From 408acb3354470e099276577a2ae7ebb4015765a7 Mon Sep 17 00:00:00 2001 From: Will Beasley Date: Sun, 19 Apr 2020 13:28:53 -0500 Subject: [PATCH] update pkgdown; include redcap_survey_link_export_oneshot --- _pkgdown.yml | 1 + docs/404.html | 61 +-- docs/CONDUCT.html | 61 +-- docs/apple-touch-icon-120x120.png | Bin 0 -> 11270 bytes docs/apple-touch-icon-152x152.png | Bin 0 -> 15963 bytes docs/apple-touch-icon-180x180.png | Bin 0 -> 20313 bytes docs/apple-touch-icon-60x60.png | Bin 0 -> 4808 bytes docs/apple-touch-icon-76x76.png | Bin 0 -> 6537 bytes docs/apple-touch-icon.png | Bin 0 -> 20313 bytes docs/articles/BasicREDCapROperations.html | 316 ++++++------- docs/articles/SecurityDatabase.html | 292 ++++-------- docs/articles/TroubleshootingApiCalls.html | 447 ++++++++---------- .../articles/advanced-redcapr-operations.html | 365 +++++++------- docs/articles/index.html | 71 ++- docs/authors.html | 63 +-- docs/bootstrap-toc.css | 60 +++ docs/bootstrap-toc.js | 159 +++++++ docs/docsearch.json | 2 +- docs/favicon-16x16.png | Bin 0 -> 1570 bytes docs/favicon-32x32.png | Bin 0 -> 2302 bytes docs/favicon.ico | Bin 0 -> 15086 bytes docs/index.html | 98 ++-- docs/news/index.html | 163 +++---- docs/pkgdown.css | 121 ++++- docs/pkgdown.js | 5 - docs/pkgdown.yml | 3 +- docs/reference/REDCapR-package.html | 66 +-- docs/reference/collapse_vector.html | 71 +-- docs/reference/constant.html | 86 ++-- docs/reference/create_batch_glossary.html | 79 ++-- docs/reference/index.html | 101 ++-- docs/reference/kernel_api.html | 72 +-- docs/reference/metadata_utilities.html | 79 ++-- docs/reference/redcap_column_sanitize.html | 72 +-- .../redcap_download_file_oneshot.html | 92 ++-- .../reference/redcap_download_instrument.html | 77 ++- docs/reference/redcap_metadata_read.html | 73 +-- docs/reference/redcap_metadata_write.html | 72 +-- .../redcap_next_free_record_name.html | 71 +-- docs/reference/redcap_project.html | 73 ++- docs/reference/redcap_read.html | 75 +-- docs/reference/redcap_read_oneshot.html | 79 ++-- docs/reference/redcap_read_oneshot_eav.html | 75 +-- .../redcap_survey_link_export_oneshot.html | 73 +-- .../reference/redcap_upload_file_oneshot.html | 75 +-- docs/reference/redcap_users_export.html | 88 ++-- docs/reference/redcap_variables.html | 73 +-- docs/reference/redcap_version.html | 70 +-- docs/reference/redcap_write.html | 79 ++-- docs/reference/redcap_write_oneshot.html | 79 ++-- docs/reference/replace_nas_with_explicit.html | 70 +-- docs/reference/retrieve_credential.html | 75 +-- docs/reference/sanitize_token.html | 72 +-- docs/reference/validate.html | 73 +-- 54 files changed, 1929 insertions(+), 2499 deletions(-) create mode 100644 docs/apple-touch-icon-120x120.png create mode 100644 docs/apple-touch-icon-152x152.png create mode 100644 docs/apple-touch-icon-180x180.png create mode 100644 docs/apple-touch-icon-60x60.png create mode 100644 docs/apple-touch-icon-76x76.png create mode 100644 docs/apple-touch-icon.png create mode 100644 docs/bootstrap-toc.css create mode 100644 docs/bootstrap-toc.js create mode 100644 docs/favicon-16x16.png create mode 100644 docs/favicon-32x32.png create mode 100644 docs/favicon.ico diff --git a/_pkgdown.yml b/_pkgdown.yml index 541ec157..0c387c97 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -50,6 +50,7 @@ reference: - redcap_next_free_record_name - redcap_metadata_read - redcap_metadata_write + - redcap_survey_link_export_oneshot - redcap_users_export - redcap_variables - redcap_version diff --git a/docs/404.html b/docs/404.html index 28be2bff..49fa6436 100644 --- a/docs/404.html +++ b/docs/404.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,15 +46,14 @@ - + - - + @@ -68,7 +71,7 @@ - +
@@ -97,26 +100,8 @@
  • Reference
    • -
  • - - +
  • + Articles
  • Changelog @@ -124,7 +109,7 @@
    • - + @@ -155,6 +140,12 @@

      Page not found (404)

    • + + @@ -165,7 +156,7 @@

    Page not found (404)

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html index 31b27e3c..8d643a98 100644 --- a/docs/CONDUCT.html +++ b/docs/CONDUCT.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,15 +46,14 @@ - + - - + @@ -68,7 +71,7 @@ - +
    @@ -97,26 +100,8 @@
  • Reference
    • -
  • - - +
  • + Articles
  • Changelog @@ -124,7 +109,7 @@
    • - + @@ -163,6 +148,12 @@

