture\" = 4059173, \"forearm_fracture\" = 4278672, \"hip_fracture\" = 4230399), name = \"fractures\") settings(cdm$fractures) %>% glimpse() #> Rows: 3 #> Columns: 2 #> $ cohort_definition_id 1, 2, 3 #> $ cohort_name \"ankle_fracture\", \"forearm_fracture\", \"hip_fractu… cohort_count(cdm$fractures) %>% glimpse() #> Rows: 3 #> Columns: 3 #> $ cohort_definition_id 1, 2, 3 #> $ number_records 464, 569, 138 #> $ number_subjects 427, 510, 132 attrition(cdm$fractures) %>% glimpse() #> Rows: 3 #> Columns: 7 #> $ cohort_definition_id 1, 2, 3 #> $ number_records 464, 569, 138 #> $ number_subjects 427, 510, 132 #> $ reason_id 1, 1, 1 #> $ reason \"Initial qualifying events\", \"Initial qualifying … #> $ excluded_records 0, 0, 0 #> $ excluded_subjects 0, 0, 0"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"require-in-date-range","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Require in date range","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"created base cohort, can start applying additional cohort requirements. example, first can require individuals’ cohort start date fall within certain date range. Now ’ve applied date restriction, can see cohort attributes updated","code":"cdm$fractures <- cdm$fractures %>% requireInDateRange(dateRange = as.Date(c(\"2000-01-01\", \"2020-01-01\"))) cohort_count(cdm$fractures) %>% glimpse() #> Rows: 3 #> Columns: 3 #> $ cohort_definition_id 1, 2, 3 #> $ number_records 108, 152, 62 #> $ number_subjects 104, 143, 60 attrition(cdm$fractures) %>% filter(reason == \"cohort_start_date between 2000-01-01 & 2020-01-01\") %>% glimpse() #> Rows: 0 #> Columns: 7 #> $ cohort_definition_id #> $ number_records #> $ number_subjects #> $ reason_id #> $ reason #> $ excluded_records #> $ excluded_subjects "},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"applying-demographic-requirements","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Applying demographic requirements","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"can also add restrictions patient characteristics age (cohort start date default) sex. can see many individuals ’ve lost applying criteria.","code":"cdm$fractures <- cdm$fractures %>% requireDemographics(ageRange = list(c(40, 65)), sex = \"Female\") attrition(cdm$fractures) %>% filter(reason == \"Age requirement: 40 to 65\") %>% glimpse() #> Rows: 3 #> Columns: 7 #> $ cohort_definition_id 1, 2, 3 #> $ number_records 43, 64, 22 #> $ number_subjects 43, 62, 22 #> $ reason_id 4, 4, 4 #> $ reason \"Age requirement: 40 to 65\", \"Age requirement: 40… #> $ excluded_records 65, 88, 40 #> $ excluded_subjects 61, 81, 38 attrition(cdm$fractures) %>% filter(reason == \"Sex requirement: Female\") %>% glimpse() #> Rows: 3 #> Columns: 7 #> $ cohort_definition_id 1, 2, 3 #> $ number_records 19, 37, 12 #> $ number_subjects 19, 36, 12 #> $ reason_id 5, 5, 5 #> $ reason \"Sex requirement: Female\", \"Sex requirement: Fema… #> $ excluded_records 24, 27, 10 #> $ excluded_subjects 24, 26, 10"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"require-presence-in-another-cohort","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Require presence in another cohort","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"can also require individuals another cohort window. example require study participants GI bleed cohort time prior entry fractures cohort.","code":"cdm$gibleed <- cdm |> conceptCohort(conceptSet = list(\"gibleed\" = 192671), name = \"gibleed\") cdm$fractures <- cdm$fractures %>% requireCohortIntersect(targetCohortTable = \"gibleed\", window = c(-Inf, 0)) attrition(cdm$fractures) %>% filter(reason == \"In cohort gibleed between -Inf & 0 days relative to cohort_start_date\") %>% glimpse() #> Rows: 3 #> Columns: 7 #> $ cohort_definition_id 1, 2, 3 #> $ number_records 5, 7, 2 #> $ number_subjects 5, 6, 2 #> $ reason_id 8, 8, 8 #> $ reason \"In cohort gibleed between -Inf & 0 days relative… #> $ excluded_records 14, 30, 10 #> $ excluded_subjects 14, 30, 10"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"combining-cohorts","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Combining cohorts","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"Currently separate fracture cohorts. Let’s say want create cohort people fractures. create cohort like :","code":"cdm$fractures <- cdm$fractures |> CohortConstructor::unionCohorts() settings(cdm$fractures) #> # A tibble: 1 × 3 #> cohort_definition_id cohort_name gap #> #> 1 1 ankle_fracture_forearm_fracture_hip_fracture 0 cohortCount(cdm$fractures) #> # A tibble: 1 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 14 13 cdmDisconnect(cdm)"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/CohortConstructor-package.html","id":null,"dir":"Reference","previous_headings":"","what":"CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model — CohortConstructor-package","title":"CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model — CohortConstructor-package","text":"Create manipulate study cohorts data mapped Observational Medical Outcomes Partnership Common Data Model.","code":""},{"path":[]},{"path":"https://ohdsi.github.io/CohortConstructor/reference/CohortConstructor-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model — CohortConstructor-package","text":"Maintainer: Edward Burn edward.burn@ndorms.ox.ac.uk (ORCID) Authors: Marti Catala marti.catalasabate@ndorms.ox.ac.uk (ORCID) Nuria Mercade-Besora nuria.mercadebesora@ndorms.ox.ac.uk (ORCID) Marta Alcalde-Herraiz marta.alcaldeherraiz@ndorms.ox.ac.uk (ORCID) Mike Du mike.du@ndorms.ox.ac.uk (ORCID) Yuchen Guo yuchen.guo@ndorms.ox.ac.uk (ORCID) Xihang Chen xihang.chen@ndorms.ox.ac.uk (ORCID) Kim Lopez kim.lopez@spc.ox.ac.uk (ORCID)","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/collapseCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","title":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","text":"collapseCohorts() concatenates cohort records, allowing number days one finishing next starting.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/collapseCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","text":"","code":"collapseCohorts(cohort, cohortId = NULL, gap = 0, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/collapseCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","text":"cohort cohort table cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. gap Number days use merging cohort entries. name Name cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/collapseCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","text":"cohort table","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Create cohorts based on a concept set — conceptCohort","title":"Create cohorts based on a concept set — conceptCohort","text":"conceptCohort() creates cohort table patient records clinical tables OMOP CDM. following tables currently supported creating concept cohorts: condition_occurrence device_exposure drug_exposure measurement observation procedure_occurrence visit_occurrence Cohort duration based record start end (e.g. condition_start_date condition_end_date records coming condition_occurrence tables). resulting table satisfies requirements OMOP CDM cohort table: Overlapping records collapsed single cohort entry. record starts outside observation period silently ignored. record ends outside observation period trimmed end preceding observation period end date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create cohorts based on a concept set — conceptCohort","text":"","code":"conceptCohort(cdm, conceptSet, name, exit = \"event_end_date\")"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create cohorts based on a concept set — conceptCohort","text":"cdm cdm reference. conceptSet conceptSet, can either codelist conceptSetExpression. name Name cohort cdm object. exit cohort end date defined. Can either \"event_end_date\" \"event_start_date\".","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create cohorts based on a concept set — conceptCohort","text":"cohort table","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create cohorts based on a concept set — conceptCohort","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(conditionOccurrence = TRUE) #> Note: method with signature ‘DBIConnection#Id’ chosen for function ‘dbExistsTable’, #> target signature ‘duckdb_connection#Id’. #> \"duckdb_connection#ANY\" would also be valid cohort <- conceptCohort(cdm = cdm, conceptSet = list(a = 1), name = \"cohort\") #> Warning: ! `codelist` contains numeric values, they are casted to integers. #> ℹ Subsetting table condition_occurrence using 1 concept with domain: condition. #> ℹ Combining tables. #> ℹ Creating cohort attributes. #> ℹ Applying cohort requirements. #> ℹ Collapsing records. #> ✔ Cohort cohort created. cohort |> attrition() #> # A tibble: 3 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 10 7 1 Initial qualify… #> 2 1 10 7 2 cohort requirem… #> 3 1 7 7 3 Overlapping rec… #> # ℹ 2 more variables: excluded_records , excluded_subjects # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Create cohorts based on patient demographics — demographicsCohort","title":"Create cohorts based on patient demographics — demographicsCohort","text":"demographicsCohort() creates cohort table based patient characteristics. individual satisfies criteria enter cohort. stop satisfying criteria cohort entry ends.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create cohorts based on patient demographics — demographicsCohort","text":"","code":"demographicsCohort( cdm, name, ageRange = NULL, sex = NULL, minPriorObservation = NULL, minFutureObservation = NULL )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create cohorts based on patient demographics — demographicsCohort","text":"cdm cdm reference. name Name new cohort table ageRange list vectors specifying minimum maximum age. sex Can \"\", \"Male\" \"Female\". minPriorObservation minimum number prior observation days database. minFutureObservation minimum number future observation days database.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create cohorts based on patient demographics — demographicsCohort","text":"cohort table","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create cohorts based on patient demographics — demographicsCohort","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cohort <- cdm |> demographicsCohort(name = \"cohort3\", ageRange = c(18,40), sex = \"Male\") #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> ℹ Building new trimmed cohort #> Adding demographics information #> Creating initial cohort #> Trim sex #> Trim age #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> ✔ Cohort trimmed attrition(cohort) #> # A tibble: 3 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 10 10 1 Initial qualify… #> 2 1 5 5 2 Sex requirement… #> 3 1 4 4 3 Age requirement… #> # ℹ 2 more variables: excluded_records , excluded_subjects # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":null,"dir":"Reference","previous_headings":"","what":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"entryAtFirstDate() resets cohort start date based set specified column dates. first date occurs chosen.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"","code":"entryAtFirstDate( cohort, dateColumns, cohortId = NULL, returnReason = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"cohort cohort table cdm reference. dateColumns Date columns cohort table consider. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. returnReason TRUE return column stating column dateColumns used new cohort end date. name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(tables = list( \"cohort\" = dplyr::tibble( cohort_definition_id = 1, subject_id = c(1, 2, 3, 4), cohort_start_date = as.Date(c(\"2000-06-03\", \"2000-01-01\", \"2015-01-15\", \"2000-12-09\")), cohort_end_date = as.Date(c(\"2001-09-01\", \"2001-01-12\", \"2015-02-15\", \"2002-12-09\")), date_1 = as.Date(c(\"2001-08-01\", \"2001-01-01\", \"2015-01-15\", \"2002-12-09\")), date_2 = as.Date(c(\"2001-08-01\", NA, \"2015-02-14\", \"2002-12-09\")) ) )) #> Warning: ! 7 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `gender_concept_id` is numeric but expected integer #> • `year_of_birth` is numeric but expected integer #> • `month_of_birth` is numeric but expected integer #> • `race_concept_id` is numeric but expected integer #> • `ethnicity_concept_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 2 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> • `period_type_concept_id` is numeric but expected integer #> Warning: ! 9 column in cdm_source do not match expected column type: #> • `cdm_source_abbreviation` is logical but expected character #> • `cdm_holder` is logical but expected character #> • `source_description` is logical but expected character #> • `source_documentation_reference` is logical but expected character #> • `cdm_etl_reference` is logical but expected character #> • `source_release_date` is logical but expected date #> • `cdm_release_date` is logical but expected date #> • `cdm_version` is numeric but expected character #> • `vocabulary_version` is logical but expected character #> Warning: ! 3 column in concept do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `valid_start_date` is character but expected date #> • `valid_end_date` is character but expected date #> Warning: ! 1 column in vocabulary do not match expected column type: #> • `vocabulary_concept_id` is numeric but expected integer #> Warning: ! 5 column in concept_relationship do not match expected column type: #> • `concept_id_1` is numeric but expected integer #> • `concept_id_2` is numeric but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> • `invalid_reason` is logical but expected character #> Warning: ! 2 column in concept_synonym do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `language_concept_id` is numeric but expected integer #> Warning: ! 4 column in concept_ancestor do not match expected column type: #> • `ancestor_concept_id` is numeric but expected integer #> • `descendant_concept_id` is numeric but expected integer #> • `min_levels_of_separation` is numeric but expected integer #> • `max_levels_of_separation` is numeric but expected integer #> Warning: ! 9 column in drug_strength do not match expected column type: #> • `drug_concept_id` is numeric but expected integer #> • `ingredient_concept_id` is numeric but expected integer #> • `amount_value` is logical but expected numeric #> • `amount_unit_concept_id` is numeric but expected integer #> • `numerator_unit_concept_id` is numeric but expected integer #> • `denominator_unit_concept_id` is numeric but expected integer #> • `box_size` is logical but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> Warning: ! 2 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 1 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer cdm$cohort |> entryAtLastDate(dateColumns = c(\"date_1\", \"date_2\")) #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> # Source: table [4 x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date entry_reason #> #> 1 1 1 2001-08-01 2001-09-01 date_1; dat… #> 2 1 3 2015-02-14 2015-02-15 date_2 #> 3 1 2 2001-01-01 2001-01-12 date_1 #> 4 1 4 2002-12-09 2002-12-09 date_1; dat… # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort start date to the last of a set of column dates — entryAtLastDate","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"Set cohort start date last set column dates","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"","code":"entryAtLastDate( cohort, dateColumns, cohortId = NULL, returnReason = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"cohort cohort table cdm reference. dateColumns description cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. returnReason TRUE return column stating column dateColumns used new cohort end date. description name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(tables = list( \"cohort\" = dplyr::tibble( cohort_definition_id = 1, subject_id = c(1, 2, 3, 4), cohort_start_date = as.Date(c(\"2000-06-03\", \"2000-01-01\", \"2015-01-15\", \"2000-12-09\")), cohort_end_date = as.Date(c(\"2001-09-01\", \"2001-01-12\", \"2015-02-15\", \"2002-12-09\")), date_1 = as.Date(c(\"2001-08-01\", \"2001-01-01\", \"2015-01-15\", \"2002-12-09\")), date_2 = as.Date(c(\"2001-08-01\", NA, \"2015-02-14\", \"2002-12-09\")) ) )) #> Warning: ! 7 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `gender_concept_id` is numeric but expected integer #> • `year_of_birth` is numeric but expected integer #> • `month_of_birth` is numeric but expected integer #> • `race_concept_id` is numeric but expected integer #> • `ethnicity_concept_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 2 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> • `period_type_concept_id` is numeric but expected integer #> Warning: ! 9 column in cdm_source do not match expected column type: #> • `cdm_source_abbreviation` is logical but expected character #> • `cdm_holder` is logical but expected character #> • `source_description` is logical but expected character #> • `source_documentation_reference` is logical but expected character #> • `cdm_etl_reference` is logical but expected character #> • `source_release_date` is logical but expected date #> • `cdm_release_date` is logical but expected date #> • `cdm_version` is numeric but expected character #> • `vocabulary_version` is logical but expected character #> Warning: ! 3 column in concept do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `valid_start_date` is character but expected date #> • `valid_end_date` is character but expected date #> Warning: ! 1 column in vocabulary do not match expected column type: #> • `vocabulary_concept_id` is numeric but expected integer #> Warning: ! 5 column in concept_relationship do not match expected column type: #> • `concept_id_1` is numeric but expected integer #> • `concept_id_2` is numeric but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> • `invalid_reason` is logical but expected character #> Warning: ! 2 column in concept_synonym do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `language_concept_id` is numeric but expected integer #> Warning: ! 4 column in concept_ancestor do not match expected column type: #> • `ancestor_concept_id` is numeric but expected integer #> • `descendant_concept_id` is numeric but expected integer #> • `min_levels_of_separation` is numeric but expected integer #> • `max_levels_of_separation` is numeric but expected integer #> Warning: ! 9 column in drug_strength do not match expected column type: #> • `drug_concept_id` is numeric but expected integer #> • `ingredient_concept_id` is numeric but expected integer #> • `amount_value` is logical but expected numeric #> • `amount_unit_concept_id` is numeric but expected integer #> • `numerator_unit_concept_id` is numeric but expected integer #> • `denominator_unit_concept_id` is numeric but expected integer #> • `box_size` is logical but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> Warning: ! 2 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 1 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer cdm$cohort |> entryAtLastDate(dateColumns = c(\"date_1\", \"date_2\")) #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> # Source: table [4 x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date entry_reason #> #> 1 1 1 2001-08-01 2001-09-01 date_2; dat… #> 2 1 3 2015-02-14 2015-02-15 date_2 #> 3 1 4 2002-12-09 2002-12-09 date_2; dat… #> 4 1 2 2001-01-01 2001-01-12 date_1 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort end date to death date — exitAtDeath","title":"Set cohort end date to death date — exitAtDeath","text":"functions changes cohort end date subject's death date. case generates overlapping records cohort, overlapping entries merged.