cdm$medications %>% filter(subject_id == 1) #> # Source: SQL [4 x 4] -#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1//tmp/Rtmp7X9hnP/file23597b1a402e.duckdb] +#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1//tmp/Rtmp63eoUI/file230130379d08.duckdb] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> <int> <int> <date> <date> -#> 1 1 1 1976-10-20 1976-11-03 -#> 2 1 1 1971-01-04 1971-01-18 -#> 3 1 1 1982-09-11 1982-10-02 -#> 4 1 1 1980-03-15 1980-03-29 +#> 1 1 1 1971-01-04 1971-01-18 +#> 2 1 1 1982-09-11 1982-10-02 +#> 3 1 1 1980-03-15 1980-03-29 +#> 4 1 1 1976-10-20 1976-11-03 cdm$medications_collapsed %>% filter(subject_id == 1) #> # Source: SQL [3 x 4] -#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1//tmp/Rtmp7X9hnP/file23597b1a402e.duckdb] +#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1//tmp/Rtmp63eoUI/file230130379d08.duckdb] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> <int> <int> <date> <date> #> 1 1 1 1976-10-20 1976-11-03 diff --git a/articles/a07_filter_cohorts.html b/articles/a07_filter_cohorts.html index 7f9f800..e8b76c8 100644 --- a/articles/a07_filter_cohorts.html +++ b/articles/a07_filter_cohorts.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 @@ -108,26 +108,26 @@ cdm$medications |> sampleCohorts(cohortId = NULL, n = 100) #> # Source: table<main.my_study_medications> [?? x 4] -#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1//tmp/Rtmp4IP3Tf/file239e6d25bc76.duckdb] +#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1//tmp/RtmpCf9KA8/file23437cc57145.duckdb] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> <int> <int> <date> <date> -#> 1 1 887 1974-10-05 1974-10-19 -#> 2 1 5048 1978-01-22 1978-01-29 -#> 3 1 1550 1981-02-07 1981-05-08 -#> 4 1 4490 1956-04-15 1956-04-29 -#> 5 1 3488 1960-04-20 1960-05-04 -#> 6 1 3655 1997-08-04 1997-08-25 -#> 7 2 1227 1980-05-31 1980-05-31 -#> 8 1 4078 1967-09-12 1967-09-19 -#> 9 1 4655 1982-11-20 1982-12-25 -#> 10 1 2228 2001-02-26 2001-03-12 +#> 1 1 1246 1947-11-06 1947-11-20 +#> 2 1 1246 2011-03-12 2011-03-26 +#> 3 1 2576 1993-10-25 1993-11-15 +#> 4 1 4758 1995-10-21 1995-11-04 +#> 5 1 4758 1999-11-11 2000-02-09 +#> 6 1 4364 2005-03-18 2005-04-01 +#> 7 1 1804 1989-07-12 1989-07-19 +#> 8 2 640 1992-11-07 1992-11-07 +#> 9 1 3389 1973-01-15 1973-02-14 +#> 10 1 3389 2005-02-04 2005-02-18 #> # ℹ more rows cohortCount(cdm$medications) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> <int> <int> <int> -#> 1 1 324 100 +#> 1 1 345 100 #> 2 2 100 100 When cohortId = NULL all cohorts in the table are used. Note that this function does not reduced the number of records in each cohort, diff --git a/articles/a08_split_cohorts.html b/articles/a08_split_cohorts.html index 35da880..98ca063 100644 --- a/articles/a08_split_cohorts.html +++ b/articles/a08_split_cohorts.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/articles/a09_combine_cohorts.html b/articles/a09_combine_cohorts.html index 755bd59..fb55323 100644 --- a/articles/a09_combine_cohorts.html +++ b/articles/a09_combine_cohorts.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/articles/a10_match_cohorts.html b/articles/a10_match_cohorts.html index c5d767c..9be8219 100644 --- a/articles/a10_match_cohorts.html +++ b/articles/a10_match_cohorts.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/articles/a11_benchmark.html b/articles/a11_benchmark.html index a7138c2..150a003 100644 --- a/articles/a11_benchmark.html +++ b/articles/a11_benchmark.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/articles/index.html b/articles/index.html index 6324593..54ee3a3 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/authors.html b/authors.html index 0b77172..aebdcab 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 @@ -90,13 +90,13 @@ Citation Burn E, Catala M, Mercade-Besora N, Alcalde-Herraiz M, Du M, Guo Y, Chen X, Lopez-Guell K, Rowlands E (2024). CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model. -R package version 0.3.1, https://ohdsi.github.io/CohortConstructor/. +R package version 0.3.1.900, https://ohdsi.github.io/CohortConstructor/. @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-Guell and