      Contributor Code of Conduct

    • + + @@ -173,7 +164,7 @@

    Contributor Code of Conduct

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

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z-{hu-hL}N7zzSHanu$mkk*-2VpsT7~fv%)!rkxJ&|Jl!a&gZl5eJ?B42Cd)pe-r+1 zlIWqs0Xv}pb`Y0(?m*o3-`AtRcJ$X3)h^CmG&HySizNR)-`cW-gJ9TN0000bbVXQn zWMOn=I%9HWVRU5xGB7bYEigGPGBH#zGCDCeIx#XUFfuwYFvi09cK`qYC3HntbYx+4 zWjbwdWNBu305UK!IV~_bEiy4wFfuwZH99deD=;!TFfg~DLCXLD09SfcSaechcOY6Cgx@ wG{a;ABePT>%h=S&#LUDT#0SfONT5nC0O}VJbn-$ql>h($07*qoM6N<$f=hH1Z2$lO literal 0 HcmV?d00001 diff --git a/docs/articles/BasicREDCapROperations.html b/docs/articles/BasicREDCapROperations.html index 7ea98e5b..9735b0ac 100644 --- a/docs/articles/BasicREDCapROperations.html +++ b/docs/articles/BasicREDCapROperations.html @@ -12,22 +12,22 @@ - - - - - + + + + + + - - - + + - +

    -

    Basic REDCapR Operations

    +

    Basic REDCapR Operations

    -

    2020-02-18

    +

    2020-04-19

    Source: vignettes/BasicREDCapROperations.Rmd @@ -127,21 +109,21 @@

    Set project-wide values

    There is some information that is specific to the REDCap project, as opposed to an individual operation. This includes the (1) uri of the server, and the (2) token for the user’s project.

    -
    library(REDCapR) #Load the package into the current R session.
-uri <- "https://bbmc.ouhsc.edu/redcap/api/"
-token <- "9A81268476645C4E5F03428B8AC3AA7B" #`UnitTestPhiFree` user and simple project (pid 153)
    +
    library(REDCapR) # Load the package into the current R session.
+uri   <- "https://bbmc.ouhsc.edu/redcap/api/"
+token <- "9A81268476645C4E5F03428B8AC3AA7B" # `UnitTestPhiFree` user and simple project (pid 153)

    Read all records and fields

    If no information is passed about the desired records or fields, then the entire data set is returned. Only two parameters are required, redcap_uri and token. Unless the verbose parameter is set to FALSE, a message will be printed on the R console with the number of records and fields returned.

    -
    #Return all records and all variables.
-ds_all_rows_all_fields <- redcap_read(redcap_uri=uri, token=token)$data
    -
    The data dictionary describing 16 fields was read from REDCap in 0.5 seconds.  The http status code was 200.
    -
    5 records and 1 columns were read from REDCap in 0.4 seconds.  The http status code was 200.
    -
    Starting to read 5 records  at 2020-02-18 10:35:33.
    +
    # Return all records and all variables.
+ds_all_rows_all_fields <- redcap_read(redcap_uri = uri, token = token)$data
    +
    The data dictionary describing 16 fields was read from REDCap in 0.4 seconds.  The http status code was 200.
    +
    5 records and 1 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    +
    Starting to read 5 records  at 2020-04-19 13:31:36.
    Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).
    -
    5 records and 24 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    +
    5 records and 24 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    Parsed with column specification:
 cols(
   .default = col_double(),
@@ -155,7 +137,7 @@ 
    
   mugshot = col_character()
 )
    See spec(...) for full column specifications.
    -
    ds_all_rows_all_fields #Inspect the returned dataset
    +
    ds_all_rows_all_fields # Inspect the returned dataset
      record_id name_first name_last                                 address
 1         1     Nutmeg  Nutmouse 14 Rose Cottage St.\nKenning UK, 323232
 2         2     Tumtum  Nutmouse 14 Rose Cottage Blvd.\nKenning UK 34243
@@ -198,18 +180,18 @@ 
    
 Read a subset of the records
    
 
    If only a subset of the records is desired, the two approaches are shown below. The first is to pass an array (where each element is an ID) to the records parameter. The second is to pass a single string (where the elements are separated by commas) to the records_collapsed parameter.
    
 
    The first format is more natural for more R users. The second format is what is expected by the REDCap API. If a value for records is specified, but records_collapsed is not specified, then redcap_read_oneshot automatically converts the array into the format needed by the API.
    
-
    #Return only records with IDs of 1 and 3
-desired_records_v1 <- c(1, 3)
-ds_some_rows_v1 <- redcap_read(
-   redcap_uri = uri,
-   token      = token,
-   records    = desired_records_v1
-)$data
    
-
    The data dictionary describing 16 fields was read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    2 records and 1 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    Starting to read 2 records  at 2020-02-18 10:35:35.
    
+
    # Return only records with IDs of 1 and 3
+desired_records_v1 <- c(1, 3)
+ds_some_rows_v1 <- redcap_read(
+  redcap_uri = uri,
+  token      = token,
+  records    = desired_records_v1
+)$data
    
+
    The data dictionary describing 16 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    2 records and 1 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    Starting to read 2 records  at 2020-04-19 13:31:37.
    
 
    Reading batch 1 of 1, with subjects 1 through 3 (ie, 2 unique subject records).
    