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort end date to death date — exitAtDeath","text":"","code":"exitAtDeath( cohort, cohortId = NULL, requireDeath = FALSE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort end date to death date — exitAtDeath","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. requireDeath TRUE, subjects without death record dropped, FALSE end date left . name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort end date to death date — exitAtDeath","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort end date to death date — exitAtDeath","text":"","code":"# \\donttest{ library(PatientProfiles) library(CohortConstructor) cdm <- mockPatientProfiles() #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. cdm$cohort1 |> exitAtDeath() #> # Source: table [10 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 2 2 1998-11-05 2008-01-27 #> 2 1 6 2006-12-25 2022-11-01 #> 3 2 1 1951-11-28 2019-01-16 #> 4 2 5 2113-08-18 2144-11-05 #> 5 2 8 1954-07-05 1955-07-17 #> 6 3 7 2029-01-30 2050-08-27 #> 7 3 10 2003-01-05 2060-02-27 #> 8 2 3 1993-12-06 1997-05-26 #> 9 2 9 2109-11-07 2115-08-03 #> 10 1 4 2017-04-18 2077-11-07 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"exitAtFirstDate() resets cohort end date based set specified column dates. first date occurs chosen.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"","code":"exitAtFirstDate( cohort, dateColumns, cohortId = NULL, returnReason = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"cohort cohort table cdm reference. dateColumns Date columns cohort table consider. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. returnReason TRUE return column stating column dateColumns used new cohort end date. name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(tables = list( \"cohort\" = dplyr::tibble( cohort_definition_id = 1, subject_id = c(1, 2, 3, 4), cohort_start_date = as.Date(c(\"2000-06-03\", \"2000-01-01\", \"2015-01-15\", \"2000-12-09\")), cohort_end_date = as.Date(c(\"2001-09-01\", \"2001-01-12\", \"2015-02-15\", \"2002-12-09\")), date_1 = as.Date(c(\"2001-08-01\", \"2001-01-01\", \"2015-01-15\", \"2002-12-09\")), date_2 = as.Date(c(\"2001-08-01\", NA, \"2015-04-15\", \"2002-12-09\")) ) )) #> Warning: ! 7 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `gender_concept_id` is numeric but expected integer #> • `year_of_birth` is numeric but expected integer #> • `month_of_birth` is numeric but expected integer #> • `race_concept_id` is numeric but expected integer #> • `ethnicity_concept_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 2 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> • `period_type_concept_id` is numeric but expected integer #> Warning: ! 9 column in cdm_source do not match expected column type: #> • `cdm_source_abbreviation` is logical but expected character #> • `cdm_holder` is logical but expected character #> • `source_description` is logical but expected character #> • `source_documentation_reference` is logical but expected character #> • `cdm_etl_reference` is logical but expected character #> • `source_release_date` is logical but expected date #> • `cdm_release_date` is logical but expected date #> • `cdm_version` is numeric but expected character #> • `vocabulary_version` is logical but expected character #> Warning: ! 3 column in concept do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `valid_start_date` is character but expected date #> • `valid_end_date` is character but expected date #> Warning: ! 1 column in vocabulary do not match expected column type: #> • `vocabulary_concept_id` is numeric but expected integer #> Warning: ! 5 column in concept_relationship do not match expected column type: #> • `concept_id_1` is numeric but expected integer #> • `concept_id_2` is numeric but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> • `invalid_reason` is logical but expected character #> Warning: ! 2 column in concept_synonym do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `language_concept_id` is numeric but expected integer #> Warning: ! 4 column in concept_ancestor do not match expected column type: #> • `ancestor_concept_id` is numeric but expected integer #> • `descendant_concept_id` is numeric but expected integer #> • `min_levels_of_separation` is numeric but expected integer #> • `max_levels_of_separation` is numeric but expected integer #> Warning: ! 9 column in drug_strength do not match expected column type: #> • `drug_concept_id` is numeric but expected integer #> • `ingredient_concept_id` is numeric but expected integer #> • `amount_value` is logical but expected numeric #> • `amount_unit_concept_id` is numeric but expected integer #> • `numerator_unit_concept_id` is numeric but expected integer #> • `denominator_unit_concept_id` is numeric but expected integer #> • `box_size` is logical but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> Warning: ! 2 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 1 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer cdm$cohort |> exitAtFirstDate(dateColumns = c(\"date_1\", \"date_2\")) #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> # Source: table [4 x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date exit_reason #> #> 1 1 3 2015-01-15 2015-01-15 date_1 #> 2 1 4 2000-12-09 2002-12-09 date_2; dat… #> 3 1 2 2000-01-01 2001-01-01 date_1 #> 4 1 1 2000-06-03 2001-08-01 date_2; dat… # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort end date to the last of a set of column dates — exitAtLastDate","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"exitAtLastDate() resets cohort end date based set specified column dates. last date occurs chosen.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"","code":"exitAtLastDate( cohort, dateColumns, cohortId = NULL, returnReason = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"cohort cohort table cdm reference. dateColumns description cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. returnReason TRUE return column stating column dateColumns used new cohort end date. description name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(tables = list( \"cohort\" = dplyr::tibble( cohort_definition_id = 1, subject_id = c(1, 2, 3, 4), cohort_start_date = as.Date(c(\"2000-06-03\", \"2000-01-01\", \"2015-01-15\", \"2000-12-09\")), cohort_end_date = as.Date(c(\"2001-09-01\", \"2001-01-12\", \"2015-02-15\", \"2002-12-09\")), date_1 = as.Date(c(\"2001-08-01\", \"2001-01-01\", \"2015-01-15\", \"2002-12-09\")), date_2 = as.Date(c(\"2001-08-01\", NA, \"2015-04-15\", \"2002-12-09\")) ) )) #> Warning: ! 7 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `gender_concept_id` is numeric but expected integer #> • `year_of_birth` is numeric but expected integer #> • `month_of_birth` is numeric but expected integer #> • `race_concept_id` is numeric but expected integer #> • `ethnicity_concept_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 2 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> • `period_type_concept_id` is numeric but expected integer #> Warning: ! 9 column in cdm_source do not match expected column type: #> • `cdm_source_abbreviation` is logical but expected character #> • `cdm_holder` is logical but expected character #> • `source_description` is logical but expected character #> • `source_documentation_reference` is logical but expected character #> • `cdm_etl_reference` is logical but expected character #> • `source_release_date` is logical but expected date #> • `cdm_release_date` is logical but expected date #> • `cdm_version` is numeric but expected character #> • `vocabulary_version` is logical but expected character #> Warning: ! 3 column in concept do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `valid_start_date` is character but expected date #> • `valid_end_date` is character but expected date #> Warning: ! 1 column in vocabulary do not match expected column type: #> • `vocabulary_concept_id` is numeric but expected integer #> Warning: ! 5 column in concept_relationship do not match expected column type: #> • `concept_id_1` is numeric but expected integer #> • `concept_id_2` is numeric but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> • `invalid_reason` is logical but expected character #> Warning: ! 2 column in concept_synonym do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `language_concept_id` is numeric but expected integer #> Warning: ! 4 column in concept_ancestor do not match expected column type: #> • `ancestor_concept_id` is numeric but expected integer #> • `descendant_concept_id` is numeric but expected integer #> • `min_levels_of_separation` is numeric but expected integer #> • `max_levels_of_separation` is numeric but expected integer #> Warning: ! 9 column in drug_strength do not match expected column type: #> • `drug_concept_id` is numeric but expected integer #> • `ingredient_concept_id` is numeric but expected integer #> • `amount_value` is logical but expected numeric #> • `amount_unit_concept_id` is numeric but expected integer #> • `numerator_unit_concept_id` is numeric but expected integer #> • `denominator_unit_concept_id` is numeric but expected integer #> • `box_size` is logical but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> Warning: ! 2 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 1 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer cdm$cohort |> exitAtLastDate(dateColumns = c(\"date_1\", \"date_2\")) #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> # Source: table [4 x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date exit_reason #> #> 1 1 2 2000-01-01 2001-01-01 date_1 #> 2 1 4 2000-12-09 2002-12-09 date_2; dat… #> 3 1 3 2015-01-15 2015-04-15 date_2 #> 4 1 1 2000-06-03 2001-08-01 date_2; dat… # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort end date to end of observation — exitAtObservationEnd","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"exitAtObservationEnd() resets cohort end date based set specified column dates. last date occurs chosen. functions changes cohort end date end date observation period corresponding cohort entry. case generates overlapping records cohort, overlapping entries merged.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"","code":"exitAtObservationEnd(cohort, cohortId = NULL, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> exitAtObservationEnd() #> # Source: table [6 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 4 1996-06-30 2013-12-31 #> 2 1 2 2000-05-04 2003-06-15 #> 3 1 7 2014-03-07 2014-04-09 #> 4 1 1 2001-05-30 2013-06-29 #> 5 1 5 2012-03-20 2013-02-10 #> 6 1 3 2015-01-27 2015-10-11 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"intersectCohorts() combines different cohort entries, records overlap combined kept. Cohort entries individual cohorts.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"","code":"intersectCohorts( cohort, cohortId = NULL, gap = 0, mutuallyExclusive = FALSE, returnOnlyComb = FALSE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. gap Number days two subsequent cohort entries merged single cohort record. mutuallyExclusive Whether generated cohorts mutually exclusive . returnOnlyComb Whether get combination cohort back name Name new cohort demographic requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort3 <- intersectCohorts( cohort = cdm$cohort2, name = \"cohort3\", ) #> Warning: ! 3 casted column in cohort3 (cohort_attrition) as do not match expected column #> type: #> • `reason_id` from numeric to integer #> • `excluded_records` from numeric to integer #> • `excluded_subjects` from numeric to integer settings(cdm$cohort3) #> # A tibble: 3 × 6 #> cohort_definition_id cohort_name cohort_1 cohort_2 mutually_exclusive gap #> #> 1 1 cohort_1 1 0 FALSE 0 #> 2 2 cohort_2 0 1 FALSE 0 #> 3 3 cohort_1_coho… 1 1 FALSE 0 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a new cohort matched cohort — matchCohorts","title":"Generate a new cohort matched cohort — matchCohorts","text":"matchCohorts() generate new cohort matched individuals existing cohort. Individuals can matched based year birth sex.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a new cohort matched cohort — matchCohorts","text":"","code":"matchCohorts( cohort, cohortId = NULL, matchSex = TRUE, matchYearOfBirth = TRUE, ratio = 1, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a new cohort matched cohort — matchCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. matchSex Whether match sex. matchYearOfBirth Whether match year birth. ratio Number allowed matches per individual target cohort. name Name new generated cohort set.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a new cohort matched cohort — matchCohorts","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a new cohort matched cohort — matchCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) library(dplyr) #> #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #> #> filter, lag #> The following objects are masked from ‘package:base’: #> #> intersect, setdiff, setequal, union cdm <- mockCohortConstructor(nPerson = 200) cdm$new_matched_cohort <- cdm$cohort2 |> matchCohorts( name = \"new_matched_cohort\", cohortId = 2, matchSex = TRUE, matchYearOfBirth = TRUE, ratio = 1) #> Starting matching #> Warning: Multiple records per person detected. The matchCohorts() function is designed #> to operate under the assumption that there is only one record per person within #> each cohort. If this assumption is not met, each record will be treated #> independently. As a result, the same individual may be matched multiple times, #> leading to inconsistent and potentially misleading results. #> ℹ Creating copy of target cohort. #> • 1 cohort to be matched. #> ℹ Creating controls cohorts. #> Warning: ! 2 casted column in tmp_004_og_039_1724749686 (cohort_attrition) as do not #> match expected column type: #> • `number_records` from numeric to integer #> • `number_subjects` from numeric to integer #> ℹ Excluding cases from controls #> • Matching by gender_concept_id and year_of_birth #> • Removing controls that were not in observation at index date #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> • Excluding target records whose pair is not in observation #> • Adjusting ratio #> Binding both cohorts #> ✔ Done cdm$new_matched_cohort #> # Source: table [?? x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date cluster_id #> #> 1 1 118 1975-11-28 1981-05-30 6 #> 2 1 56 2007-09-28 2008-07-15 18 #> 3 1 63 2008-08-23 2008-09-02 19 #> 4 1 20 1985-08-15 1990-06-06 26 #> 5 1 19 2003-06-22 2005-07-21 36 #> 6 1 84 2000-04-13 2006-06-11 42 #> 7 1 121 2007-10-25 2010-01-05 47 #> 8 1 113 2015-09-05 2016-01-10 50 #> 9 1 24 2016-12-17 2016-12-29 59 #> 10 1 62 2017-01-18 2017-04-26 74 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Create cohorts measurement based cohorts — measurementCohort","title":"Create cohorts measurement based cohorts — measurementCohort","text":"measurementCohort() creates cohorts based patient records contained measurement table. function extends conceptCohort() allows measurement values associated records specified. valueAsConcept valueAsNumber NULL requirements values associated measurement records using measurementCohort() lead result using conceptCohort() (long concepts measurement domain). one valueAsConcept valueAsNumber NULL records required values satisfy requirement specified. valueAsConcept valueAsNumber NULL, records required values fulfill either requirements","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create cohorts measurement based cohorts — measurementCohort","text":"","code":"measurementCohort( cdm, conceptSet, name, valueAsConcept = NULL, valueAsNumber = NULL )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create cohorts measurement based cohorts — measurementCohort","text":"cdm cdm reference. conceptSet conceptSet, can either codelist conceptSetExpression. name Name cohort cdm object. valueAsConcept vector cohort IDs used filter measurements. measurements values value_as_concept_id column measurement table included. NULL entries independently value concept considered. valueAsNumber named list indicating range values unit correspond , follows: list(\"unit_concept_id\" = c(rangeValue1, rangeValue2)). NULL, entries independently value number included.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create cohorts measurement based cohorts — measurementCohort","text":"cohort table","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create cohorts measurement based cohorts — measurementCohort","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(con = NULL) cdm$concept <- cdm$concept |> dplyr::union_all( dplyr::tibble( concept_id = c(4326744, 4298393, 45770407, 8876, 4124457), concept_name = c(\"Blood pressure\", \"Systemic blood pressure\", \"Baseline blood pressure\", \"millimeter mercury column\", \"Normal range\"), domain_id = \"Measurement\", vocabulary_id = c(\"SNOMED\", \"SNOMED\", \"SNOMED\", \"UCUM\", \"SNOMED\"), standard_concept = \"S\", concept_class_id = c(\"Observable Entity\", \"Observable Entity\", \"Observable Entity\", \"Unit\", \"Qualifier Value\"), concept_code = NA, valid_start_date = NA, valid_end_date = NA, invalid_reason = NA ) ) cdm$measurement <- dplyr::tibble( measurement_id = 1:4, person_id = c(1, 1, 2, 3), measurement_concept_id = c(4326744, 4298393, 4298393, 45770407), measurement_date = as.Date(c(\"2000-07-01\", \"2000-12-11\", \"2002-09-08\", \"2015-02-19\")), measurement_type_concept_id = NA, value_as_number = c(100, 125, NA, NA), value_as_concept_id = c(0, 0, 0, 4124457), unit_concept_id = c(8876, 8876, 0, 0) ) cdm <- CDMConnector::copyCdmTo( con = DBI::dbConnect(duckdb::duckdb()), cdm = cdm, schema = \"main\") cdm$cohort <- measurementCohort( cdm = cdm, name = \"cohort\", conceptSet = list(\"normal_blood_pressure\" = c(4326744, 4298393, 45770407)), valueAsConcept = c(4124457), valueAsNumber = list(\"8876\" = c(70, 120)) ) #> Warning: ! `codelist` contains numeric values, they are casted to integers. #> ℹ Getting records in observation. #> ℹ Applying measurement requirements. #> ℹ Creating cohort attributes. #> Warning: ! 1 column in cohort do not match expected column type: #> • `subject_id` is numeric but expected integer #> ✔ Cohort cohort created. cdm$cohort #> # Source: table [2 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2000-07-01 2000-07-01 #> 2 1 3 2015-02-19 2015-02-19 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"mockCohortConstructor() creates example dataset can used demonstrating testing package","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"","code":"mockCohortConstructor( nPerson = 10, conceptTable = NULL, tables = NULL, conceptId = NULL, conceptIdClass = NULL, drugExposure = FALSE, conditionOccurrence = FALSE, measurement = FALSE, death = FALSE, otherTables = NULL, con = DBI::dbConnect(duckdb::duckdb()), writeSchema = \"main\", seed = 123 )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"nPerson number person cdm conceptTable user defined concept table tables list tables include cdm conceptId list concept id conceptIdClass domain class conceptId drugExposure T/F include drug exposure table cdm conditionOccurrence T/F include condition occurrence cdm measurement T/F include measurement cdm death T/F include death table cdm otherTables takes list single tibble names include tables cdm con DBI connection create cdm mock object. writeSchema Name schema connection writing permissions. seed Seed passed omock::mockCdmFromTable","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"cdm object","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm #> #> ── # OMOP CDM reference (duckdb) of mock database ────────────────────────────── #> • omop tables: person, observation_period, cdm_source, concept, vocabulary, #> concept_relationship, concept_synonym, concept_ancestor, drug_strength #> • cohort tables: cohort1, cohort2 #> • achilles tables: - #> • other tables: - # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. omopgenerics attrition, bind, cohortCodelist, cohortCount, settings, tableName PatientProfiles endDateColumn, startDateColumn","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on age — requireAge","title":"Restrict cohort on age — requireAge","text":"requireAge() filters cohort records, keeping records individuals satisfy specified age criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on age — requireAge","text":"","code":"requireAge( cohort, ageRange, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on age — requireAge","text":"cohort cohort table cdm reference. ageRange list minimum maximum age. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains date compute demographics characteristics restrict . name Name new cohort age requirement.