Elin Rowlands}, year = {2024}, - note = {R package version 0.3.1}, + note = {R package version 0.3.1.900}, url = {https://ohdsi.github.io/CohortConstructor/}, } diff --git a/index.html b/index.html index 9385ede..3373601 100644 --- a/index.html +++ b/index.html @@ -29,7 +29,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/pkgdown.yml b/pkgdown.yml index dad9b05..46fc45a 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -14,7 +14,7 @@ articles: a09_combine_cohorts: a09_combine_cohorts.html a10_match_cohorts: a10_match_cohorts.html a11_benchmark: a11_benchmark.html -last_built: 2024-10-11T14:52Z +last_built: 2024-10-11T15:31Z urls: reference: https://ohdsi.github.io/CohortConstructor/reference article: https://ohdsi.github.io/CohortConstructor/articles diff --git a/reference/CohortConstructor-package.html b/reference/CohortConstructor-package.html index 0fc0c10..096463e 100644 --- a/reference/CohortConstructor-package.html +++ b/reference/CohortConstructor-package.html @@ -9,7 +9,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/benchmarkData.html b/reference/benchmarkData.html index 097fc19..06e197d 100644 --- a/reference/benchmarkData.html +++ b/reference/benchmarkData.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/cdmDoc.html b/reference/cdmDoc.html index 2134bf9..771e974 100644 --- a/reference/cdmDoc.html +++ b/reference/cdmDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/cohortDoc.html b/reference/cohortDoc.html index c8ab3cf..8364922 100644 --- a/reference/cohortDoc.html +++ b/reference/cohortDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/cohortIdModifyDoc.html b/reference/cohortIdModifyDoc.html index 1ac353a..951e840 100644 --- a/reference/cohortIdModifyDoc.html +++ b/reference/cohortIdModifyDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/cohortIdSubsetDoc.html b/reference/cohortIdSubsetDoc.html index 9327a0f..b7319b7 100644 --- a/reference/cohortIdSubsetDoc.html +++ b/reference/cohortIdSubsetDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/collapseCohorts.html b/reference/collapseCohorts.html index 1e48519..4a8210e 100644 --- a/reference/collapseCohorts.html +++ b/reference/collapseCohorts.html @@ -9,7 +9,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/columnDateDoc.html b/reference/columnDateDoc.html index 331c1e3..31842d5 100644 --- a/reference/columnDateDoc.html +++ b/reference/columnDateDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/conceptCohort.html b/reference/conceptCohort.html index 7cc2b20..54155db 100644 --- a/reference/conceptCohort.html +++ b/reference/conceptCohort.html @@ -53,7 +53,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/conceptSetDoc.html b/reference/conceptSetDoc.html index 3f205c7..934e317 100644 --- a/reference/conceptSetDoc.html +++ b/reference/conceptSetDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/demographicsCohort.html b/reference/demographicsCohort.html index 4a27b6c..c1df445 100644 --- a/reference/demographicsCohort.html +++ b/reference/demographicsCohort.html @@ -13,7 +13,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/entryAtFirstDate.html b/reference/entryAtFirstDate.html index 75ce1d9..4ca43a6 100644 --- a/reference/entryAtFirstDate.html +++ b/reference/entryAtFirstDate.html @@ -9,7 +9,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 @@ -181,10 +181,10 @@ Examples#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-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… +#> 1 1 2 2001-01-01 2001-01-12 date_1 #> 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 +#> 3 1 1 2001-08-01 2001-09-01 date_1; dat… +#> 4 1 4 2002-12-09 2002-12-09 date_1; dat… # }