-
    2 records and 24 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
+
    2 records and 24 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
 
    Parsed with column specification:
 cols(
   .default = col_double(),
@@ -223,18 +205,18 @@ 
    
   mugshot = col_character()
 )
    
 
    See spec(...) for full column specifications.
    
-
    #Return only records with IDs of 1 and 3 (alternate way)
-desired_records_v2 <- "1, 3"
-ds_some_rows_v2 <- redcap_read(
-   redcap_uri        = uri,
-   token             = token,
-   records_collapsed = desired_records_v2
-)$data
    
-
    The data dictionary describing 16 fields was read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    2 records and 1 columns were read from REDCap in 0.7 seconds.  The http status code was 200.
    
-
    Starting to read 2 records  at 2020-02-18 10:35:37.
    
+
    # Return only records with IDs of 1 and 3 (alternate way)
+desired_records_v2 <- "1, 3"
+ds_some_rows_v2 <- redcap_read(
+  redcap_uri        = uri,
+  token             = token,
+  records_collapsed = desired_records_v2
+)$data
    
+
    The data dictionary describing 16 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    2 records and 1 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
+
    Starting to read 2 records  at 2020-04-19 13:31:38.
    
 
    Reading batch 1 of 1, with subjects 1 through 3 (ie, 2 unique subject records).
    
-
    2 records and 24 columns were read from REDCap in 0.4 seconds.  The http status code was 200.
    
+
    2 records and 24 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
 
    Parsed with column specification:
 cols(
   .default = col_double(),
@@ -248,7 +230,7 @@ 
    
   mugshot = col_character()
 )
    
 
    See spec(...) for full column specifications.
    
-
    ds_some_rows_v2 #Inspect the returned dataset
    
+
    ds_some_rows_v2 # Inspect the returned dataset
    
 
      record_id name_first name_last                                 address
 1         1     Nutmeg  Nutmouse 14 Rose Cottage St.\nKenning UK, 323232
 2         3     Marcus      Wood          243 Hill St.\nGuthrie OK 73402
@@ -269,43 +251,43 @@ 
    
 
    
 Read a subset of the fields
    
 
    If only a subset of the fields is desired, then two approaches exist. The first is to pass an array (where each element is an field) to the fields parameter. The second is to pass a single string (where the elements are separated by commas) to the fields_collapsed parameter. Like with records and records_collapsed described above, this function converts the more natural format (i.e., fields) to the format required by the API (ie, fields_collapsed) if fields is specified and fields_collapsed is not.
    
-
    #Return only the fields record_id, name_first, and age
-desired_fields_v1 <- c("record_id", "name_first", "age")
-ds_some_fields_v1 <- redcap_read(
-   redcap_uri = uri,
-   token      = token,
-   fields     = desired_fields_v1
-)$data
    
-
    The data dictionary describing 16 fields was read from REDCap in 0.3 seconds.  The http status code was 200.
    
+
    #Return only the fields record_id, name_first, and age
+desired_fields_v1 <- c("record_id", "name_first", "age")
+ds_some_fields_v1 <- redcap_read(
+  redcap_uri = uri,
+  token      = token,
+  fields     = desired_fields_v1
+)$data
    
+
    The data dictionary describing 16 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
    
 
    5 records and 1 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    Starting to read 5 records  at 2020-02-18 10:35:38.
    
+
    Starting to read 5 records  at 2020-04-19 13:31:40.
    
 
    Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).
    
-
    5 records and 3 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
+
    5 records and 3 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
 
    Parsed with column specification:
 cols(
   record_id = col_double(),
   name_first = col_character(),
   age = col_double()
 )
    
-
    #Return only the fields record_id, name_first, and age (alternate way)
-desired_fields_v2 <- "record_id, name_first, age"
-ds_some_fields_v2 <- redcap_read(
-   redcap_uri       = uri,
-   token            = token,
-   fields_collapsed = desired_fields_v2
-)$data
    
-
    The data dictionary describing 16 fields was read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    5 records and 1 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    Starting to read 5 records  at 2020-02-18 10:35:40.
    
+
    #Return only the fields record_id, name_first, and age (alternate way)
+desired_fields_v2 <- "record_id, name_first, age"
+ds_some_fields_v2 <- redcap_read(
+  redcap_uri       = uri,
+  token            = token,
+  fields_collapsed = desired_fields_v2
+)$data
    
+
    The data dictionary describing 16 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    5 records and 1 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    Starting to read 5 records  at 2020-04-19 13:31:41.
    
 
    Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).
    
-
    5 records and 3 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
+
    5 records and 3 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
 
    Parsed with column specification:
 cols(
   record_id = col_double(),
   name_first = col_character(),
   age = col_double()
 )
    
-
    ds_some_fields_v2 #Inspect the returned dataset
    
+
    ds_some_fields_v2 #Inspect the returned dataset
    
 
      record_id name_first age
 1         1     Nutmeg  11
 2         2     Tumtum  11
@@ -317,51 +299,51 @@ 
    
 
    
 Read a subset of records, conditioned on the values in some variables
    
 
    The two techniques above can be combined when your datasets are large and you don’t want to pull records with certain values. Suppose you want to select subjects from the previous dataset if the were born before 1960 and their weight was over 70kg. Two calls to the server are required. The first call to REDCap pulls all the records, but for only three columns: record_id, dob, and weight. From this subset, identify the records that you want to pull all the data for; in this case, the desired record_id values are 3 & 5. The second call to REDCap pulls all the columns, but only for the identified records.
    