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on age — requireAge","text":"cohort table records individuals satisfying age requirement","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on age — requireAge","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requireAge(indexDate = \"cohort_start_date\", ageRange = list(c(18, 65))) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [7 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 2 2000-05-04 2000-05-17 #> 2 1 2 2000-05-18 2001-01-23 #> 3 1 3 2015-01-27 2015-06-28 #> 4 1 5 2012-03-20 2012-04-30 #> 5 1 5 2012-05-01 2012-07-24 #> 6 1 7 2014-03-07 2014-03-07 #> 7 1 7 2014-03-08 2014-03-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":null,"dir":"Reference","previous_headings":"","what":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"requireCohortIntersect() filters cohort table based requirement individual seen (seen) another cohort time window around index date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"","code":"requireCohortIntersect( cohort, targetCohortTable, window, intersections = c(1, Inf), cohortId = NULL, targetCohortId = NULL, indexDate = \"cohort_start_date\", targetStartDate = \"cohort_start_date\", targetEndDate = \"cohort_end_date\", censorDate = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"cohort cohort table cdm reference. targetCohortTable Name cohort want check intersect. window Window consider events . intersections range indicating number intersections criteria fulfilled. single number passed, number intersections must match . cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. targetCohortId Vector cohort definition ids include. indexDate Variable x contains date compute intersection. targetStartDate Date reference cohort table, either start (overlap) (incidence). targetEndDate Date reference cohort table, either end (overlap) NULL (incidence). censorDate Whether censor overlap events specific date column date x. name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"Cohort table isatisfying criteria kept","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requireCohortIntersect(targetCohortTable = \"cohort2\", targetCohortId = 1, indexDate = \"cohort_start_date\", window = c(-Inf, 0)) #> # Source: table [10 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2001-05-30 2003-05-01 #> 2 1 1 2003-05-02 2006-06-10 #> 3 1 2 2000-05-04 2000-05-17 #> 4 1 2 2000-05-18 2001-01-23 #> 5 1 3 2015-01-27 2015-06-28 #> 6 1 4 1996-06-30 1998-11-20 #> 7 1 5 2012-03-20 2012-04-30 #> 8 1 5 2012-05-01 2012-07-24 #> 9 1 7 2014-03-07 2014-03-07 #> 10 1 7 2014-03-08 2014-03-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":null,"dir":"Reference","previous_headings":"","what":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"requireConceptIntersect() filters cohort table based requirement individual seen (seen) events related concept list time window around index date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"","code":"requireConceptIntersect( cohort, conceptSet, window, intersections = c(1, Inf), cohortId = NULL, indexDate = \"cohort_start_date\", targetStartDate = \"event_start_date\", targetEndDate = \"event_end_date\", censorDate = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"cohort cohort table cdm reference. conceptSet Concept set list. window Window consider events . intersections range indicating number intersections criteria fulfilled. single number passed, number intersections must match . cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged.. indexDate Variable x contains date compute intersection. targetStartDate Date reference cohort table, either start (overlap) (incidence). targetEndDate Date reference cohort table, either end (overlap) NULL (incidence). censorDate Whether censor overlap events specific date column date x. name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"Cohort table events concept list kept (without event negate = TRUE)","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(conditionOccurrence = TRUE) cdm$cohort2 <- requireConceptIntersect( cohort = cdm$cohort1, conceptSet = list(a = 1), window = c(-Inf, 0), name = \"cohort2\") #> Warning: ! `codelist` contains numeric values, they are casted to integers. # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":null,"dir":"Reference","previous_headings":"","what":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"requireDeathFlag() filters cohort table based requirement individual seen (seen) death time window around index date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"","code":"requireDeathFlag( cohort, window, cohortId = NULL, indexDate = \"cohort_start_date\", censorDate = NULL, negate = FALSE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"cohort cohort table cdm reference. window Window consider events . cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable x contains date compute intersection. censorDate Whether censor overlap events specific date column date x. negate set TRUE, criteria applied exclusion rather inclusion (.e. require absence another cohort). name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"Cohort table death event kept (without negate = TRUE)","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"","code":"# \\donttest{ library(CDMConnector) #> #> Attaching package: ‘CDMConnector’ #> The following objects are masked from ‘package:CohortConstructor’: #> #> intersectCohorts, unionCohorts library(CohortConstructor) cdm <- mockCohortConstructor(death = TRUE) cdm$cohort1 <- cdm$cohort1 |> requireDeathFlag(window = list(c(0, Inf))) attrition(cdm$cohort1) #> # A tibble: 2 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 10 6 1 Initial qualify… #> 2 1 10 6 2 Death between 0… #> # ℹ 2 more variables: excluded_records , excluded_subjects # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on patient demographics — requireDemographics","title":"Restrict cohort on patient demographics — requireDemographics","text":"requireDemographics() filters cohort records, keeping records individuals satisfy specified demographic criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on patient demographics — requireDemographics","text":"","code":"requireDemographics( cohort, cohortId = NULL, indexDate = \"cohort_start_date\", ageRange = list(c(0, 150)), sex = c(\"Both\"), minPriorObservation = 0, minFutureObservation = 0, requirementInteractions = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on patient demographics — requireDemographics","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains date compute demographics characteristics restrict . ageRange list minimum maximum age. sex Can \"\", \"Male\" \"Female\". one latter, sex included. minPriorObservation minimum number prior observation days database. minFutureObservation minimum number future observation days database. requirementInteractions TRUE, cohorts created combinations ageGroup, sex, daysPriorObservation. FALSE, first value specified factors used. Consequently, order values matters requirementInteractions FALSE. name Name new cohort demographic requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on patient demographics — requireDemographics","text":"cohort table records individuals satisfying demographic requirements","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on patient demographics — requireDemographics","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 |> requireDemographics(indexDate = \"cohort_start_date\", ageRange = list(c(18, 65)), sex = \"Female\", minPriorObservation = 365) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [3 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 32 1991-09-11 2002-11-15 #> 2 1 38 1990-05-01 1994-07-14 #> 3 1 85 2000-05-09 2001-11-16 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on future observation — requireFutureObservation","title":"Restrict cohort on future observation — requireFutureObservation","text":"requireFutureObservation() filters cohort records, keeping records individuals satisfy specified future observation criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on future observation — requireFutureObservation","text":"","code":"requireFutureObservation( cohort, minFutureObservation, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on future observation — requireFutureObservation","text":"cohort cohort table cdm reference. minFutureObservation minimum number future observation days database. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains date compute demographics characteristics restrict . name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on future observation — requireFutureObservation","text":"cohort table records individuals satisfying future observation requirement","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on future observation — requireFutureObservation","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requireFutureObservation(indexDate = \"cohort_start_date\", minFutureObservation = 30) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [10 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2001-05-30 2003-05-01 #> 2 1 1 2003-05-02 2006-06-10 #> 3 1 2 2000-05-04 2000-05-17 #> 4 1 2 2000-05-18 2001-01-23 #> 5 1 3 2015-01-27 2015-06-28 #> 6 1 4 1996-06-30 1998-11-20 #> 7 1 5 2012-03-20 2012-04-30 #> 8 1 5 2012-05-01 2012-07-24 #> 9 1 7 2014-03-07 2014-03-07 #> 10 1 7 2014-03-08 2014-03-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":null,"dir":"Reference","previous_headings":"","what":"Require that an index date is within a date range — requireInDateRange","title":"Require that an index date is within a date range — requireInDateRange","text":"requireInDateRange() filters cohort records, keeping index date within specified date range.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require that an index date is within a date range — requireInDateRange","text":"","code":"requireInDateRange( cohort, dateRange, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require that an index date is within a date range — requireInDateRange","text":"cohort cohort table cdm reference. dateRange window time index date must observed. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains index date interest name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require that an index date is within a date range — requireInDateRange","text":"cohort table cohort entries outside date range dropped","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require that an index date is within a date range — requireInDateRange","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 |> requireInDateRange(indexDate = \"cohort_start_date\", dateRange = as.Date(c(\"2010-01-01\", \"2019-01-01\"))) #> # Source: table [?? x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 6 2011-03-07 2014-01-24 #> 2 1 7 2014-03-08 2014-03-19 #> 3 1 13 2014-06-24 2014-06-29 #> 4 1 13 2014-06-30 2014-08-07 #> 5 1 17 2017-03-28 2017-04-05 #> 6 1 18 2012-01-30 2012-05-21 #> 7 1 24 2016-11-15 2016-11-22 #> 8 1 24 2016-11-23 2016-11-29 #> 9 1 24 2016-11-30 2017-01-25 #> 10 1 31 2013-03-29 2014-02-09 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort to first entry — requireIsFirstEntry","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"requireIsFirstEntry() filters cohort records, keeping first cohort entry per person.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"","code":"requireIsFirstEntry( cohort, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Column name cohort contains date restrict . name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"cohort table cdm reference.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 <- requireIsFirstEntry(cdm$cohort1) # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort to last entry per person — requireIsLastEntry","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"requireIsLastEntry() filters cohort records, keeping last cohort entry per person.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"","code":"requireIsLastEntry( cohort, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Column name cohort contains date restrict . name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"cohort table cdm reference.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 <- requireIsLastEntry(cdm$cohort1) # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on prior observation — requirePriorObservation","title":"Restrict cohort on prior observation — requirePriorObservation","text":"requirePriorObservation() filters cohort records, keeping records individuals satisfy specified prior observation criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on prior observation — requirePriorObservation","text":"","code":"requirePriorObservation( cohort, minPriorObservation, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on prior observation — requirePriorObservation","text":"cohort cohort table cdm reference. minPriorObservation minimum number prior observation days database. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains date compute demographics characteristics restrict . name Name new cohort prior observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on prior observation — requirePriorObservation","text":"cohort table records individuals satisfying prior observation requirement","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on prior observation — requirePriorObservation","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requirePriorObservation(indexDate = \"cohort_start_date\", minPriorObservation = 365) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [4 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2003-05-02 2006-06-10 #> 2 1 2 2000-05-04 2000-05-17 #> 3 1 2 2000-05-18 2001-01-23 #> 4 1 4 1996-06-30 1998-11-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on sex — requireSex","title":"Restrict cohort on sex — requireSex","text":"requireSex() filters cohort records, keeping records individuals satisfy specified sex criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on sex — requireSex","text":"","code":"requireSex(cohort, sex, cohortId = NULL, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on sex — requireSex","text":"cohort cohort table cdm reference. sex Can \"\", \"Male\" \"Female\". one latter, sex included. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. name Name new cohort sex requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on sex — requireSex","text":"cohort table records individuals satisfying sex requirement","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on sex — requireSex","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requireSex(sex = \"Female\") #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [5 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 2 2000-05-04 2000-05-17 #> 2 1 2 2000-05-18 2001-01-23 #> 3 1 3 2015-01-27 2015-06-28 #> 4 1 5 2012-03-20 2012-04-30 #> 5 1 5 2012-05-01 2012-07-24 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":null,"dir":"Reference","previous_headings":"","what":"Require cohort subjects are present in another clinical table — requireTableIntersect","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"requireTableIntersect() filters cohort table based requirement individual seen (seen) record (records) clinical table time window around index date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"","code":"requireTableIntersect( cohort, tableName, window, intersections = c(1, Inf), cohortId = NULL, indexDate = \"cohort_start_date\", targetStartDate = startDateColumn(tableName), targetEndDate = endDateColumn(tableName), censorDate = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"cohort cohort table cdm reference. tableName Name table check intersect. window Window consider events . intersections range indicating number intersections criteria fulfilled. single number passed, number intersections must match . cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable x contains date compute intersection. targetStartDate Date reference cohort table, either start (overlap) (incidence). targetEndDate Date reference cohort table, either end (overlap) NULL (incidence). censorDate Whether censor overlap events specific date column date x. name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"Cohort table table kept (table negate = TRUE)","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(drugExposure = TRUE) #> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 90% | ETA: 0s cdm$cohort1 |> requireTableIntersect(tableName = \"drug_exposure\", indexDate = \"cohort_start_date\", window = c(-Inf, 0)) #> # Source: table [7 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2003-05-02 2006-06-10 #> 2 1 2 2000-05-04 2000-05-17 #> 3 1 2 2000-05-18 2001-01-23 #> 4 1 3 2015-01-27 2015-06-28 #> 5 1 4 1996-06-30 1998-11-20 #> 6 1 5 2012-05-01 2012-07-24 #> 7 1 7 2014-03-08 2014-03-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample a cohort table for a given number of individuals. — sampleCohorts","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"sampleCohorts() samples existing cohort table given number people. records individuals preserved.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"","code":"sampleCohorts(cohort, cohortId = NULL, n, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included sampled. n Number people sampled included cohort. name Name new sampled cohort.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"Cohort table specified cohorts sampled.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort2 |> sampleCohorts(cohortId = 1, n = 10) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [?? x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2001-02-15 2001-10-28 #> 2 1 1 2001-10-29 2003-03-15 #> 3 1 1 2003-03-16 2005-02-08 #> 4 1 2 1999-11-11 2002-04-09 #> 5 1 28 2005-04-01 2005-04-03 #> 6 1 28 2005-04-04 2005-08-23 #> 7 1 48 1964-01-15 1966-03-08 #> 8 1 48 1966-03-09 1966-08-01 #> 9 1 48 1966-08-02 1967-04-16 #> 10 1 48 1967-04-17 1974-01-28 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a new cohort table from stratifying an existing one — stratifyCohorts","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"stratifyCohorts() creates new cohorts, splitting existing cohort based specified columns stratify .","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"","code":"stratifyCohorts( cohort, strata, cohortId = NULL, removeStrata = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"cohort cohort table cdm reference. strata strata list point columns cohort table. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. removeStrata Whether remove strata columns final cohort table. name Name new cohort.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"Cohort table stratified.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) library(PatientProfiles) cdm <- mockCohortConstructor() cdm$my_cohort <- cdm$cohort1 |> addAge(ageGroup = list(\"child\" = c(0, 17), \"adult\" = c(18, Inf))) |> addSex() |> stratifyCohorts( strata = list(\"sex\", c(\"sex\", \"age_group\")), name = \"my_cohort\" ) #> Warning: ! 5 casted column in my_cohort (cohort_attrition) as do not match expected #> column type: #> • `number_records` from numeric to integer #> • `number_subjects` from numeric to integer #> • `reason_id` from numeric to integer #> • `excluded_records` from numeric to integer #> • `excluded_subjects` from numeric to integer #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. cdm$my_cohort #> # Source: table [?? x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date age #> #> 1 2 1 2001-05-30 2003-05-01 3 #> 2 2 1 2003-05-02 2006-06-10 5 #> 3 1 2 2000-05-04 2000-05-17 37 #> 4 1 2 2000-05-18 2001-01-23 37 #> 5 1 3 2015-01-27 2015-06-28 28 #> 6 2 4 1996-06-30 1998-11-20 17 #> 7 1 5 2012-03-20 2012-04-30 39 #> 8 1 5 2012-05-01 2012-07-24 39 #> 9 2 7 2014-03-07 2014-03-07 27 #> 10 2 7 2014-03-08 2014-03-20 27 #> # ℹ more rows settings(cdm$my_cohort) #> # A tibble: 6 × 8 #> cohort_definition_id cohort_name target_cohort_id target_cohort_name #> #> 1 1 cohort_1_female 1 cohort_1 #> 2 2 cohort_1_male 1 cohort_1 #> 3 3 cohort_1_female_adult 1 cohort_1 #> 4 4 cohort_1_female_child 1 cohort_1 #> 5 5 cohort_1_male_adult 1 cohort_1 #> 6 6 cohort_1_male_child 1 cohort_1 #> # ℹ 4 more variables: target_cohort_table_name , strata_columns , #> # sex , age_group attrition(cdm$my_cohort) #> # A tibble: 16 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 10 6 1 Initial qualif… #> 2 1 5 3 2 filter strata:… #> 3 2 10 6 1 Initial qualif… #> 4 2 5 3 2 filter strata:… #> 5 3 10 6 1 Initial qualif… #> 6 3 5 3 2 filter strata:… #> 7 3 5 3 3 filter strata:… #> 8 4 10 6 1 Initial qualif… #> 9 4 5 3 2 filter strata:… #> 10 4 0 0 3 filter strata:… #> 11 5 10 6 1 Initial qualif… #> 12 5 5 3 2 filter strata:… #> 13 5 2 1 3 filter strata:… #> 14 6 10 6 1 Initial qualif… #> 15 6 5 3 2 filter strata:… #> 16 6 3 2 3 filter strata:… #> # ℹ 2 more variables: excluded_records , excluded_subjects # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"subsetCohorts() filters existing cohort table, keeping records cohorts specified.