cdm$medications |> sampleCohorts(cohortId = NULL, n = 100) #> # Source: table<main.my_study_medications> [?? x 4] -#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1//tmp/Rtmp4IP3Tf/file239e6d25bc76.duckdb] +#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1//tmp/RtmpCf9KA8/file23437cc57145.duckdb] #> cohort_definition_id subject_id cohort_start_date cohort_end_date #> <int> <int> <date> <date> -#> 1 1 887 1974-10-05 1974-10-19 -#> 2 1 5048 1978-01-22 1978-01-29 -#> 3 1 1550 1981-02-07 1981-05-08 -#> 4 1 4490 1956-04-15 1956-04-29 -#> 5 1 3488 1960-04-20 1960-05-04 -#> 6 1 3655 1997-08-04 1997-08-25 -#> 7 2 1227 1980-05-31 1980-05-31 -#> 8 1 4078 1967-09-12 1967-09-19 -#> 9 1 4655 1982-11-20 1982-12-25 -#> 10 1 2228 2001-02-26 2001-03-12 +#> 1 1 1246 1947-11-06 1947-11-20 +#> 2 1 1246 2011-03-12 2011-03-26 +#> 3 1 2576 1993-10-25 1993-11-15 +#> 4 1 4758 1995-10-21 1995-11-04 +#> 5 1 4758 1999-11-11 2000-02-09 +#> 6 1 4364 2005-03-18 2005-04-01 +#> 7 1 1804 1989-07-12 1989-07-19 +#> 8 2 640 1992-11-07 1992-11-07 +#> 9 1 3389 1973-01-15 1973-02-14 +#> 10 1 3389 2005-02-04 2005-02-18 #> # ℹ more rows cohortCount(cdm$medications) #> # A tibble: 2 × 3 #> cohort_definition_id number_records number_subjects #> <int> <int> <int> -#> 1 1 324 100 +#> 1 1 345 100 #> 2 2 100 100
When cohortId = NULL all cohorts in the table are used. Note that this function does not reduced the number of records in each cohort, diff --git a/articles/a08_split_cohorts.html b/articles/a08_split_cohorts.html index 35da880..98ca063 100644 --- a/articles/a08_split_cohorts.html +++ b/articles/a08_split_cohorts.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/articles/a09_combine_cohorts.html b/articles/a09_combine_cohorts.html index 755bd59..fb55323 100644 --- a/articles/a09_combine_cohorts.html +++ b/articles/a09_combine_cohorts.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/articles/a10_match_cohorts.html b/articles/a10_match_cohorts.html index c5d767c..9be8219 100644 --- a/articles/a10_match_cohorts.html +++ b/articles/a10_match_cohorts.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/articles/a11_benchmark.html b/articles/a11_benchmark.html index a7138c2..150a003 100644 --- a/articles/a11_benchmark.html +++ b/articles/a11_benchmark.html @@ -26,7 +26,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/articles/index.html b/articles/index.html index 6324593..54ee3a3 100644 --- a/articles/index.html +++ b/articles/index.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/authors.html b/authors.html index 0b77172..aebdcab 100644 --- a/authors.html +++ b/authors.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 @@ -90,13 +90,13 @@ Citation Burn E, Catala M, Mercade-Besora N, Alcalde-Herraiz M, Du M, Guo Y, Chen X, Lopez-Guell K, Rowlands E (2024). CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model. -R package version 0.3.1, https://ohdsi.github.io/CohortConstructor/. +R package version 0.3.1.900, https://ohdsi.github.io/CohortConstructor/. @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-Guell and Elin Rowlands}, year = {2024}, - note = {R package version 0.3.1}, + note = {R package version 0.3.1.900}, url = {https://ohdsi.github.io/CohortConstructor/}, } diff --git a/index.html b/index.html index 9385ede..3373601 100644 --- a/index.html +++ b/index.html @@ -29,7 +29,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/pkgdown.yml b/pkgdown.yml index dad9b05..46fc45a 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -14,7 +14,7 @@ articles: a09_combine_cohorts: a09_combine_cohorts.html a10_match_cohorts: a10_match_cohorts.html a11_benchmark: a11_benchmark.html -last_built: 2024-10-11T14:52Z +last_built: 2024-10-11T15:31Z urls: reference: https://ohdsi.github.io/CohortConstructor/reference article: https://ohdsi.github.io/CohortConstructor/articles diff --git a/reference/CohortConstructor-package.html b/reference/CohortConstructor-package.html index 0fc0c10..096463e 100644 --- a/reference/CohortConstructor-package.html +++ b/reference/CohortConstructor-package.html @@ -9,7 +9,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/benchmarkData.html b/reference/benchmarkData.html index 097fc19..06e197d 100644 --- a/reference/benchmarkData.html +++ b/reference/benchmarkData.