-
    ######
-## Step 1: First call to REDCap
-desired_fields_v3 <- c("record_id", "dob", "weight")
-ds_some_fields_v3 <- redcap_read(
-   redcap_uri = uri,
-   token      = token,
-   fields     = desired_fields_v3
-)$data
    
-
    The data dictionary describing 16 fields was read from REDCap in 0.3 seconds.  The http status code was 200.
    
+
    ######
+## Step 1: First call to REDCap
+desired_fields_v3 <- c("record_id", "dob", "weight")
+ds_some_fields_v3 <- redcap_read(
+  redcap_uri = uri,
+  token      = token,
+  fields     = desired_fields_v3
+)$data
    
+
    The data dictionary describing 16 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
    
 
    5 records and 1 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
-
    Starting to read 5 records  at 2020-02-18 10:35:41.
    
+
    Starting to read 5 records  at 2020-04-19 13:31:42.
    
 
    Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).
    
-
    5 records and 3 columns were read from REDCap in 0.4 seconds.  The http status code was 200.
    
+
    5 records and 3 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
 
    Parsed with column specification:
 cols(
   record_id = col_double(),
   dob = col_date(format = ""),
   weight = col_double()
 )
    
-
    ds_some_fields_v3 #Examine the these three variables.
    
+
    ds_some_fields_v3 #Examine the these three variables.
    
 
      record_id        dob weight
 1         1 2003-08-30      1
 2         2 2003-03-10      1
 3         3 1934-04-09     80
 4         4 1952-11-02     54
 5         5 1955-04-15    104
    
-
    ######
-## Step 2: identify desired records, based on age & weight
-before_1960 <- (ds_some_fields_v3$dob <= as.Date("1960-01-01"))
-heavier_than_70_kg <- (ds_some_fields_v3$weight > 70)
-desired_records_v3 <- ds_some_fields_v3[before_1960 & heavier_than_70_kg, ]$record_id
-
-desired_records_v3 #Peek at IDs of the identified records
    
+
    ######
+## Step 2: identify desired records, based on age & weight
+before_1960 <- (ds_some_fields_v3$dob <= as.Date("1960-01-01"))
+heavier_than_70_kg <- (ds_some_fields_v3$weight > 70)
+desired_records_v3 <- ds_some_fields_v3[before_1960 & heavier_than_70_kg, ]$record_id
+
+desired_records_v3 #Peek at IDs of the identified records
    
 
    [1] 3 5
    
-
    ######
-## Step 3: second call to REDCap
-#Return only records that met the age & weight criteria.
-ds_some_rows_v3 <- redcap_read(
-   redcap_uri = uri,
-   token      = token,
-   records    = desired_records_v3
-)$data
    
-
    The data dictionary describing 16 fields was read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    2 records and 1 columns were read from REDCap in 0.4 seconds.  The http status code was 200.
    
-
    Starting to read 2 records  at 2020-02-18 10:35:43.
    
+
    ######
+## Step 3: second call to REDCap
+#Return only records that met the age & weight criteria.
+ds_some_rows_v3 <- redcap_read(
+  redcap_uri = uri,
+  token      = token,
+  records    = desired_records_v3
+)$data
    
+
    The data dictionary describing 16 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    2 records and 1 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    Starting to read 2 records  at 2020-04-19 13:31:44.
    
 
    Reading batch 1 of 1, with subjects 3 through 5 (ie, 2 unique subject records).
    
 
    2 records and 24 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
 
    Parsed with column specification:
@@ -377,7 +359,7 @@ 
    
   mugshot = col_character()
 )
    
 
    See spec(...) for full column specifications.
    
-
    ds_some_rows_v3 #Examine the results.
    
+
    ds_some_rows_v3 #Examine the results.
    
 
      record_id name_first name_last                            address
 1         3     Marcus      Wood     243 Hill St.\nGuthrie OK 73402
 2         5   John Lee    Walker Hotel Suite\nNew Orleans LA, 70115
@@ -410,24 +392,24 @@ 
    
 
  • The fields_collapsed fields passed to the API. This shows which field subsets, if any, were requested.
    • 
 
  • The elapsed_seconds measures the duration of the call.
    • 
 
-
    #Return only the fields record_id, name_first, and age
-all_information <- redcap_read(
-   redcap_uri = uri,
-   token      = token,
-   fields     = desired_fields_v1
-)
    
-
    The data dictionary describing 16 fields was read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    5 records and 1 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
-
    Starting to read 5 records  at 2020-02-18 10:35:44.
    
+
    #Return only the fields record_id, name_first, and age
+all_information <- redcap_read(
+  redcap_uri = uri,
+  token      = token,
+  fields     = desired_fields_v1
+)
    
+
    The data dictionary describing 16 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    5 records and 1 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
+
    Starting to read 5 records  at 2020-04-19 13:31:45.
    
 
    Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).
    