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"","code":"subsetCohorts(cohort, cohortId, minCohortCount = 0, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. minCohortCount minimum count cohort included. Default 0, meaning non-empty cohorts included. Cohorts included removed cohort set. name Name new cohort demographic requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"Cohort table cohorts cohortId.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 |> subsetCohorts(cohortId = 1) #> # Source: table [?? x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2001-02-15 2001-10-28 #> 2 1 1 2001-10-29 2003-03-15 #> 3 1 1 2003-03-16 2005-02-08 #> 4 1 2 1999-11-11 2002-04-09 #> 5 1 6 2011-03-07 2014-01-24 #> 6 1 7 2014-03-08 2014-03-19 #> 7 1 10 2019-12-04 2019-12-14 #> 8 1 13 2014-06-24 2014-06-29 #> 9 1 13 2014-06-30 2014-08-07 #> 10 1 14 1986-11-29 1987-12-14 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on patient demographics — trimDemographics","title":"Restrict cohort on patient demographics — trimDemographics","text":"trimDemographics() resets cohort start end date based specified demographic criteria satisfied.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on patient demographics — trimDemographics","text":"","code":"trimDemographics( cohort, cohortId = NULL, ageRange = NULL, sex = NULL, minPriorObservation = NULL, minFutureObservation = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on patient demographics — trimDemographics","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. ageRange list minimum maximum age. sex Can \"\", \"Male\" \"Female\". one latter, sex included. minPriorObservation minimum number prior observation days database. minFutureObservation minimum number future observation days database. name Name new cohort demographic requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on patient demographics — trimDemographics","text":"cohort table records individuals satisfying demographic requirements","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on patient demographics — trimDemographics","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 |> trimDemographics(ageRange = list(c(10, 30))) #> ℹ Building new trimmed cohort #> Adding demographics information #> Creating initial cohort #> Trim age #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> ✔ Cohort trimmed #> # Source: table [?? x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 14 1987-12-15 1988-03-19 #> 2 1 20 1990-10-19 1997-01-08 #> 3 1 28 2005-04-04 2005-08-23 #> 4 1 60 1974-02-12 1979-10-10 #> 5 1 79 1991-10-01 1996-02-15 #> 6 1 81 2009-08-24 2010-07-01 #> 7 1 14 1987-03-20 1987-12-14 #> 8 1 20 1990-03-24 1990-10-18 #> 9 1 28 2005-04-01 2005-04-03 #> 10 1 79 1991-02-24 1991-09-30 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":null,"dir":"Reference","previous_headings":"","what":"Trim cohort dates to be within a date range — trimToDateRange","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"trimToDateRange() resets cohort start end date based specified date range.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"","code":"trimToDateRange( cohort, dateRange, cohortId = NULL, startDate = \"cohort_start_date\", endDate = \"cohort_end_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"cohort cohort table cdm reference. dateRange window time index date must observed. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. startDate Variable earliest date. endDate Variable latest date. name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"cohort table record timings updated within date range. records time outside range dropped.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> trimToDateRange(startDate = \"cohort_start_date\", endDate = \"cohort_end_date\", dateRange = as.Date(c(\"2015-01-01\", \"2015-12-31\"))) #> # Source: table [1 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 3 2015-01-27 2015-06-28 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate cohort from the union of different cohorts — unionCohorts","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"unionCohorts() combines different cohort entries, records overlap combined kept. Cohort entries individual either cohorts.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"","code":"unionCohorts( cohort, cohortId = NULL, gap = 0, cohortName = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. gap Number days two subsequent cohort entries subject merged single cohort entry cohortName Name returned cohort. NULL, cohort name created collapsing individual cohort names, separated \"_\". name Name new cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort2 <- cdm$cohort2 |> unionCohorts() #> Warning: `union_cohorts()` was deprecated in CDMConnector 1.1.0. #> ℹ Please use `cohort_union()` instead. settings(cdm$cohort2) #> Error in UseMethod(\"settings\"): no applicable method for 'settings' applied to an object of class \"c('cdm_table', 'GeneratedCohortSet', 'tbl_duckdb_connection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')\" # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"yearCohorts() splits cohort multiple cohorts, one year.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"","code":"yearCohorts(cohort, years, cohortId = NULL, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"cohort cohort table cdm reference. years Numeric vector years use restrict observation . cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. name Name new cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 <- cdm$cohort1 |> yearCohorts(years = 2000:2002) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. settings(cdm$cohort1) #> # A tibble: 3 × 5 #> cohort_definition_id cohort_name target_cohort_definition_id year #> #> 1 1 cohort_1_2000 1 2000 #> 2 2 cohort_1_2001 1 2001 #> 3 3 cohort_1_2002 1 2002 #> # ℹ 1 more variable: target_cohort_name # }"}] +[{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"Apache License","title":"Apache License","text":"Version 2.0, January 2004 ","code":""},{"path":[]},{"path":"https://ohdsi.github.io/CohortConstructor/LICENSE.html","id":"id_1-definitions","dir":"","previous_headings":"Terms and Conditions for use, reproduction, and distribution","what":"1. 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(Don’t include brackets!) text enclosed appropriate comment syntax file format. also recommend file class name description purpose included “printed page” copyright notice easier identification within third-party archives.","code":"Copyright [yyyy] [name of copyright owner] Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a00_introduction.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Introduction","text":"CohortConstructor package designed support cohort building pipelines. using package general workflow first build set base cohorts subsequently apply inclusion criteria derive final study cohorts interest. Base cohorts built domain (rather cohort definition) one base cohort many study cohorts can derived.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a00_introduction.html","id":"building-a-cohort-set-by-domain","dir":"Articles","previous_headings":"","what":"Building a cohort set by domain","title":"Introduction","text":"Let´s say want build 5 cohorts 3 (asthma, copd, diabetes) defined based concepts seen condition occurrence table 2 (acetaminophen warfarin) based concepts recorded drug exposure table. can build cohorts independently, one . However, approach mean repeating 3 joins condition occurrence tables 2 joins drug exposure table (concepts concept sets). make less computationally expensive, instead create cohorts domain. case instead make one join condition occurrence table one drug exposure (using concept sets together).","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a00_introduction.html","id":"deriving-study-cohorts-from-base-cohorts","dir":"Articles","previous_headings":"","what":"Deriving study cohorts from base cohorts","title":"Introduction","text":"making study cohorts often concept sets define clinical event along various study-specific inclusion criteria, example criteria around amount prior observation age. Often may sensitivity analysis concept set remains inclusion criteria change. situations can make cohorts one--one. However, can lead duplication can see example identify asthma records multiple times. alternative approach build base cohort, case based asthma records, derive multiple cohorts different inclusion criteria applied.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a00_introduction.html","id":"considerations-when-building-cohorts","dir":"Articles","previous_headings":"","what":"Considerations when building cohorts","title":"Introduction","text":"CohortConstructor provides means building cohorts via pipeline, cohorts created application sequence functions. important note order sequence often important implications. example just one individual three recorded diagnoses asthma. One diagnosis 2008 two 2009, last coming individual´s 18th birthday. three cohort pipelines shown restrictions around calendar dates, age, record first. cohort pipeline , however, individual included final cohort, third diagnosis used cohort start. pipeline B C individual excluded.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a01_building_base_cohorts.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Building base cohorts","text":"Let’s first create cdm reference Eunomia synthetic data.","code":"library(CDMConnector) library(CodelistGenerator) library(PatientProfiles) library(CohortConstructor) library(dplyr) con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) cdm <- cdm_from_con(con, cdm_schema = \"main\", write_schema = c(prefix = \"my_study_\", schema = \"main\"))"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a01_building_base_cohorts.html","id":"demographic-based-cohort-creation","dir":"Articles","previous_headings":"","what":"Demographic based cohort creation","title":"Building base cohorts","text":"One base cohort can create based around patient demographics. example create cohort people enter 18th birthday leave age 65 ","code":"cdm$working_age_cohort <- demographicsCohort(cdm = cdm, ageRange = c(18, 65), name = \"working_age_cohort\") settings(cdm$working_age_cohort) #> # A tibble: 1 × 3 #> cohort_definition_id cohort_name age_range #> #> 1 1 demographics 18_65 cohortCount(cdm$working_age_cohort) #> # A tibble: 1 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 2694 2694 attrition(cdm$working_age_cohort) #> # A tibble: 2 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 2694 2694 1 Initial qualify… #> 2 1 2694 2694 2 Age requirement… #> # ℹ 2 more variables: excluded_records , excluded_subjects cdm$working_age_cohort |> addAge(indexDate = \"cohort_start_date\") |> summarise(min_start_age = min(age), median_start_age = median(age), max_start_age = max(age)) #> # Source: SQL [1 x 3] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1//tmp/RtmpIHhO79/file1a5632d75182.duckdb] #> min_start_age median_start_age max_start_age #> #> 1 17 18 18 cdm$working_age_cohort |> addAge(indexDate = \"cohort_end_date\") |> summarise(min_start_age = min(age), median_start_age = median(age), max_start_age = max(age)) #> # Source: SQL [1 x 3] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1//tmp/RtmpIHhO79/file1a5632d75182.duckdb] #> min_start_age median_start_age max_start_age #> #> 1 31 57 65"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a01_building_base_cohorts.html","id":"concept-based-cohort-creation","dir":"Articles","previous_headings":"","what":"Concept based cohort creation","title":"Building base cohorts","text":"","code":"drug_codes <- getDrugIngredientCodes(cdm, name = c(\"diclofenac\", \"acetaminophen\")) drug_codes #> #> - 161_acetaminophen (7 codes) #> - 3355_diclofenac (1 codes) cdm$medications <- conceptCohort(cdm = cdm, conceptSet = drug_codes, name = \"medications\") settings(cdm$medications) #> # A tibble: 2 × 4 #> cohort_definition_id cohort_name cdm_version vocabulary_version #> #> 1 1 161_acetaminophen 5.3 v5.0 18-JAN-19 #> 2 2 3355_diclofenac 5.3 v5.0 18-JAN-19 cohortCount(cdm$medications) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 13908 2679 #> 2 2 830 830"},{"path":[]},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a02_applying_cohort_restrictions.html","id":"keep-only-the-first-record-per-person","dir":"Articles","previous_headings":"","what":"Keep only the first record per person","title":"Applying cohort restrictions","text":"Individuals can contribute multiple records per cohort. However now ’ll keep earliest cohort entry remaining records using requireIsFirstEntry() CohortConstructor. can see one record per person cohort. Note, applying criteria later applying criteria result different result. ’re requiring individuals meet inclusion criteria time first use diclofenac acetaminophen.","code":"cdm$medications <- cdm$medications %>% requireIsFirstEntry(indexDate = \"cohort_start_date\") cohortCount(cdm$medications) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 2580 2580 #> 2 2 830 830"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a02_applying_cohort_restrictions.html","id":"applying-restrictions-on-patient-demographics","dir":"Articles","previous_headings":"","what":"Applying restrictions on patient demographics","title":"Applying cohort restrictions","text":"Using requireDemographics() ’ll require individuals medications cohort female , relative cohort start date, 18 85 least 30 days prior observation time database. can see many people people excluded based demographic requirements.","code":"cdm$medications <- cdm$medications %>% requireDemographics(indexDate = \"cohort_start_date\", ageRange = list(c(18, 85)), sex = \"Female\", minPriorObservation = 30) cohort_attrition(cdm$medications) %>% dplyr::filter(reason == \"Demographic requirements\") %>% dplyr::glimpse() #> Rows: 0 #> Columns: 7 #> $ cohort_definition_id #> $ number_records #> $ number_subjects #> $ reason_id #> $ reason #> $ excluded_records #> $ excluded_subjects "},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a02_applying_cohort_restrictions.html","id":"restrictions-on-calendar-dates","dir":"Articles","previous_headings":"","what":"Restrictions on calendar dates","title":"Applying cohort restrictions","text":"Next can use requireInDateRange() keep records cohort entry particular date range. , can track cohort attrition","code":"cdm$medications <- cdm$medications %>% requireInDateRange(indexDate = \"cohort_start_date\", dateRange = as.Date(c(\"2000-01-01\", \"2015-01-01\"))) cohort_attrition(cdm$medications) %>% dplyr::filter(reason == \"cohort_start_date between 2000-01-01 and 2015-01-01\") %>% dplyr::glimpse() #> Rows: 0 #> Columns: 7 #> $ cohort_definition_id #> $ number_records #> $ number_subjects #> $ reason_id #> $ reason #> $ excluded_records #> $ excluded_subjects "},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a02_applying_cohort_restrictions.html","id":"restrictions-on-cohort-presence","dir":"Articles","previous_headings":"","what":"Restrictions on cohort presence","title":"Applying cohort restrictions","text":"require individuals medication cohorts history GI bleed. can use requireCohortIntersect() function, requiring individuals one intersections GI bleed cohort. Instead requiring individuals history GI bleed, instead require don’t history . case can use requireCohortIntersect() function, time set intersections argument 0 require individuals’ absence cohort rather presence .","code":"cdm$medications_gi_bleed <- cdm$medications %>% requireCohortIntersect(intersections = c(1,Inf), targetCohortTable = \"gi_bleed\", targetCohortId = 1, indexDate = \"cohort_start_date\", window = c(-Inf, 0), name = \"medications_gi_bleed\") cohort_count(cdm$medications_gi_bleed) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 0 0 #> 2 2 0 0 cdm$medications_no_gi_bleed <- cdm$medications %>% requireCohortIntersect(intersections = 0, targetCohortTable = \"gi_bleed\", targetCohortId = 1, indexDate = \"cohort_start_date\", window = c(-Inf, 0), name = \"medications_no_gi_bleed\") cohort_count(cdm$medications_no_gi_bleed) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 101 101 #> 2 2 179 179"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Generate a matched age and sex cohort","text":"CohortConstructor packages includes function obtain age sex matched cohort, generateMatchedCohortSet() function. vignette, explore usage function.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"create-mock-data","dir":"Articles","previous_headings":"Introduction","what":"Create mock data","title":"Generate a matched age and sex cohort","text":"first use mockDrugUtilisation() function DrugUtilisation package create mock data. use cohort1 explore generateMatchedCohortSet(), let us first use cohort_attrition() CDMConnector package explore cohort:","code":"library(CohortConstructor) library(dplyr) cdm <- mockCohortConstructor(nPerson = 1000) CDMConnector::cohort_set(cdm$cohort1)"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"use-generatematchedcohortset-to-create-an-age-sex-matched-cohort","dir":"Articles","previous_headings":"","what":"Use generateMatchedCohortSet() to create an age-sex matched cohort","title":"Generate a matched age and sex cohort","text":"Let us first see example function works. usage, need provide cdm object, targetCohortName, name table containing cohort interest, name new generated tibble containing cohort matched cohort. also use argument targetCohortId specify want matched cohort cohort_definition_id = 1. Notice generated tibble, two cohorts: cohort_definition_id = 1 (original cohort), cohort_definition_id = 4 (matched cohort). target_cohort_name column indicates original cohort. match_sex match_year_of_birth adopt boolean values (TRUE/FALSE) indicating matched sex age, . match_status indicate original cohort (target) matched cohort (matched). target_cohort_id indicates cohort_id original cohort. Check exclusion criteria applied generate new cohorts using cohort_attrition() CDMConnector package: Briefly, original cohort, exclude first individuals match, individuals matching pair observation assigned cohort_start_date. matched cohort, start whole database first exclude individuals original cohort. Afterwards, exclude individuals match, individuals observation assigned cohort_start_date, finally remove many individuals required fulfill ratio. Notice matching pairs randomly assigned, probable every time execute function, generated cohorts change. Use set.seed() avoid .","code":"cdm$matched_cohort1 <- matchCohorts( cohort = cdm$cohort1, cohortId = 1, name = \"matched_cohort1\") CDMConnector::cohort_set(cdm$matched_cohort1) # Original cohort CDMConnector::cohort_attrition(cdm$matched_cohort1) %>% filter(cohort_definition_id == 1) # Matched cohort CDMConnector::cohort_attrition(cdm$matched_cohort1) %>% filter(cohort_definition_id == 4)"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"matchsex-parameter","dir":"Articles","previous_headings":"Use generateMatchedCohortSet() to create an age-sex matched cohort","what":"matchSex parameter","title":"Generate a matched age and sex cohort","text":"matchSex boolean parameter (TRUE/FALSE) indicating want match sex (TRUE) want (FALSE).","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"matchyear-parameter","dir":"Articles","previous_headings":"Use generateMatchedCohortSet() to create an age-sex matched cohort","what":"matchYear parameter","title":"Generate a matched age and sex cohort","text":"matchYear another boolean parameter (TRUE/FALSE) indicating want match age (TRUE) want (FALSE). Notice matchSex = FALSE matchYear = FALSE, obtain unmatched comparator cohort.