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/cdmDoc.html b/reference/cdmDoc.html index 2134bf9..771e974 100644 --- a/reference/cdmDoc.html +++ b/reference/cdmDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/cohortDoc.html b/reference/cohortDoc.html index c8ab3cf..8364922 100644 --- a/reference/cohortDoc.html +++ b/reference/cohortDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/cohortIdModifyDoc.html b/reference/cohortIdModifyDoc.html index 1ac353a..951e840 100644 --- a/reference/cohortIdModifyDoc.html +++ b/reference/cohortIdModifyDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/cohortIdSubsetDoc.html b/reference/cohortIdSubsetDoc.html index 9327a0f..b7319b7 100644 --- a/reference/cohortIdSubsetDoc.html +++ b/reference/cohortIdSubsetDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/collapseCohorts.html b/reference/collapseCohorts.html index 1e48519..4a8210e 100644 --- a/reference/collapseCohorts.html +++ b/reference/collapseCohorts.html @@ -9,7 +9,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/columnDateDoc.html b/reference/columnDateDoc.html index 331c1e3..31842d5 100644 --- a/reference/columnDateDoc.html +++ b/reference/columnDateDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/conceptCohort.html b/reference/conceptCohort.html index 7cc2b20..54155db 100644 --- a/reference/conceptCohort.html +++ b/reference/conceptCohort.html @@ -53,7 +53,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/conceptSetDoc.html b/reference/conceptSetDoc.html index 3f205c7..934e317 100644 --- a/reference/conceptSetDoc.html +++ b/reference/conceptSetDoc.html @@ -7,7 +7,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/demographicsCohort.html b/reference/demographicsCohort.html index 4a27b6c..c1df445 100644 --- a/reference/demographicsCohort.html +++ b/reference/demographicsCohort.html @@ -13,7 +13,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 diff --git a/reference/entryAtFirstDate.html b/reference/entryAtFirstDate.html index 75ce1d9..4ca43a6 100644 --- a/reference/entryAtFirstDate.html +++ b/reference/entryAtFirstDate.html @@ -9,7 +9,7 @@ CohortConstructor - 0.3.1 + 0.3.1.900 @@ -181,10 +181,10 @@ Examples#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-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… +#> 1 1 2 2001-01-01 2001-01-12 date_1 #> 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 +#> 3 1 1 2001-08-01 2001-09-01 date_1; dat… +#> 4 1 4 2002-12-09 2002-12-09 date_1; dat… # }
Burn E, Catala M, Mercade-Besora N, Alcalde-Herraiz M, Du M, Guo Y, Chen X, Lopez-Guell K, Rowlands E (2024). CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model. -R package version 0.3.1, https://ohdsi.github.io/CohortConstructor/. +R package version 0.3.1.900, https://ohdsi.github.io/CohortConstructor/.
@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-Guell and Elin Rowlands}, year = {2024}, - note = {R package version 0.3.1}, + note = {R package version 0.3.1.900}, url = {https://ohdsi.github.io/CohortConstructor/}, }
padCohortEnd()
padCohortStart()
padCohortEnd.Rd
padCohortStart() Adds (or subtracts) a certain number of days to the cohort +end date. Note:
If the days added means that cohort end would be after observation +period end date, then observation period end date will be used for cohort +exit.
If the days added means that cohort exit would be after the next cohort +start then these overlapping cohort entries will be collapsed.
If days subtracted means that cohort end would be before cohort start then +the cohort entry will be dropped.
padCohortEnd(cohort, days, cohortId = NULL, name = tableName(cohort))
A cohort table in a cdm reference.
Number of day to add to the cohort end date.
Vector identifying which cohorts to modify +(cohort_definition_id or cohort_name). If NULL, all cohorts will be +used; otherwise, only the specified cohorts will be modified, and the +rest will remain unchanged.
Name of the new cohort table created in the cdm object.
Cohort table
# \donttest{ +library(CohortConstructor) +cdm <- mockCohortConstructor() +# add 10 days to each cohort exit +cdm$cohort1 |> + padCohortEnd(days = 10) +#> # Source: table<main.cohort1> [6 x 4] +#> # Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1015-azure:R 4.4.1/:memory:] +#> cohort_definition_id subject_id cohort_start_date cohort_end_date +#> <int> <int> <date> <date> +#> 1 1 2 1964-09-18 1965-09-09 +#> 2 1 6 2003-10-31 2004-04-20 +#> 3 1 9 2012-01-18 2012-03-18 +#> 4 1 4 1998-06-22 2001-02-22 +#> 5 1 5 2007-10-19 2011-09-22 +#> 6 1 3 1976-11-28 1987-03-08 +# } +