-
    5 records and 3 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    
+
    5 records and 3 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    
 
    Parsed with column specification:
 cols(
   record_id = col_double(),
   name_first = col_character(),
   age = col_double()
 )
    
-
    all_information #Inspect the additional information
    
+
    all_information #Inspect the additional information
    
 
    $data
   record_id name_first age
 1         1     Nutmeg  11
@@ -443,7 +425,7 @@ 
    
 [1] "200"
 
 $outcome_messages
-[1] "5 records and 3 columns were read from REDCap in 0.3 seconds.  The http status code was 200."
+[1] "5 records and 3 columns were read from REDCap in 0.2 seconds.  The http status code was 200."
 
 $records_collapsed
 [1] ""
@@ -461,7 +443,7 @@ 
    
 [1] ""
 
 $elapsed_seconds
-[1] 1.400878
    
+[1] 1.284016
    @@ -471,7 +453,7 @@

    Environment 

    ─ Session info ───────────────────────────────────────────────────────────────
  setting  value                       
- version  R version 3.6.2 (2019-12-12)
+ version  R version 3.6.3 (2020-02-29)
  os       Ubuntu 19.10                
  system   x86_64, linux-gnu           
  ui       X11                         
@@ -479,102 +461,76 @@ 
    
  collate  en_US.UTF-8                 
  ctype    en_US.UTF-8                 
  tz       America/Chicago             
- date     2020-02-18                  
+ date     2020-04-19                  
 
 ─ Packages ───────────────────────────────────────────────────────────────────
  package     * version     date       lib source        
  assertthat    0.2.1       2019-03-21 [2] CRAN (R 3.6.1)
- backports     1.1.5       2019-10-02 [2] CRAN (R 3.6.1)
- callr         3.4.2       2020-02-12 [2] CRAN (R 3.6.2)
+ backports     1.1.6       2020-04-05 [2] CRAN (R 3.6.3)
  checkmate     2.0.0       2019-12-03 [2] local         
- cli           2.0.1       2020-01-08 [2] CRAN (R 3.6.1)
+ cli           2.0.2       2020-02-28 [2] CRAN (R 3.6.2)
  colorspace    1.4-1       2019-03-18 [2] CRAN (R 3.6.1)
  crayon        1.3.4       2017-09-16 [2] CRAN (R 3.6.1)
  curl          4.3         2019-12-02 [2] CRAN (R 3.6.1)
  desc          1.2.0       2018-05-01 [2] CRAN (R 3.6.1)
- devtools      2.2.1       2019-09-24 [2] CRAN (R 3.6.1)
- digest        0.6.24      2020-02-12 [2] CRAN (R 3.6.2)
- dplyr         0.8.4       2020-01-31 [2] CRAN (R 3.6.2)
+ digest        0.6.25      2020-02-23 [2] CRAN (R 3.6.2)
+ dplyr         0.8.5       2020-03-07 [2] CRAN (R 3.6.3)
  ellipsis      0.3.0       2019-09-20 [2] CRAN (R 3.6.1)
  evaluate      0.14        2019-05-28 [2] CRAN (R 3.6.1)
  fansi         0.4.1       2020-01-08 [2] CRAN (R 3.6.1)
- fs            1.3.1       2019-05-06 [2] CRAN (R 3.6.1)
- glue          1.3.1       2019-03-12 [2] CRAN (R 3.6.1)
+ fs            1.4.1       2020-04-04 [2] CRAN (R 3.6.3)
+ glue          1.4.0       2020-04-03 [2] CRAN (R 3.6.3)
  hms           0.5.3       2020-01-08 [2] CRAN (R 3.6.1)
  htmltools     0.4.0       2019-10-04 [2] CRAN (R 3.6.1)
  httr          1.4.1       2019-08-05 [2] CRAN (R 3.6.1)
  kableExtra    1.1.0       2019-03-16 [2] CRAN (R 3.6.1)
  knitr       * 1.28        2020-02-06 [2] CRAN (R 3.6.2)
- lifecycle     0.1.0       2019-08-01 [2] CRAN (R 3.6.1)
+ lifecycle     0.2.0       2020-03-06 [2] CRAN (R 3.6.3)
  magrittr    * 1.5         2014-11-22 [2] CRAN (R 3.6.1)
  MASS          7.3-51.5    2019-12-20 [5] CRAN (R 3.6.2)
  memoise       1.1.0       2017-04-21 [2] CRAN (R 3.6.1)
  munsell       0.5.0       2018-06-12 [2] CRAN (R 3.6.1)
  pillar        1.4.3       2019-12-20 [2] CRAN (R 3.6.1)
- pkgbuild      1.0.6       2019-10-09 [2] CRAN (R 3.6.1)
  pkgconfig     2.0.3       2019-09-22 [2] CRAN (R 3.6.1)
- pkgdown       1.4.1       2019-09-15 [2] CRAN (R 3.6.1)
- pkgload       1.0.2       2018-10-29 [2] CRAN (R 3.6.1)
- prettyunits   1.1.1       2020-01-24 [2] CRAN (R 3.6.2)
- processx      3.4.2       2020-02-09 [2] CRAN (R 3.6.2)
- ps            1.3.2       2020-02-13 [2] CRAN (R 3.6.2)
+ pkgdown       1.5.0       2020-03-25 [2] CRAN (R 3.6.3)
  purrr         0.3.3       2019-10-18 [2] CRAN (R 3.6.1)
  R6            2.4.1       2019-11-12 [2] CRAN (R 3.6.1)
- Rcpp          1.0.3       2019-11-08 [2] CRAN (R 3.6.1)
+ Rcpp          1.0.4       2020-03-17 [2] CRAN (R 3.6.3)
  readr         1.3.1       2018-12-21 [2] CRAN (R 3.6.1)
- REDCapR     * 0.10.2.9005 2020-02-18 [1] local         
- remotes       2.1.1       2020-02-15 [2] CRAN (R 3.6.2)
- rlang         0.4.4       2020-01-28 [2] CRAN (R 3.6.2)
+ REDCapR     * 0.10.2.9006 2020-04-19 [1] local         
+ rlang         0.4.5       2020-03-01 [2] CRAN (R 3.6.2)
  rmarkdown     2.1         2020-01-20 [2] CRAN (R 3.6.2)
  rprojroot     1.3-2       2018-01-03 [2] CRAN (R 3.6.1)
  rstudioapi    0.11        2020-02-07 [2] CRAN (R 3.6.2)
  rvest         0.3.5       2019-11-08 [2] CRAN (R 3.6.1)
  scales        1.1.0       2019-11-18 [2] CRAN (R 3.6.1)
  sessioninfo   1.1.1       2018-11-05 [2] CRAN (R 3.6.1)
- stringi       1.4.5       2020-01-11 [2] CRAN (R 3.6.1)
+ stringi       1.4.6       2020-02-17 [2] CRAN (R 3.6.2)
  stringr       1.4.0       2019-02-10 [2] CRAN (R 3.6.1)
- testthat      2.3.1       2019-12-01 [2] CRAN (R 3.6.1)
- tibble        2.1.3       2019-06-06 [2] CRAN (R 3.6.1)
+ tibble        3.0.0       2020-03-30 [2] CRAN (R 3.6.3)
  tidyselect    1.0.0       2020-01-27 [2] CRAN (R 3.6.2)
- usethis       1.5.1       2019-07-04 [2] CRAN (R 3.6.1)
- vctrs         0.2.2       2020-01-24 [2] CRAN (R 3.6.2)
+ vctrs         0.2.4       2020-03-10 [2] CRAN (R 3.6.3)
  viridisLite   0.3.0       2018-02-01 [2] CRAN (R 3.6.1)
  webshot       0.5.2       2019-11-22 [2] CRAN (R 3.6.1)
  withr         2.1.2       2018-03-15 [2] CRAN (R 3.6.1)
  xfun          0.12        2020-01-13 [2] CRAN (R 3.6.1)
- xml2          1.2.2       2019-08-09 [2] CRAN (R 3.6.1)
+ xml2          1.3.0       2020-04-01 [2] CRAN (R 3.6.3)
  yaml          2.2.1       2020-02-01 [2] CRAN (R 3.6.2)
 