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"ratio-parameter","dir":"Articles","previous_headings":"Use generateMatchedCohortSet() to create an age-sex matched cohort","what":"ratio parameter","title":"Generate a matched age and sex cohort","text":"default matching ratio 1:1 (ratio = 1). Use cohort_counts() CDMConnector check matching done desired. can modify ratio parameter tailor matched cohort. ratio can adopt values 1 Inf.","code":"CDMConnector::cohort_count(cdm$matched_cohort1) cdm$matched_cohort2 <- matchCohorts( cohort = cdm$cohort1, cohortId = 1, name = \"matched_cohort2\", ratio = Inf) CDMConnector::cohort_count(cdm$matched_cohort2)"},{"path":"https://ohdsi.github.io/CohortConstructor/articles/a03_age_sex_matching.html","id":"generate-matched-cohorts-simultaneously-across-multiple-cohorts","dir":"Articles","previous_headings":"Use generateMatchedCohortSet() to create an age-sex matched cohort","what":"Generate matched cohorts simultaneously across multiple cohorts","title":"Generate a matched age and sex cohort","text":"functionalities can implemented across multiple cohorts simultaneously. Specify targetCohortId parameter cohorts interest. set NULL, cohorts present targetCohortName matched. Notice cohort (independent cohorts) matched cohort.","code":"cdm$matched_cohort3 <- matchCohorts( cohort = cdm$cohort1, cohortId = c(1,3), name = \"matched_cohort3\", ratio = 2) CDMConnector::cohort_set(cdm$matched_cohort3) %>% arrange(cohort_definition_id) CDMConnector::cohort_count(cdm$matched_cohort3) %>% arrange(cohort_definition_id)"},{"path":"https://ohdsi.github.io/CohortConstructor/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Edward Burn. Author, maintainer. Marti Catala. Author. Nuria Mercade-Besora. Author. Marta Alcalde-Herraiz. Author. Mike Du. Author. Yuchen Guo. Author. Xihang Chen. Author. Kim Lopez. Author.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Burn E, Catala M, Mercade-Besora N, Alcalde-Herraiz M, Du M, Guo Y, Chen X, Lopez K (2024). CohortConstructor: Build Manipulate Study Cohorts Using Common Data Model. R package version 0.2.2, https://ohdsi.github.io/CohortConstructor/.","code":"@Manual{, title = {CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model}, author = {Edward Burn and Marti Catala and Nuria Mercade-Besora and Marta Alcalde-Herraiz and Mike Du and Yuchen Guo and Xihang Chen and Kim Lopez}, year = {2024}, note = {R package version 0.2.2}, url = {https://ohdsi.github.io/CohortConstructor/}, }"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"cohortconstructor-","dir":"","previous_headings":"","what":"Build and Manipulate Study Cohorts Using a Common Data Model","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"goal CohortConstructor support creation manipulation study cohorts data mapped OMOP CDM.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"package can installed CRAN: can install development version CohortConstructor GitHub:","code":"install.packages(\"CohortConstructor\") # install.packages(\"devtools\") devtools::install_github(\"ohdsi/CohortConstructor\")"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"creating-and-manipulating-cohorts","dir":"","previous_headings":"","what":"Creating and manipulating cohorts","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"illustrate functionality let’s create set fracture cohorts using Eunomia dataset. ’ll first load required packages create cdm reference data.","code":"library(omopgenerics) library(CDMConnector) library(PatientProfiles) library(dplyr) library(CohortConstructor) library(CohortCharacteristics) con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomia_dir()) cdm <- cdm_from_con(con, cdm_schema = \"main\", write_schema = c(prefix = \"my_study_\", schema = \"main\")) cdm #> #> ── # OMOP CDM reference (duckdb) of Synthea synthetic health database ────────── #> • omop tables: person, observation_period, visit_occurrence, visit_detail, #> condition_occurrence, drug_exposure, procedure_occurrence, device_exposure, #> measurement, observation, death, note, note_nlp, specimen, fact_relationship, #> location, care_site, provider, payer_plan_period, cost, drug_era, dose_era, #> condition_era, metadata, cdm_source, concept, vocabulary, domain, #> concept_class, concept_relationship, relationship, concept_synonym, #> concept_ancestor, source_to_concept_map, drug_strength #> • cohort tables: - #> • achilles tables: - #> • other tables: -"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"generating-concept-based-fracture-cohorts","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Generating concept-based fracture cohorts","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"start making simple concept-based cohort fracture interest. First create codelist ankle, forearm hip fractures (note, just use one code using synthetic data). Now can quickly create set cohorts fracture type. need provide codes defined get cohort back, cohort end date set event date associated records, overlapping records collapsed, records observation kept. can see starting cohorts, add additional restrictions, following associated settings, counts, attrition.","code":"fracture_codes <- newCodelist(list(\"ankle_fracture\" = 4059173L, \"forearm_fracture\" = 4278672L, \"hip_fracture\" = 4230399L)) fracture_codes #> #> ── 3 codelists ───────────────────────────────────────────────────────────────── #> #> - ankle_fracture (1 codes) #> - forearm_fracture (1 codes) #> - hip_fracture (1 codes) cdm$fractures <- cdm |> conceptCohort(conceptSet = fracture_codes, name = \"fractures\") settings(cdm$fractures) %>% glimpse() #> Rows: 3 #> Columns: 2 #> $ cohort_definition_id 1, 2, 3 #> $ cohort_name \"ankle_fracture\", \"forearm_fracture\", \"hip_fractu… cohort_count(cdm$fractures) %>% glimpse() #> Rows: 3 #> Columns: 3 #> $ cohort_definition_id 1, 2, 3 #> $ number_records 464, 569, 138 #> $ number_subjects 427, 510, 132 attrition(cdm$fractures) %>% glimpse() #> Rows: 3 #> Columns: 7 #> $ cohort_definition_id 1, 2, 3 #> $ number_records 464, 569, 138 #> $ number_subjects 427, 510, 132 #> $ reason_id 1, 1, 1 #> $ reason \"Initial qualifying events\", \"Initial qualifying … #> $ excluded_records 0, 0, 0 #> $ excluded_subjects 0, 0, 0"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"create-an-overall-fracture-cohort","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Create an overall fracture cohort","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"far created three separate fracture cohorts. Let’s say also want cohort people fractures. union three cohorts create overall cohort like :","code":"cdm$any_fracture <- cdm$fractures |> CohortConstructor::unionCohorts(cohortName = \"any_fracture\", name = \"any_fracture\") #> Warning: ! 1 casted column in any_fracture (cohort_set) as do not match expected column #> type: #> • `cohort_definition_id` from numeric to integer #> Warning: ! 6 casted column in any_fracture (cohort_attrition) as do not match expected #> column type: #> • `cohort_definition_id` from numeric to integer #> • `number_records` from numeric to integer #> • `number_subjects` from numeric to integer #> • `reason_id` from numeric to integer #> • `excluded_records` from numeric to integer #> • `excluded_subjects` from numeric to integer #> Warning: ! 1 casted column in any_fracture (cohort_codelist) as do not match expected #> column type: #> • `cohort_definition_id` from numeric to integer #> Warning: ! 1 column in any_fracture do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer cdm <- bind(cdm$fractures, cdm$any_fracture, name = \"fractures\") settings(cdm$fractures) #> # A tibble: 4 × 3 #> cohort_definition_id cohort_name gap #> #> 1 1 ankle_fracture NA #> 2 2 forearm_fracture NA #> 3 3 hip_fracture NA #> 4 4 any_fracture 0 cohortCount(cdm$fractures) #> # A tibble: 4 × 3 #> cohort_definition_id number_records number_subjects #> #> 1 1 464 427 #> 2 2 569 510 #> 3 3 138 132 #> 4 4 1171 924"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"require-in-date-range","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Require in date range","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"created base fracture cohort, can start applying additional cohort requirements. example, first can require individuals’ cohort start date fall within certain date range. Now ’ve applied date restriction, can see cohort attributes updated","code":"cdm$fractures <- cdm$fractures %>% requireInDateRange(dateRange = as.Date(c(\"2000-01-01\", \"2020-01-01\"))) cohort_count(cdm$fractures) %>% glimpse() #> Rows: 4 #> Columns: 3 #> $ cohort_definition_id 1, 2, 3, 4 #> $ number_records 108, 152, 62, 322 #> $ number_subjects 104, 143, 60, 287 attrition(cdm$fractures) %>% filter(reason == \"cohort_start_date between 2000-01-01 & 2020-01-01\") %>% glimpse() #> Rows: 0 #> Columns: 7 #> $ cohort_definition_id #> $ number_records #> $ number_subjects #> $ reason_id #> $ reason #> $ excluded_records #> $ excluded_subjects "},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"applying-demographic-requirements","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Applying demographic requirements","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"can also add restrictions patient characteristics age (cohort start date default) sex. can see many individuals ’ve lost applying criteria.","code":"cdm$fractures <- cdm$fractures %>% requireDemographics(ageRange = list(c(40, 65)), sex = \"Female\") attrition(cdm$fractures) %>% filter(reason == \"Age requirement: 40 to 65\") %>% glimpse() #> Rows: 4 #> Columns: 7 #> $ cohort_definition_id 1, 2, 3, 4 #> $ number_records 43, 64, 22, 129 #> $ number_subjects 43, 62, 22, 122 #> $ reason_id 4, 4, 4, 4 #> $ reason \"Age requirement: 40 to 65\", \"Age requirement: 40… #> $ excluded_records 65, 88, 40, 193 #> $ excluded_subjects 61, 81, 38, 165 attrition(cdm$fractures) %>% filter(reason == \"Sex requirement: Female\") %>% glimpse() #> Rows: 4 #> Columns: 7 #> $ cohort_definition_id 1, 2, 3, 4 #> $ number_records 19, 37, 12, 68 #> $ number_subjects 19, 36, 12, 65 #> $ reason_id 5, 5, 5, 5 #> $ reason \"Sex requirement: Female\", \"Sex requirement: Fema… #> $ excluded_records 24, 27, 10, 61 #> $ excluded_subjects 24, 26, 10, 57"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"require-presence-in-another-cohort","dir":"","previous_headings":"Creating and manipulating cohorts","what":"Require presence in another cohort","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"can also require individuals () another cohort window. example require study participants GI bleed cohort time prior entry fractures cohort.","code":"cdm$gibleed <- cdm |> conceptCohort(conceptSet = list(\"gibleed\" = 192671L), name = \"gibleed\") cdm$fractures <- cdm$fractures %>% requireCohortIntersect(targetCohortTable = \"gibleed\", intersections = 0, window = c(-Inf, 0)) attrition(cdm$fractures) %>% filter(reason == \"Not in cohort gibleed between -Inf & 0 days relative to cohort_start_date\") %>% glimpse() #> Rows: 4 #> Columns: 7 #> $ cohort_definition_id 1, 2, 3, 4 #> $ number_records 14, 30, 10, 54 #> $ number_subjects 14, 30, 10, 52 #> $ reason_id 8, 8, 8, 8 #> $ reason \"Not in cohort gibleed between -Inf & 0 days rela… #> $ excluded_records 5, 7, 2, 14 #> $ excluded_subjects 5, 6, 2, 13 cdmDisconnect(cdm)"},{"path":"https://ohdsi.github.io/CohortConstructor/index.html","id":"more-information","dir":"","previous_headings":"Creating and manipulating cohorts","what":"More information","title":"Build and Manipulate Study Cohorts Using a Common Data Model","text":"CohortConstructor provides much functionality creating manipulating cohorts. See package website details.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/CohortConstructor-package.html","id":null,"dir":"Reference","previous_headings":"","what":"CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model — CohortConstructor-package","title":"CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model — CohortConstructor-package","text":"Create manipulate study cohorts data mapped Observational Medical Outcomes Partnership Common Data Model.","code":""},{"path":[]},{"path":"https://ohdsi.github.io/CohortConstructor/reference/CohortConstructor-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model — CohortConstructor-package","text":"Maintainer: Edward Burn edward.burn@ndorms.ox.ac.uk (ORCID) Authors: Marti Catala marti.catalasabate@ndorms.ox.ac.uk (ORCID) Nuria Mercade-Besora nuria.mercadebesora@ndorms.ox.ac.uk (ORCID) Marta Alcalde-Herraiz marta.alcaldeherraiz@ndorms.ox.ac.uk (ORCID) Mike Du mike.du@ndorms.ox.ac.uk (ORCID) Yuchen Guo yuchen.guo@ndorms.ox.ac.uk (ORCID) Xihang Chen xihang.chen@ndorms.ox.ac.uk (ORCID) Kim Lopez kim.lopez@spc.ox.ac.uk (ORCID)","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/collapseCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","title":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","text":"collapseCohorts() concatenates cohort records, allowing number days one finishing next starting.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/collapseCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","text":"","code":"collapseCohorts(cohort, cohortId = NULL, gap = 0, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/collapseCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","text":"cohort cohort table cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. gap Number days use merging cohort entries. name Name cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/collapseCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collapse cohort entries using a certain gap to concatenate records. — collapseCohorts","text":"cohort table","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Create cohorts based on a concept set — conceptCohort","title":"Create cohorts based on a concept set — conceptCohort","text":"conceptCohort() creates cohort table patient records clinical tables OMOP CDM. following tables currently supported creating concept cohorts: condition_occurrence device_exposure drug_exposure measurement observation procedure_occurrence visit_occurrence Cohort duration based record start end (e.g. condition_start_date condition_end_date records coming condition_occurrence tables). resulting table satisfies requirements OMOP CDM cohort table: Overlapping records collapsed single cohort entry. record starts outside observation period silently ignored. record ends outside observation period trimmed end preceding observation period end date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create cohorts based on a concept set — conceptCohort","text":"","code":"conceptCohort(cdm, conceptSet, name, exit = \"event_end_date\")"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create cohorts based on a concept set — conceptCohort","text":"cdm cdm reference. conceptSet conceptSet, can either codelist conceptSetExpression. name Name cohort cdm object. exit cohort end date defined. Can either \"event_end_date\" \"event_start_date\".","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create cohorts based on a concept set — conceptCohort","text":"cohort table","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/conceptCohort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create cohorts based on a concept set — conceptCohort","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(conditionOccurrence = TRUE) #> Note: method with signature ‘DBIConnection#Id’ chosen for function ‘dbExistsTable’, #> target signature ‘duckdb_connection#Id’. #> \"duckdb_connection#ANY\" would also be valid #> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 90% | ETA: 0s cohort <- conceptCohort(cdm = cdm, conceptSet = list(a = 1), name = \"cohort\") #> Warning: ! `codelist` contains numeric values, they are casted to integers. #> ℹ Subsetting table condition_occurrence using 1 concept with domain: condition. #> ℹ Combining tables. #> ℹ Creating cohort attributes. #> ℹ Applying cohort requirements. #> ℹ Collapsing records. #> ✔ Cohort cohort created. cohort |> attrition() #> # A tibble: 3 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 10 7 1 Initial qualify… #> 2 1 10 7 2 cohort requirem… #> 3 1 7 7 3 Overlapping rec… #> # ℹ 2 more variables: excluded_records , excluded_subjects # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Create cohorts based on patient demographics — demographicsCohort","title":"Create cohorts based on patient demographics — demographicsCohort","text":"demographicsCohort() creates cohort table based patient characteristics. individual satisfies criteria enter cohort. stop satisfying criteria cohort entry ends.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create cohorts based on patient demographics — demographicsCohort","text":"","code":"demographicsCohort( cdm, name, ageRange = NULL, sex = NULL, minPriorObservation = NULL, minFutureObservation = NULL )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create cohorts based on patient demographics — demographicsCohort","text":"cdm cdm reference. name Name new cohort table ageRange list vectors specifying minimum maximum age. sex Can \"\", \"Male\" \"Female\". minPriorObservation minimum number prior observation days database. minFutureObservation minimum number future observation days database.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create cohorts based on patient demographics — demographicsCohort","text":"cohort table","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/demographicsCohort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create cohorts based on patient demographics — demographicsCohort","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cohort <- cdm |> demographicsCohort(name = \"cohort3\", ageRange = c(18,40), sex = \"Male\") #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> ℹ Building new trimmed cohort #> Adding demographics information #> Creating initial cohort #> Trim sex #> Trim age #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> ✔ Cohort trimmed attrition(cohort) #> # A tibble: 3 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 10 10 1 Initial qualify… #> 2 1 5 5 2 Sex requirement… #> 3 1 4 4 3 Age requirement… #> # ℹ 2 more variables: excluded_records , excluded_subjects # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":null,"dir":"Reference","previous_headings":"","what":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"entryAtFirstDate() resets cohort start date based set specified column dates. first date occurs chosen.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"","code":"entryAtFirstDate( cohort, dateColumns, cohortId = NULL, returnReason = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"cohort cohort table cdm reference. dateColumns Date columns cohort table consider. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. returnReason TRUE return column stating column dateColumns used new cohort end date. name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtFirstDate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update cohort start date to be the first date from of a set of column dates — entryAtFirstDate","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(tables = list( \"cohort\" = dplyr::tibble( cohort_definition_id = 1, subject_id = c(1, 2, 3, 4), cohort_start_date = as.Date(c(\"2000-06-03\", \"2000-01-01\", \"2015-01-15\", \"2000-12-09\")), cohort_end_date = as.Date(c(\"2001-09-01\", \"2001-01-12\", \"2015-02-15\", \"2002-12-09\")), date_1 = as.Date(c(\"2001-08-01\", \"2001-01-01\", \"2015-01-15\", \"2002-12-09\")), date_2 = as.Date(c(\"2001-08-01\", NA, \"2015-02-14\", \"2002-12-09\")) ) )) #> Warning: ! 7 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `gender_concept_id` is numeric but expected integer #> • `year_of_birth` is numeric but expected integer #> • `month_of_birth` is numeric but expected integer #> • `race_concept_id` is numeric but expected integer #> • `ethnicity_concept_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 2 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> • `period_type_concept_id` is numeric but expected integer #> Warning: ! 