-[1] /tmp/RtmpQwpj1Q/temp_libpath20fe13c92d77
+[1] /tmp/Rtmp5avAp4/temp_libpath4e6a183ad817
 [2] /home/wibeasley/R/x86_64-pc-linux-gnu-library/3.6
 [3] /usr/local/lib/R/site-library
 [4] /usr/lib/R/site-library
 [5] /usr/lib/R/library
    -

    Report rendered by wibeasley at 2020-02-18, 10:35 -0600 in 15 seconds.

    +

    Report rendered by wibeasley at 2020-04-19, 13:31 -0500 in 15 seconds.

    - @@ -585,7 +541,7 @@

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/articles/SecurityDatabase.html b/docs/articles/SecurityDatabase.html index 360ce19f..27c5a7de 100644 --- a/docs/articles/SecurityDatabase.html +++ b/docs/articles/SecurityDatabase.html @@ -12,22 +12,22 @@ - - - - - + + + + + + - - - + + - +
    -

    Security Database

    +

    Security Database

    -

    2020-02-18

    +

    2020-04-19

    Source: vignettes/SecurityDatabase.Rmd @@ -281,161 +263,78 @@

  • Combine & groom the credentials.
  • Upload to SQL Server (called auxiliary_security here).
    • -
    rm(list=ls(all=TRUE)) #Clear the memory for any variables set from any previous runs.
-
-# ---- load-sources ------------------------------------------------------------
-
-# ---- load-packages -----------------------------------------------------------
-if( !require(OuhscMunge) )
-  stop('The `OuhscMunge` package needs to be installed with `devtools::install_github("OuhscBbmc/OuhscMunge")`.')
-
-testit::assert(
-  "The `OuhscMunge` package should meet a minimal version.",
-  compareVersion( as.character(packageVersion("OuhscMunge")), "0.1.9.9009") >= 0L
-)
-
-library(magrittr)
-requireNamespace("DBI")
-requireNamespace("odbc")
-requireNamespace("dplyr")
-requireNamespace("readr")
-requireNamespace("tibble")
-requireNamespace("testit")
-requireNamespace("checkmate")
-requireNamespace("OuhscMunge")  # devtools::install_github("OuhscBbmc/OuhscMunge")
-
-
-# ---- declare-globals ---------------------------------------------------------
-# This file assume your campus has two REDCap instances.
-# Modify each (a) database name, (b) REDCap URL, and (c) DSN name.
-
-name_production <- "production"
-name_dev        <- "dev"
-
-uri_production  <- "https://redcap-production.ouhsc.edu/redcap/api/",
-uri_dev         <- "https://redcap-dev.ouhsc.edu/redcap/api/"
-
-dsn_production  <- "redcap-production"
-dsn_dev         <- "redcap-dev"
-dsn_source      <- "auxiliary_security" # The DSN of the token server.
-
-# The Activity Directory name that should precede each username.
-#   This should correspond with the result of SQL Server's `SYSTEM_USER` function
-#   (https://msdn.microsoft.com/en-us/library/ms179930.aspx)
-ldap_prefix <- "OUHSC\\"
-
-####
-# Nothing below this line should need to change, assuming:
-# 1. the vignette was followed exactly (https://ouhscbbmc.github.io/REDCapR/articles/SecurityDatabase.html),
-# 2. your campus has exactly two REDCap instances.
-
-# SQL sent to the MySQL database underneath each REDCap instance.
-sql <- "
-  SELECT username, project_id, api_token
-  FROM redcap_user_rights
-  WHERE api_token IS NOT NULL
-"
-
-# Update this ad-hoc CSV.  Each row should represent one REDCap instance.
-ds_url <- tibble::tribble(
-  ~instance         , ~redcap_uri,
-  name_production   , uri_production,
-  name_dev          , uri_dev
-)
-
-# Remove variables that aren't used below.
-rm(uri_production, uri_dev)
-
-
-# ---- load-data ---------------------------------------------------------------
-
-# Load the credentials from the first/production REDCap instance.
-cnn_production  <- DBI::dbConnect(odbc::odbc(), dsn=dsn_production)
-ds_production   <- DBI::dbGetQuery(cnn_production, sql)
-DBI::dbDisconnect(cnn_production); rm(cnn_production, dsn_production)
-
-# Load the credentials from the second/dev REDCap instance.
-cnn_dev         <- DBI::dbConnect(odbc::odbc(), dsn=dsn_dev)
-ds_dev          <- DBI::dbGetQuery(cnn_dev, sql)
-DBI::dbDisconnect(cnn_dev); rm(cnn_dev, dsn_dev)
-
-rm(sql)
-
-# Assert these are valid datasets and contain at least 5 rows.
-#   Adjust '5' to smaller value if necessary.  It's just to catch blatant retrieval problems.
-checkmate::assert_data_frame(ds_production, min.rows=5)
-checkmate::assert_data_frame(ds_dev       , min.rows=5)
-
-
-# ---- tweak-data --------------------------------------------------------------
-
-# Label each instance, so they're distinguishable later.
-ds_production$instance <- name_production
-ds_dev$instance        <- name_dev
-
-# Stack the token collection from each instance.  Then prefix the username and include the URL of each instance.
-ds <-
-  ds_production %>%
-  dplyr::union(ds_dev) %>%                                # Remove union if the dev instance isn't included.
-  tibble::as_tibble() %>%
-  dplyr::select(
-    username        = username,
-    project_id      = project_id,
-    instance        = instance,
-    token           = api_token
-  ) %>%
-  dplyr::mutate(
-    username        = paste0(ldap_prefix, username), # Qualify for the Active Directory.
-  ) %>%
-  dplyr::left_join( ds_url, by="instance") %>%            # Include the instance URL.
-  dplyr::arrange(instance, project_id, username) %>%
-  tibble::rowid_to_column("id")                           # For the sake of a clustered primary key.
-
-rm(ds_production, ds_dev, ds_url)
-rm(name_production, name_dev)
-rm(ldap_prefix)
-
-
-# ---- verify-values -----------------------------------------------------------
-
-# Assert that the dataset is well-behaved.
-# OuhscMunge::verify_value_headstart(ds)
-checkmate::assert_integer(  ds$id         , any.missing=FALSE, lower=1, upper=.Machine$integer.max, unique=TRUE)
-checkmate::assert_character(ds$username   , any.missing=FALSE, pattern="^.{1,255}$"                         )
-checkmate::assert_integer(  ds$project_id , any.missing=FALSE, lower=1, upper=.Machine$integer.max          )
-checkmate::assert_character(ds$token      , any.missing=FALSE, pattern="^[A-Z0-9]{32}$"           , unique=TRUE)
-checkmate::assert_character(ds$instance   , any.missing=FALSE, pattern="^.{1,255}$"                         )
-checkmate::assert_character(ds$redcap_uri , any.missing=FALSE, pattern="^.{1,255}$"                         )
-
-testit::assert(
-  "The `username` x `project_id` x `instance` must be unique.",
-  sum(duplicated(paste0(ds$username, "-", ds$project_id, "-", ds$instance))) == 0L
-)
-
-testit::assert("At least 10 tokens should be ready to write." , 10L <= nrow(ds))
-
-
-# ---- specify-columns-to-upload -----------------------------------------------
-
-# Dictate the exact columns and order that will be uploaded.
-columns_to_write <- c("id", "username", "project_id", "instance", "token", "redcap_uri")
-ds_slim          <- ds[, columns_to_write]
-rm(columns_to_write)
-
-
-# ---- upload-to-db ------------------------------------------------------------------
-
-OuhscMunge::upload_sqls_odbc(
-  d               = ds_slim,
-  schema_name     = "redcap_private",
-  table_name      = "tbl_credential",
-  dsn_name        = dsn_source,
-  create_table    = FALSE,
-  clear_table     = TRUE,
-  transaction     = TRUE,
-  verbose         = TRUE
-)
-# Uploading 252 tokens takes 0.004 minutes.
    +
    rm(list=ls(all=TRUE)) #Clear the memory for any variables set from any previous runs.
+
+# ---- load-sources ------------------------------------------------------------
+
+# ---- load-packages -----------------------------------------------------------
+if (!require(OuhscMunge))
+  stop('The `OuhscMunge` package needs to be installed with `remotes::install_github("OuhscBbmc/OuhscMunge")`.')
+
+testit::assert(
+  "The `OuhscMunge` package should meet a minimal version.",
+  compareVersion( as.character(packageVersion("OuhscMunge")), "0.1.9.9009") >= 0L
+)
+
+library(magrittr)
+requireNamespace("DBI")
+requireNamespace("odbc")
+requireNamespace("dplyr")
+requireNamespace("readr")
+requireNamespace("tibble")
+requireNamespace("testit")
+requireNamespace("checkmate")
+requireNamespace("OuhscMunge")  # remotes::install_github("OuhscBbmc/OuhscMunge")
+
+
+# ---- declare-globals ---------------------------------------------------------
+# This file assume your campus has two REDCap instances.
+# Modify each (a) database name, (b) REDCap URL, and (c) DSN name.
+
+name_production %
+  dplyr::union(ds_dev) %>%                                # Remove union if the dev instance isn't included.
+  tibble::as_tibble() %>%
+  dplyr::select(
+    username        = username,
+    project_id      = project_id,
+    instance        = instance,
+    token           = api_token
+  ) %>%
+  dplyr::mutate(
+    username        = paste0(ldap_prefix, username), # Qualify for the Active Directory.
+  ) %>%
+  dplyr::left_join( ds_url, by="instance") %>%            # Include the instance URL.
+  dplyr::arrange(instance, project_id, username) %>%
+  tibble::rowid_to_column("id")                           # For the sake of a clustered primary key.
+
+rm(ds_production, ds_dev, ds_url)
+rm(name_production, name_dev)
+rm(ldap_prefix)
+
+
+# ---- verify-values -----------------------------------------------------------
+
+# Assert that the dataset is well-behaved.
+# OuhscMunge::verify_value_headstart(ds)
+checkmate::assert_integer(  ds$id         , any.missing=FALSE, lower=1, upper=.Machine$integer.max, unique=TRUE)
+checkmate::assert_character(ds$username   , any.missing=FALSE, pattern="^.{1,255}$"                         )
+checkmate::assert_integer(  ds$project_id , any.missing=FALSE, lower=1, upper=.Machine$integer.max          )
+checkmate::assert_character(ds$token      , any.missing=FALSE, pattern="^[A-Z0-9]{32}$"           , unique=TRUE)
+checkmate::assert_character(ds$instance   , any.missing=FALSE, pattern="^.{1,255}$"                         )
+checkmate::assert_character(ds$redcap_uri , any.missing=FALSE, pattern="^.{1,255}$"                         )
+
+testit::assert(
+  "The `username` x `project_id` x `instance` must be unique.",
+  sum(duplicated(paste0(ds$username, "-", ds$project_id, "-", ds$instance))) == 0L
+)
+
+testit::assert("At least 10 tokens should be ready to write." , 10L <= nrow(ds))
+
+
+# ---- specify-columns-to-upload -----------------------------------------------
+
+# Dictate the exact columns and order that will be uploaded.
+columns_to_write