9 column in cdm_source do not match expected column type: #> • `cdm_source_abbreviation` is logical but expected character #> • `cdm_holder` is logical but expected character #> • `source_description` is logical but expected character #> • `source_documentation_reference` is logical but expected character #> • `cdm_etl_reference` is logical but expected character #> • `source_release_date` is logical but expected date #> • `cdm_release_date` is logical but expected date #> • `cdm_version` is numeric but expected character #> • `vocabulary_version` is logical but expected character #> Warning: ! 3 column in concept do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `valid_start_date` is character but expected date #> • `valid_end_date` is character but expected date #> Warning: ! 1 column in vocabulary do not match expected column type: #> • `vocabulary_concept_id` is numeric but expected integer #> Warning: ! 5 column in concept_relationship do not match expected column type: #> • `concept_id_1` is numeric but expected integer #> • `concept_id_2` is numeric but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> • `invalid_reason` is logical but expected character #> Warning: ! 2 column in concept_synonym do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `language_concept_id` is numeric but expected integer #> Warning: ! 4 column in concept_ancestor do not match expected column type: #> • `ancestor_concept_id` is numeric but expected integer #> • `descendant_concept_id` is numeric but expected integer #> • `min_levels_of_separation` is numeric but expected integer #> • `max_levels_of_separation` is numeric but expected integer #> Warning: ! 9 column in drug_strength do not match expected column type: #> • `drug_concept_id` is numeric but expected integer #> • `ingredient_concept_id` is numeric but expected integer #> • `amount_value` is logical but expected numeric #> • `amount_unit_concept_id` is numeric but expected integer #> • `numerator_unit_concept_id` is numeric but expected integer #> • `denominator_unit_concept_id` is numeric but expected integer #> • `box_size` is logical but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> Warning: ! 2 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 1 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer cdm$cohort |> entryAtLastDate(dateColumns = c(\"date_1\", \"date_2\")) #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> # Source: table [4 x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date entry_reason #> #> 1 1 2 2001-01-01 2001-01-12 date_1 #> 2 1 3 2015-02-14 2015-02-15 date_2 #> 3 1 1 2001-08-01 2001-09-01 date_1; dat… #> 4 1 4 2002-12-09 2002-12-09 date_1; dat… # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort start date to the last of a set of column dates — entryAtLastDate","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"Set cohort start date last set column dates","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"","code":"entryAtLastDate( cohort, dateColumns, cohortId = NULL, returnReason = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"cohort cohort table cdm reference. dateColumns description cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. returnReason TRUE return column stating column dateColumns used new cohort end date. description name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/entryAtLastDate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort start date to the last of a set of column dates — entryAtLastDate","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(tables = list( \"cohort\" = dplyr::tibble( cohort_definition_id = 1, subject_id = c(1, 2, 3, 4), cohort_start_date = as.Date(c(\"2000-06-03\", \"2000-01-01\", \"2015-01-15\", \"2000-12-09\")), cohort_end_date = as.Date(c(\"2001-09-01\", \"2001-01-12\", \"2015-02-15\", \"2002-12-09\")), date_1 = as.Date(c(\"2001-08-01\", \"2001-01-01\", \"2015-01-15\", \"2002-12-09\")), date_2 = as.Date(c(\"2001-08-01\", NA, \"2015-02-14\", \"2002-12-09\")) ) )) #> Warning: ! 7 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `gender_concept_id` is numeric but expected integer #> • `year_of_birth` is numeric but expected integer #> • `month_of_birth` is numeric but expected integer #> • `race_concept_id` is numeric but expected integer #> • `ethnicity_concept_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 2 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> • `period_type_concept_id` is numeric but expected integer #> Warning: ! 9 column in cdm_source do not match expected column type: #> • `cdm_source_abbreviation` is logical but expected character #> • `cdm_holder` is logical but expected character #> • `source_description` is logical but expected character #> • `source_documentation_reference` is logical but expected character #> • `cdm_etl_reference` is logical but expected character #> • `source_release_date` is logical but expected date #> • `cdm_release_date` is logical but expected date #> • `cdm_version` is numeric but expected character #> • `vocabulary_version` is logical but expected character #> Warning: ! 3 column in concept do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `valid_start_date` is character but expected date #> • `valid_end_date` is character but expected date #> Warning: ! 1 column in vocabulary do not match expected column type: #> • `vocabulary_concept_id` is numeric but expected integer #> Warning: ! 5 column in concept_relationship do not match expected column type: #> • `concept_id_1` is numeric but expected integer #> • `concept_id_2` is numeric but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> • `invalid_reason` is logical but expected character #> Warning: ! 2 column in concept_synonym do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `language_concept_id` is numeric but expected integer #> Warning: ! 4 column in concept_ancestor do not match expected column type: #> • `ancestor_concept_id` is numeric but expected integer #> • `descendant_concept_id` is numeric but expected integer #> • `min_levels_of_separation` is numeric but expected integer #> • `max_levels_of_separation` is numeric but expected integer #> Warning: ! 9 column in drug_strength do not match expected column type: #> • `drug_concept_id` is numeric but expected integer #> • `ingredient_concept_id` is numeric but expected integer #> • `amount_value` is logical but expected numeric #> • `amount_unit_concept_id` is numeric but expected integer #> • `numerator_unit_concept_id` is numeric but expected integer #> • `denominator_unit_concept_id` is numeric but expected integer #> • `box_size` is logical but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> Warning: ! 2 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 1 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer cdm$cohort |> entryAtLastDate(dateColumns = c(\"date_1\", \"date_2\")) #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> # Source: table [4 x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date entry_reason #> #> 1 1 2 2001-01-01 2001-01-12 date_1 #> 2 1 4 2002-12-09 2002-12-09 date_2; dat… #> 3 1 3 2015-02-14 2015-02-15 date_2 #> 4 1 1 2001-08-01 2001-09-01 date_2; dat… # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort end date to death date — exitAtDeath","title":"Set cohort end date to death date — exitAtDeath","text":"functions changes cohort end date subject's death date. case generates overlapping records cohort, overlapping entries merged.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort end date to death date — exitAtDeath","text":"","code":"exitAtDeath( cohort, cohortId = NULL, requireDeath = FALSE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort end date to death date — exitAtDeath","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. requireDeath TRUE, subjects without death record dropped, FALSE end date left . name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort end date to death date — exitAtDeath","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtDeath.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort end date to death date — exitAtDeath","text":"","code":"# \\donttest{ library(PatientProfiles) library(CohortConstructor) cdm <- mockPatientProfiles() #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. cdm$cohort1 |> exitAtDeath() #> # Source: table [10 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 2 2 1998-11-05 2008-01-27 #> 2 2 1 1951-11-28 2019-01-16 #> 3 1 6 2006-12-25 2022-11-01 #> 4 2 5 2113-08-18 2144-11-05 #> 5 2 8 1954-07-05 1955-07-17 #> 6 3 7 2029-01-30 2050-08-27 #> 7 3 10 2003-01-05 2060-02-27 #> 8 1 4 2017-04-18 2077-11-07 #> 9 2 3 1993-12-06 1997-05-26 #> 10 2 9 2109-11-07 2115-08-03 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"exitAtFirstDate() resets cohort end date based set specified column dates. first date occurs chosen.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"","code":"exitAtFirstDate( cohort, dateColumns, cohortId = NULL, returnReason = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"cohort cohort table cdm reference. dateColumns Date columns cohort table consider. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. returnReason TRUE return column stating column dateColumns used new cohort end date. name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtFirstDate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort end date to the first of a set of column dates — exitAtFirstDate","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(tables = list( \"cohort\" = dplyr::tibble( cohort_definition_id = 1, subject_id = c(1, 2, 3, 4), cohort_start_date = as.Date(c(\"2000-06-03\", \"2000-01-01\", \"2015-01-15\", \"2000-12-09\")), cohort_end_date = as.Date(c(\"2001-09-01\", \"2001-01-12\", \"2015-02-15\", \"2002-12-09\")), date_1 = as.Date(c(\"2001-08-01\", \"2001-01-01\", \"2015-01-15\", \"2002-12-09\")), date_2 = as.Date(c(\"2001-08-01\", NA, \"2015-04-15\", \"2002-12-09\")) ) )) #> Warning: ! 7 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `gender_concept_id` is numeric but expected integer #> • `year_of_birth` is numeric but expected integer #> • `month_of_birth` is numeric but expected integer #> • `race_concept_id` is numeric but expected integer #> • `ethnicity_concept_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 2 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> • `period_type_concept_id` is numeric but expected integer #> Warning: ! 9 column in cdm_source do not match expected column type: #> • `cdm_source_abbreviation` is logical but expected character #> • `cdm_holder` is logical but expected character #> • `source_description` is logical but expected character #> • `source_documentation_reference` is logical but expected character #> • `cdm_etl_reference` is logical but expected character #> • `source_release_date` is logical but expected date #> • `cdm_release_date` is logical but expected date #> • `cdm_version` is numeric but expected character #> • `vocabulary_version` is logical but expected character #> Warning: ! 3 column in concept do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `valid_start_date` is character but expected date #> • `valid_end_date` is character but expected date #> Warning: ! 1 column in vocabulary do not match expected column type: #> • `vocabulary_concept_id` is numeric but expected integer #> Warning: ! 5 column in concept_relationship do not match expected column type: #> • `concept_id_1` is numeric but expected integer #> • `concept_id_2` is numeric but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> • `invalid_reason` is logical but expected character #> Warning: ! 2 column in concept_synonym do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `language_concept_id` is numeric but expected integer #> Warning: ! 4 column in concept_ancestor do not match expected column type: #> • `ancestor_concept_id` is numeric but expected integer #> • `descendant_concept_id` is numeric but expected integer #> • `min_levels_of_separation` is numeric but expected integer #> • `max_levels_of_separation` is numeric but expected integer #> Warning: ! 9 column in drug_strength do not match expected column type: #> • `drug_concept_id` is numeric but expected integer #> • `ingredient_concept_id` is numeric but expected integer #> • `amount_value` is logical but expected numeric #> • `amount_unit_concept_id` is numeric but expected integer #> • `numerator_unit_concept_id` is numeric but expected integer #> • `denominator_unit_concept_id` is numeric but expected integer #> • `box_size` is logical but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> Warning: ! 2 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 1 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer cdm$cohort |> exitAtFirstDate(dateColumns = c(\"date_1\", \"date_2\")) #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> # Source: table [4 x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date exit_reason #> #> 1 1 3 2015-01-15 2015-01-15 date_1 #> 2 1 1 2000-06-03 2001-08-01 date_1; dat… #> 3 1 2 2000-01-01 2001-01-01 date_1 #> 4 1 4 2000-12-09 2002-12-09 date_1; dat… # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort end date to the last of a set of column dates — exitAtLastDate","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"exitAtLastDate() resets cohort end date based set specified column dates. last date occurs chosen.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"","code":"exitAtLastDate( cohort, dateColumns, cohortId = NULL, returnReason = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"cohort cohort table cdm reference. dateColumns description cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. returnReason TRUE return column stating column dateColumns used new cohort end date. description name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtLastDate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort end date to the last of a set of column dates — exitAtLastDate","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(tables = list( \"cohort\" = dplyr::tibble( cohort_definition_id = 1, subject_id = c(1, 2, 3, 4), cohort_start_date = as.Date(c(\"2000-06-03\", \"2000-01-01\", \"2015-01-15\", \"2000-12-09\")), cohort_end_date = as.Date(c(\"2001-09-01\", \"2001-01-12\", \"2015-02-15\", \"2002-12-09\")), date_1 = as.Date(c(\"2001-08-01\", \"2001-01-01\", \"2015-01-15\", \"2002-12-09\")), date_2 = as.Date(c(\"2001-08-01\", NA, \"2015-04-15\", \"2002-12-09\")) ) )) #> Warning: ! 7 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `gender_concept_id` is numeric but expected integer #> • `year_of_birth` is numeric but expected integer #> • `month_of_birth` is numeric but expected integer #> • `race_concept_id` is numeric but expected integer #> • `ethnicity_concept_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 2 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> • `period_type_concept_id` is numeric but expected integer #> Warning: ! 9 column in cdm_source do not match expected column type: #> • `cdm_source_abbreviation` is logical but expected character #> • `cdm_holder` is logical but expected character #> • `source_description` is logical but expected character #> • `source_documentation_reference` is logical but expected character #> • `cdm_etl_reference` is logical but expected character #> • `source_release_date` is logical but expected date #> • `cdm_release_date` is logical but expected date #> • `cdm_version` is numeric but expected character #> • `vocabulary_version` is logical but expected character #> Warning: ! 3 column in concept do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `valid_start_date` is character but expected date #> • `valid_end_date` is character but expected date #> Warning: ! 1 column in vocabulary do not match expected column type: #> • `vocabulary_concept_id` is numeric but expected integer #> Warning: ! 5 column in concept_relationship do not match expected column type: #> • `concept_id_1` is numeric but expected integer #> • `concept_id_2` is numeric but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> • `invalid_reason` is logical but expected character #> Warning: ! 2 column in concept_synonym do not match expected column type: #> • `concept_id` is numeric but expected integer #> • `language_concept_id` is numeric but expected integer #> Warning: ! 4 column in concept_ancestor do not match expected column type: #> • `ancestor_concept_id` is numeric but expected integer #> • `descendant_concept_id` is numeric but expected integer #> • `min_levels_of_separation` is numeric but expected integer #> • `max_levels_of_separation` is numeric but expected integer #> Warning: ! 9 column in drug_strength do not match expected column type: #> • `drug_concept_id` is numeric but expected integer #> • `ingredient_concept_id` is numeric but expected integer #> • `amount_value` is logical but expected numeric #> • `amount_unit_concept_id` is numeric but expected integer #> • `numerator_unit_concept_id` is numeric but expected integer #> • `denominator_unit_concept_id` is numeric but expected integer #> • `box_size` is logical but expected integer #> • `valid_start_date` is logical but expected date #> • `valid_end_date` is logical but expected date #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> Warning: ! 2 column in person do not match expected column type: #> • `person_id` is numeric but expected integer #> • `location_id` is numeric but expected integer #> Warning: ! 1 column in observation_period do not match expected column type: #> • `person_id` is numeric but expected integer #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer cdm$cohort |> exitAtLastDate(dateColumns = c(\"date_1\", \"date_2\")) #> Warning: ! 2 column in cohort do not match expected column type: #> • `cohort_definition_id` is numeric but expected integer #> • `subject_id` is numeric but expected integer #> # Source: table [4 x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date exit_reason #> #> 1 1 2 2000-01-01 2001-01-01 date_1 #> 2 1 1 2000-06-03 2001-08-01 date_1; dat… #> 3 1 3 2015-01-15 2015-04-15 date_2 #> 4 1 4 2000-12-09 2002-12-09 date_1; dat… # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cohort end date to end of observation — exitAtObservationEnd","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"exitAtObservationEnd() resets cohort end date based set specified column dates. last date occurs chosen. functions changes cohort end date end date observation period corresponding cohort entry. case generates overlapping records cohort, overlapping entries merged.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"","code":"exitAtObservationEnd(cohort, cohortId = NULL, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/exitAtObservationEnd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cohort end date to end of observation — exitAtObservationEnd","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> exitAtObservationEnd() #> # Source: table [6 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 4 1996-06-30 2013-12-31 #> 2 1 2 2000-05-04 2003-06-15 #> 3 1 7 2014-03-07 2014-04-09 #> 4 1 5 2012-03-20 2013-02-10 #> 5 1 3 2015-01-27 2015-10-11 #> 6 1 1 2001-05-30 2013-06-29 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"intersectCohorts() combines different cohort entries, records overlap combined kept. Cohort entries individual cohorts.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"","code":"intersectCohorts( cohort, cohortId = NULL, gap = 0, mutuallyExclusive = FALSE, returnOnlyComb = FALSE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. gap Number days two subsequent cohort entries merged single cohort record. mutuallyExclusive Whether generated cohorts mutually exclusive . returnOnlyComb Whether get combination cohort back name Name new cohort demographic requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/intersectCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a combination cohort set between the intersection of different cohorts. — intersectCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort3 <- intersectCohorts( cohort = cdm$cohort2, name = \"cohort3\", ) #> Warning: ! 3 casted column in cohort3 (cohort_attrition) as do not match expected column #> type: #> • `reason_id` from numeric to integer #> • `excluded_records` from numeric to integer #> • `excluded_subjects` from numeric to integer settings(cdm$cohort3) #> # A tibble: 3 × 6 #> cohort_definition_id cohort_name cohort_1 cohort_2 mutually_exclusive gap #> #> 1 1 cohort_1 1 0 FALSE 0 #> 2 2 cohort_2 0 1 FALSE 0 #> 3 3 cohort_1_coho… 1 1 FALSE 0 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a new cohort matched cohort — matchCohorts","title":"Generate a new cohort matched cohort — matchCohorts","text":"matchCohorts() generate new cohort matched individuals existing cohort. Individuals can matched based year birth sex.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a new cohort matched cohort — matchCohorts","text":"","code":"matchCohorts( cohort, cohortId = NULL, matchSex = TRUE, matchYearOfBirth = TRUE, ratio = 1, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a new cohort matched cohort — matchCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. matchSex Whether match sex. matchYearOfBirth Whether match year birth. ratio Number allowed matches per individual target cohort. name Name new generated cohort set.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a new cohort matched cohort — matchCohorts","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/matchCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a new cohort matched cohort — matchCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) library(dplyr) #> #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #> #> filter, lag #> The following objects are masked from ‘package:base’: #> #> intersect, setdiff, setequal, union cdm <- mockCohortConstructor(nPerson = 200) cdm$new_matched_cohort <- cdm$cohort2 |> matchCohorts( name = \"new_matched_cohort\", cohortId = 2, matchSex = TRUE, matchYearOfBirth = TRUE, ratio = 1) #> Starting matching #> Warning: Multiple records per person detected. The matchCohorts() function is designed #> to operate under the assumption that there is only one record per person within #> each cohort. If this assumption is not met, each record will be treated #> independently. As a result, the same individual may be matched multiple times, #> leading to inconsistent and potentially misleading results. #> ℹ Creating copy of target cohort. #> • 1 cohort to be matched. #> ℹ Creating controls cohorts. #> Warning: ! 2 casted column in tmp_004_og_039_1724761022 (cohort_attrition) as do not #> match expected column type: #> • `number_records` from numeric to integer #> • `number_subjects` from numeric to integer #> ℹ Excluding cases from controls #> • Matching by gender_concept_id and year_of_birth #> • Removing controls that were not in observation at index date #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> • Excluding target records whose pair is not in observation #> • Adjusting ratio #> Binding both cohorts #> ✔ Done cdm$new_matched_cohort #> # Source: table [?? x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date cluster_id #> #> 1 1 19 2003-06-22 2005-07-21 36 #> 2 1 84 1995-08-28 1999-04-05 42 #> 3 1 113 2015-09-05 2016-01-10 50 #> 4 1 94 2017-11-01 2018-07-05 59 #> 5 1 118 1975-11-28 1981-05-30 6 #> 6 1 56 2007-09-28 2008-07-15 18 #> 7 1 63 2008-08-23 2008-09-02 19 #> 8 1 20 1990-06-07 1993-11-05 26 #> 9 1 83 2011-01-15 2011-02-06 94 #> 10 1 7 2014-03-06 2014-03-08 98 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":null,"dir":"Reference","previous_headings":"","what":"Create cohorts measurement based cohorts — measurementCohort","title":"Create cohorts measurement based cohorts — measurementCohort","text":"measurementCohort() creates cohorts based patient records contained measurement table. function extends conceptCohort() allows measurement values associated records specified. valueAsConcept valueAsNumber NULL requirements values associated measurement records using measurementCohort() lead result using conceptCohort() (long concepts measurement domain). one valueAsConcept valueAsNumber NULL records required values satisfy requirement specified. valueAsConcept valueAsNumber NULL, records required values fulfill either requirements","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create cohorts measurement based cohorts — measurementCohort","text":"","code":"measurementCohort( cdm, conceptSet, name, valueAsConcept = NULL, valueAsNumber = NULL )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create cohorts measurement based cohorts — measurementCohort","text":"cdm cdm reference. conceptSet conceptSet, can either codelist conceptSetExpression. name Name cohort cdm object. valueAsConcept vector cohort IDs used filter measurements. measurements values value_as_concept_id column measurement table included. NULL entries independently value concept considered. valueAsNumber named list indicating range values unit correspond , follows: list(\"unit_concept_id\" = c(rangeValue1, rangeValue2)). NULL, entries independently value number included.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create cohorts measurement based cohorts — measurementCohort","text":"cohort table","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/measurementCohort.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create cohorts measurement based cohorts — measurementCohort","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(con = NULL) cdm$concept <- cdm$concept |> dplyr::union_all( dplyr::tibble( concept_id = c(4326744, 4298393, 45770407, 8876, 4124457), concept_name = c(\"Blood pressure\", \"Systemic blood pressure\", \"Baseline blood pressure\", \"millimeter mercury column\", \"Normal range\"), domain_id = \"Measurement\", vocabulary_id = c(\"SNOMED\", \"SNOMED\", \"SNOMED\", \"UCUM\", \"SNOMED\"), standard_concept = \"S\", concept_class_id = c(\"Observable Entity\", \"Observable Entity\", \"Observable Entity\", \"Unit\", \"Qualifier Value\"), concept_code = NA, valid_start_date = NA, valid_end_date = NA, invalid_reason = NA ) ) cdm$measurement <- dplyr::tibble( measurement_id = 1:4, person_id = c(1, 1, 2, 3), measurement_concept_id = c(4326744, 4298393, 4298393, 45770407), measurement_date = as.Date(c(\"2000-07-01\", \"2000-12-11\", \"2002-09-08\", \"2015-02-19\")), measurement_type_concept_id = NA, value_as_number = c(100, 125, NA, NA), value_as_concept_id = c(0, 0, 0, 4124457), unit_concept_id = c(8876, 8876, 0, 0) ) cdm <- CDMConnector::copyCdmTo( con = DBI::dbConnect(duckdb::duckdb()), cdm = cdm, schema = \"main\") cdm$cohort <- measurementCohort( cdm = cdm, name = \"cohort\", conceptSet = list(\"normal_blood_pressure\" = c(4326744, 4298393, 45770407)), valueAsConcept = c(4124457), valueAsNumber = list(\"8876\" = c(70, 120)) ) #> Warning: ! `codelist` contains numeric values, they are casted to integers. #> ℹ Getting records in observation. #> ℹ Applying measurement requirements. #> ℹ Creating cohort attributes. #> Warning: ! 1 column in cohort do not match expected column type: #> • `subject_id` is numeric but expected integer #> ✔ Cohort cohort created. cdm$cohort #> # Source: table [2 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 3 2015-02-19 2015-02-19 #> 2 1 1 2000-07-01 2000-07-01 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"mockCohortConstructor() creates example dataset can used demonstrating testing package","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"","code":"mockCohortConstructor( nPerson = 10, conceptTable = NULL, tables = NULL, conceptId = NULL, conceptIdClass = NULL, drugExposure = FALSE, conditionOccurrence = FALSE, measurement = FALSE, death = FALSE, otherTables = NULL, con = DBI::dbConnect(duckdb::duckdb()), writeSchema = \"main\", seed = 123 )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"nPerson number person cdm conceptTable user defined concept table tables list tables include cdm conceptId list concept id conceptIdClass domain class conceptId drugExposure T/F include drug exposure table cdm conditionOccurrence T/F include condition occurrence cdm measurement T/F include measurement cdm death T/F include death table cdm otherTables takes list single tibble names include tables cdm con DBI connection create cdm mock object. writeSchema Name schema connection writing permissions. seed Seed passed omock::mockCdmFromTable","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"cdm object","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/mockCohortConstructor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to create a mock cdm reference for CohortConstructor — mockCohortConstructor","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm #> #> ── # OMOP CDM reference (duckdb) of mock database ────────────────────────────── #> • omop tables: person, observation_period, cdm_source, concept, vocabulary, #> concept_relationship, concept_synonym, concept_ancestor, drug_strength #> • cohort tables: cohort1, cohort2 #> • achilles tables: - #> • other tables: - # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. omopgenerics attrition, bind, cohortCodelist, cohortCount, settings, tableName PatientProfiles endDateColumn, startDateColumn","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on age — requireAge","title":"Restrict cohort on age — requireAge","text":"requireAge() filters cohort records, keeping records individuals satisfy specified age criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on age — requireAge","text":"","code":"requireAge( cohort, ageRange, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on age — requireAge","text":"cohort cohort table cdm reference. ageRange list minimum maximum age. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains date compute demographics characteristics restrict . name Name new cohort age requirement.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on age — requireAge","text":"cohort table records individuals satisfying age requirement","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireAge.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on age — requireAge","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requireAge(indexDate = \"cohort_start_date\", ageRange = list(c(18, 65))) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [7 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 2 2000-05-04 2000-05-17 #> 2 1 2 2000-05-18 2001-01-23 #> 3 1 3 2015-01-27 2015-06-28 #> 4 1 5 2012-03-20 2012-04-30 #> 5 1 5 2012-05-01 2012-07-24 #> 6 1 7 2014-03-07 2014-03-07 #> 7 1 7 2014-03-08 2014-03-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":null,"dir":"Reference","previous_headings":"","what":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"requireCohortIntersect() filters cohort table based requirement individual seen (seen) another cohort time window around index date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"","code":"requireCohortIntersect( cohort, targetCohortTable, window, intersections = c(1, Inf), cohortId = NULL, targetCohortId = NULL, indexDate = \"cohort_start_date\", targetStartDate = \"cohort_start_date\", targetEndDate = \"cohort_end_date\", censorDate = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"cohort cohort table cdm reference. targetCohortTable Name cohort want check intersect. window Window consider events . intersections range indicating number intersections criteria fulfilled. single number passed, number intersections must match . cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. targetCohortId Vector cohort definition ids include. indexDate Variable x contains date compute intersection. targetStartDate Date reference cohort table, either start (overlap) (incidence). targetEndDate Date reference cohort table, either end (overlap) NULL (incidence). censorDate Whether censor overlap events specific date column date x. name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"Cohort table isatisfying criteria kept","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireCohortIntersect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require cohort subjects are present (or absence) in another cohort — requireCohortIntersect","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requireCohortIntersect(targetCohortTable = \"cohort2\", targetCohortId = 1, indexDate = \"cohort_start_date\", window = c(-Inf, 0)) #> # Source: table [10 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2001-05-30 2003-05-01 #> 2 1 1 2003-05-02 2006-06-10 #> 3 1 2 2000-05-04 2000-05-17 #> 4 1 2 2000-05-18 2001-01-23 #> 5 1 3 2015-01-27 2015-06-28 #> 6 1 4 1996-06-30 1998-11-20 #> 7 1 5 2012-03-20 2012-04-30 #> 8 1 5 2012-05-01 2012-07-24 #> 9 1 7 2014-03-07 2014-03-07 #> 10 1 7 2014-03-08 2014-03-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":null,"dir":"Reference","previous_headings":"","what":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"requireConceptIntersect() filters cohort table based requirement individual seen (seen) events related concept list time window around index date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"","code":"requireConceptIntersect( cohort, conceptSet, window, intersections = c(1, Inf), cohortId = NULL, indexDate = \"cohort_start_date\", targetStartDate = \"event_start_date\", targetEndDate = \"event_end_date\", censorDate = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"cohort cohort table cdm reference. conceptSet Concept set list. window Window consider events . intersections range indicating number intersections criteria fulfilled. single number passed, number intersections must match . cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged.. indexDate Variable x contains date compute intersection. targetStartDate Date reference cohort table, either start (overlap) (incidence). targetEndDate Date reference cohort table, either end (overlap) NULL (incidence). censorDate Whether censor overlap events specific date column date x. name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"Cohort table events concept list kept (without event negate = TRUE)","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireConceptIntersect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require cohort subjects to have (or not have) events of a concept list — requireConceptIntersect","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(conditionOccurrence = TRUE) cdm$cohort2 <- requireConceptIntersect( cohort = cdm$cohort1, conceptSet = list(a = 1), window = c(-Inf, 0), name = \"cohort2\") #> Warning: ! `codelist` contains numeric values, they are casted to integers. # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":null,"dir":"Reference","previous_headings":"","what":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"requireDeathFlag() filters cohort table based requirement individual seen (seen) death time window around index date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"","code":"requireDeathFlag( cohort, window, cohortId = NULL, indexDate = \"cohort_start_date\", censorDate = NULL, negate = FALSE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"cohort cohort table cdm reference. window Window consider events . cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable x contains date compute intersection. censorDate Whether censor overlap events specific date column date x. negate set TRUE, criteria applied exclusion rather inclusion (.e. require absence another cohort). name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"Cohort table death event kept (without negate = TRUE)","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDeathFlag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require cohort subjects have (or do not have) a death record — requireDeathFlag","text":"","code":"# \\donttest{ library(CDMConnector) #> #> Attaching package: ‘CDMConnector’ #> The following objects are masked from ‘package:CohortConstructor’: #> #> intersectCohorts, unionCohorts library(CohortConstructor) cdm <- mockCohortConstructor(death = TRUE) #> ■■■■■■■■■■■■■■■■■■■■■■■■■■■■ 90% | ETA: 0s cdm$cohort1 <- cdm$cohort1 |> requireDeathFlag(window = list(c(0, Inf))) attrition(cdm$cohort1) #> # A tibble: 2 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 10 6 1 Initial qualify… #> 2 1 10 6 2 Death between 0… #> # ℹ 2 more variables: excluded_records , excluded_subjects # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on patient demographics — requireDemographics","title":"Restrict cohort on patient demographics — requireDemographics","text":"requireDemographics() filters cohort records, keeping records individuals satisfy specified demographic criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on patient demographics — requireDemographics","text":"","code":"requireDemographics( cohort, cohortId = NULL, indexDate = \"cohort_start_date\", ageRange = list(c(0, 150)), sex = c(\"Both\"), minPriorObservation = 0, minFutureObservation = 0, requirementInteractions = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on patient demographics — requireDemographics","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains date compute demographics characteristics restrict . ageRange list minimum maximum age. sex Can \"\", \"Male\" \"Female\". one latter, sex included. minPriorObservation minimum number prior observation days database. minFutureObservation minimum number future observation days database. requirementInteractions TRUE, cohorts created combinations ageGroup, sex, daysPriorObservation. FALSE, first value specified factors used. Consequently, order values matters requirementInteractions FALSE. name Name new cohort demographic requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on patient demographics — requireDemographics","text":"cohort table records individuals satisfying demographic requirements","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireDemographics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on patient demographics — requireDemographics","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 |> requireDemographics(indexDate = \"cohort_start_date\", ageRange = list(c(18, 65)), sex = \"Female\", minPriorObservation = 365) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [3 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 32 1991-09-11 2002-11-15 #> 2 1 38 1990-05-01 1994-07-14 #> 3 1 85 2000-05-09 2001-11-16 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on future observation — requireFutureObservation","title":"Restrict cohort on future observation — requireFutureObservation","text":"requireFutureObservation() filters cohort records, keeping records individuals satisfy specified future observation criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on future observation — requireFutureObservation","text":"","code":"requireFutureObservation( cohort, minFutureObservation, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on future observation — requireFutureObservation","text":"cohort cohort table cdm reference. minFutureObservation minimum number future observation days database. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains date compute demographics characteristics restrict . name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on future observation — requireFutureObservation","text":"cohort table records individuals satisfying future observation requirement","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireFutureObservation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on future observation — requireFutureObservation","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requireFutureObservation(indexDate = \"cohort_start_date\", minFutureObservation = 30) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [10 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2001-05-30 2003-05-01 #> 2 1 1 2003-05-02 2006-06-10 #> 3 1 2 2000-05-04 2000-05-17 #> 4 1 2 2000-05-18 2001-01-23 #> 5 1 3 2015-01-27 2015-06-28 #> 6 1 4 1996-06-30 1998-11-20 #> 7 1 5 2012-03-20 2012-04-30 #> 8 1 5 2012-05-01 2012-07-24 #> 9 1 7 2014-03-07 2014-03-07 #> 10 1 7 2014-03-08 2014-03-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":null,"dir":"Reference","previous_headings":"","what":"Require that an index date is within a date range — requireInDateRange","title":"Require that an index date is within a date range — requireInDateRange","text":"requireInDateRange() filters cohort records, keeping index date within specified date range.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require that an index date is within a date range — requireInDateRange","text":"","code":"requireInDateRange( cohort, dateRange, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require that an index date is within a date range — requireInDateRange","text":"cohort cohort table cdm reference. dateRange window time index date must observed. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains index date interest name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require that an index date is within a date range — requireInDateRange","text":"cohort table cohort entries outside date range dropped","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireInDateRange.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require that an index date is within a date range — requireInDateRange","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 |> requireInDateRange(indexDate = \"cohort_start_date\", dateRange = as.Date(c(\"2010-01-01\", \"2019-01-01\"))) #> # Source: table [?? x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 6 2011-03-07 2014-01-24 #> 2 1 7 2014-03-08 2014-03-19 #> 3 1 13 2014-06-24 2014-06-29 #> 4 1 13 2014-06-30 2014-08-07 #> 5 1 17 2017-03-28 2017-04-05 #> 6 1 18 2012-01-30 2012-05-21 #> 7 1 24 2016-11-15 2016-11-22 #> 8 1 24 2016-11-23 2016-11-29 #> 9 1 24 2016-11-30 2017-01-25 #> 10 1 31 2013-03-29 2014-02-09 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort to first entry — requireIsFirstEntry","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"requireIsFirstEntry() filters cohort records, keeping first cohort entry per person.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"","code":"requireIsFirstEntry( cohort, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Column name cohort contains date restrict . name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"cohort table cdm reference.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsFirstEntry.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort to first entry — requireIsFirstEntry","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 <- requireIsFirstEntry(cdm$cohort1) # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort to last entry per person — requireIsLastEntry","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"requireIsLastEntry() filters cohort records, keeping last cohort entry per person.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"","code":"requireIsLastEntry( cohort, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Column name cohort contains date restrict . name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"cohort table cdm reference.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireIsLastEntry.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort to last entry per person — requireIsLastEntry","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 <- requireIsLastEntry(cdm$cohort1) # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on prior observation — requirePriorObservation","title":"Restrict cohort on prior observation — requirePriorObservation","text":"requirePriorObservation() filters cohort records, keeping records individuals satisfy specified prior observation criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on prior observation — requirePriorObservation","text":"","code":"requirePriorObservation( cohort, minPriorObservation, cohortId = NULL, indexDate = \"cohort_start_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on prior observation — requirePriorObservation","text":"cohort cohort table cdm reference. minPriorObservation minimum number prior observation days database. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable cohort contains date compute demographics characteristics restrict . name Name new cohort prior observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on prior observation — requirePriorObservation","text":"cohort table records individuals satisfying prior observation requirement","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requirePriorObservation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on prior observation — requirePriorObservation","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requirePriorObservation(indexDate = \"cohort_start_date\", minPriorObservation = 365) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [4 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2003-05-02 2006-06-10 #> 2 1 2 2000-05-04 2000-05-17 #> 3 1 2 2000-05-18 2001-01-23 #> 4 1 4 1996-06-30 1998-11-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on sex — requireSex","title":"Restrict cohort on sex — requireSex","text":"requireSex() filters cohort records, keeping records individuals satisfy specified sex criteria.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on sex — requireSex","text":"","code":"requireSex(cohort, sex, cohortId = NULL, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on sex — requireSex","text":"cohort cohort table cdm reference. sex Can \"\", \"Male\" \"Female\". one latter, sex included. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. name Name new cohort sex requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on sex — requireSex","text":"cohort table records individuals satisfying sex requirement","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireSex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on sex — requireSex","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> requireSex(sex = \"Female\") #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [5 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 2 2000-05-04 2000-05-17 #> 2 1 2 2000-05-18 2001-01-23 #> 3 1 3 2015-01-27 2015-06-28 #> 4 1 5 2012-03-20 2012-04-30 #> 5 1 5 2012-05-01 2012-07-24 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":null,"dir":"Reference","previous_headings":"","what":"Require cohort subjects are present in another clinical table — requireTableIntersect","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"requireTableIntersect() filters cohort table based requirement individual seen (seen) record (records) clinical table time window around index date.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"","code":"requireTableIntersect( cohort, tableName, window, intersections = c(1, Inf), cohortId = NULL, indexDate = \"cohort_start_date\", targetStartDate = startDateColumn(tableName), targetEndDate = endDateColumn(tableName), censorDate = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"cohort cohort table cdm reference. tableName Name table check intersect. window Window consider events . intersections range indicating number intersections criteria fulfilled. single number passed, number intersections must match . cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. indexDate Variable x contains date compute intersection. targetStartDate Date reference cohort table, either start (overlap) (incidence). targetEndDate Date reference cohort table, either end (overlap) NULL (incidence). censorDate Whether censor overlap events specific date column date x. name Name new cohort future observation restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"Cohort table table kept (table negate = TRUE)","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/requireTableIntersect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Require cohort subjects are present in another clinical table — requireTableIntersect","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(drugExposure = TRUE) cdm$cohort1 |> requireTableIntersect(tableName = \"drug_exposure\", indexDate = \"cohort_start_date\", window = c(-Inf, 0)) #> # Source: table [7 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2003-05-02 2006-06-10 #> 2 1 2 2000-05-04 2000-05-17 #> 3 1 2 2000-05-18 2001-01-23 #> 4 1 3 2015-01-27 2015-06-28 #> 5 1 4 1996-06-30 1998-11-20 #> 6 1 5 2012-05-01 2012-07-24 #> 7 1 7 2014-03-08 2014-03-20 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample a cohort table for a given number of individuals. — sampleCohorts","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"sampleCohorts() samples existing cohort table given number people. records individuals preserved.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"","code":"sampleCohorts(cohort, cohortId = NULL, n, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included sampled. n Number people sampled included cohort. name Name new sampled cohort.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"Cohort table specified cohorts sampled.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/sampleCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample a cohort table for a given number of individuals. — sampleCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort2 |> sampleCohorts(cohortId = 1, n = 10) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> # Source: table [?? x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 6 2011-03-07 2014-01-24 #> 2 1 7 2014-03-08 2014-03-19 #> 3 1 14 1986-11-29 1987-12-14 #> 4 1 14 1987-12-15 1988-03-19 #> 5 1 15 1978-07-09 2000-06-12 #> 6 1 22 1993-09-22 1994-04-10 #> 7 1 22 1994-04-11 1996-04-26 #> 8 1 22 1996-04-27 1999-08-31 #> 9 1 59 2014-08-29 2015-04-10 #> 10 1 59 2015-04-11 2016-01-05 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a new cohort table from stratifying an existing one — stratifyCohorts","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"stratifyCohorts() creates new cohorts, splitting existing cohort based specified columns stratify .","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"","code":"stratifyCohorts( cohort, strata, cohortId = NULL, removeStrata = TRUE, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"cohort cohort table cdm reference. strata strata list point columns cohort table. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. removeStrata Whether remove strata columns final cohort table. name Name new cohort.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"Cohort table stratified.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/stratifyCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a new cohort table from stratifying an existing one — stratifyCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) library(PatientProfiles) cdm <- mockCohortConstructor() cdm$my_cohort <- cdm$cohort1 |> addAge(ageGroup = list(\"child\" = c(0, 17), \"adult\" = c(18, Inf))) |> addSex() |> stratifyCohorts( strata = list(\"sex\", c(\"sex\", \"age_group\")), name = \"my_cohort\" ) #> Warning: ! 5 casted column in my_cohort (cohort_attrition) as do not match expected #> column type: #> • `number_records` from numeric to integer #> • `number_subjects` from numeric to integer #> • `reason_id` from numeric to integer #> • `excluded_records` from numeric to integer #> • `excluded_subjects` from numeric to integer #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. cdm$my_cohort #> # Source: table [?? x 5] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date age #> #> 1 2 1 2001-05-30 2003-05-01 3 #> 2 2 1 2003-05-02 2006-06-10 5 #> 3 1 2 2000-05-04 2000-05-17 37 #> 4 1 2 2000-05-18 2001-01-23 37 #> 5 1 3 2015-01-27 2015-06-28 28 #> 6 2 4 1996-06-30 1998-11-20 17 #> 7 1 5 2012-03-20 2012-04-30 39 #> 8 1 5 2012-05-01 2012-07-24 39 #> 9 2 7 2014-03-07 2014-03-07 27 #> 10 2 7 2014-03-08 2014-03-20 27 #> # ℹ more rows settings(cdm$my_cohort) #> # A tibble: 6 × 8 #> cohort_definition_id cohort_name target_cohort_id target_cohort_name #> #> 1 1 cohort_1_female 1 cohort_1 #> 2 2 cohort_1_male 1 cohort_1 #> 3 3 cohort_1_female_adult 1 cohort_1 #> 4 4 cohort_1_female_child 1 cohort_1 #> 5 5 cohort_1_male_adult 1 cohort_1 #> 6 6 cohort_1_male_child 1 cohort_1 #> # ℹ 4 more variables: target_cohort_table_name , strata_columns , #> # sex , age_group attrition(cdm$my_cohort) #> # A tibble: 16 × 7 #> cohort_definition_id number_records number_subjects reason_id reason #> #> 1 1 10 6 1 Initial qualif… #> 2 1 5 3 2 filter strata:… #> 3 2 10 6 1 Initial qualif… #> 4 2 5 3 2 filter strata:… #> 5 3 10 6 1 Initial qualif… #> 6 3 5 3 2 filter strata:… #> 7 3 5 3 3 filter strata:… #> 8 4 10 6 1 Initial qualif… #> 9 4 5 3 2 filter strata:… #> 10 4 0 0 3 filter strata:… #> 11 5 10 6 1 Initial qualif… #> 12 5 5 3 2 filter strata:… #> 13 5 2 1 3 filter strata:… #> 14 6 10 6 1 Initial qualif… #> 15 6 5 3 2 filter strata:… #> 16 6 3 2 3 filter strata:… #> # ℹ 2 more variables: excluded_records , excluded_subjects # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"subsetCohorts() filters existing cohort table, keeping records cohorts specified.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"","code":"subsetCohorts(cohort, cohortId, minCohortCount = 0, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. minCohortCount minimum count cohort included. Default 0, meaning non-empty cohorts included. Cohorts included removed cohort set. name Name new cohort demographic requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"Cohort table cohorts cohortId.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/subsetCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a cohort table using a subset of cohorts from another table. — subsetCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 |> subsetCohorts(cohortId = 1) #> # Source: table [?? x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 1 2001-02-15 2001-10-28 #> 2 1 1 2001-10-29 2003-03-15 #> 3 1 1 2003-03-16 2005-02-08 #> 4 1 2 1999-11-11 2002-04-09 #> 5 1 6 2011-03-07 2014-01-24 #> 6 1 7 2014-03-08 2014-03-19 #> 7 1 10 2019-12-04 2019-12-14 #> 8 1 13 2014-06-24 2014-06-29 #> 9 1 13 2014-06-30 2014-08-07 #> 10 1 14 1986-11-29 1987-12-14 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":null,"dir":"Reference","previous_headings":"","what":"Restrict cohort on patient demographics — trimDemographics","title":"Restrict cohort on patient demographics — trimDemographics","text":"trimDemographics() resets cohort start end date based specified demographic criteria satisfied.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Restrict cohort on patient demographics — trimDemographics","text":"","code":"trimDemographics( cohort, cohortId = NULL, ageRange = NULL, sex = NULL, minPriorObservation = NULL, minFutureObservation = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Restrict cohort on patient demographics — trimDemographics","text":"cohort cohort table cdm reference. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. ageRange list minimum maximum age. sex Can \"\", \"Male\" \"Female\". one latter, sex included. minPriorObservation minimum number prior observation days database. minFutureObservation minimum number future observation days database. name Name new cohort demographic requirements.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Restrict cohort on patient demographics — trimDemographics","text":"cohort table records individuals satisfying demographic requirements","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimDemographics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Restrict cohort on patient demographics — trimDemographics","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 |> trimDemographics(ageRange = list(c(10, 30))) #> ℹ Building new trimmed cohort #> Adding demographics information #> Creating initial cohort #> Trim age #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. #> ✔ Cohort trimmed #> # Source: table [?? x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 43 2014-10-05 2015-09-27 #> 2 1 48 1970-07-29 1974-01-28 #> 3 1 64 1993-05-18 2001-05-18 #> 4 1 75 1974-01-17 1974-10-19 #> 5 1 43 2014-07-21 2014-10-04 #> 6 1 29 2006-11-24 2008-03-21 #> 7 1 43 2014-07-06 2014-07-20 #> 8 1 29 2006-10-02 2006-11-23 #> 9 1 29 2006-07-07 2006-10-01 #> 10 1 14 1987-12-15 1988-03-19 #> # ℹ more rows # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":null,"dir":"Reference","previous_headings":"","what":"Trim cohort dates to be within a date range — trimToDateRange","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"trimToDateRange() resets cohort start end date based specified date range.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"","code":"trimToDateRange( cohort, dateRange, cohortId = NULL, startDate = \"cohort_start_date\", endDate = \"cohort_end_date\", name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"cohort cohort table cdm reference. dateRange window time index date must observed. cohortId IDs cohorts modify. NULL, cohorts used; otherwise, specified cohorts modified, rest remain unchanged. startDate Variable earliest date. endDate Variable latest date. name Name new cohort restriction.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"cohort table record timings updated within date range. records time outside range dropped.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/trimToDateRange.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Trim cohort dates to be within a date range — trimToDateRange","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor() cdm$cohort1 |> trimToDateRange(startDate = \"cohort_start_date\", endDate = \"cohort_end_date\", dateRange = as.Date(c(\"2015-01-01\", \"2015-12-31\"))) #> # Source: table [1 x 4] #> # Database: DuckDB v1.0.0 [unknown@Linux 6.5.0-1025-azure:R 4.4.1/:memory:] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> #> 1 1 3 2015-01-27 2015-06-28 # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate cohort from the union of different cohorts — unionCohorts","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"unionCohorts() combines different cohort entries, records overlap combined kept. Cohort entries individual either cohorts.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"","code":"unionCohorts( cohort, cohortId = NULL, gap = 0, cohortName = NULL, name = tableName(cohort) )"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"cohort cohort table cdm reference. cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. gap Number days two subsequent cohort entries subject merged single cohort entry cohortName Name returned cohort. NULL, cohort name created collapsing individual cohort names, separated \"_\". name Name new cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/unionCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate cohort from the union of different cohorts — unionCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort2 <- cdm$cohort2 |> unionCohorts() #> Warning: `union_cohorts()` was deprecated in CDMConnector 1.1.0. #> ℹ Please use `cohort_union()` instead. settings(cdm$cohort2) #> Error in UseMethod(\"settings\"): no applicable method for 'settings' applied to an object of class \"c('cdm_table', 'GeneratedCohortSet', 'tbl_duckdb_connection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')\" # }"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"yearCohorts() splits cohort multiple cohorts, one year.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"","code":"yearCohorts(cohort, years, cohortId = NULL, name = tableName(cohort))"},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"cohort cohort table cdm reference. years Numeric vector years use restrict observation . cohortId IDs cohorts include. NULL cohorts considered. Cohorts included removed cohort set. name Name new cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"cohort table.","code":""},{"path":"https://ohdsi.github.io/CohortConstructor/reference/yearCohorts.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate a new cohort table restricting cohort entries to certain years — yearCohorts","text":"","code":"# \\donttest{ library(CohortConstructor) cdm <- mockCohortConstructor(nPerson = 100) cdm$cohort1 <- cdm$cohort1 |> yearCohorts(years = 2000:2002) #> ! cohort columns will be reordered to match the expected order: #> cohort_definition_id, subject_id, cohort_start_date, and cohort_end_date. settings(cdm$cohort1) #> # A tibble: 3 × 5 #> cohort_definition_id cohort_name target_cohort_definition_id year #> #> 1 1 cohort_1_2000 1 2000 #> 2 2 cohort_1_2001 1 2001 #> 3 3 cohort_1_2002 1 2002 #> # ℹ 1 more variable: target_cohort_name # }"}]