    @@ -444,22 +343,11 @@

    - @@ -470,7 +358,7 @@

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/articles/TroubleshootingApiCalls.html b/docs/articles/TroubleshootingApiCalls.html index b1ee5f83..c286a245 100644 --- a/docs/articles/TroubleshootingApiCalls.html +++ b/docs/articles/TroubleshootingApiCalls.html @@ -12,22 +12,22 @@ - - - - - + + + + + + - - - + + - +
    -

    Troubleshooting REDCap API Calls

    +

    Troubleshooting REDCap API Calls

    -

    2020-02-18

    +

    2020-04-19

    Source: vignettes/TroubleshootingApiCalls.Rmd @@ -219,90 +201,90 @@

    There are several ways to call REDCap’s API from R. The packages redcapAPI and REDCapR both rely on the httr package, which calls the curl package, which calls cURL.

    1. -

      Is httr installed on the user’s local machine? If so, running library(httr) should not produce any error messages if you’re starting with a fresh session of R:

      -
      library(httr)
      +

      Is httr installed on the user’s local machine? If so, running library(httr) should not produce any error messages if you’re starting with a fresh session of R:

      +
      library(httr)

    2. Do you have the most recent version of httr? There are several ways to do this, but the easiest is probably to run update.packages(ask = FALSE, repos = "https://cran.rstudio.com"). The optional argument ask prevents the user from needing to respond ‘Y’ to each outdated package.

    3. Can you query a test project using httr? Both the redcapAPI and REDCapR packages employ something similar to the following function in httr. If you’re curious, here is the relevant source code for redcapAPI and REDCapR.

      If this check fails, consider attempting again with the url and token used above in the Postman example.

      -
      redcap_uri <- "https://bbmc.ouhsc.edu/redcap/api/"
-token      <- "9A81268476645C4E5F03428B8AC3AA7B"
-
-post_body <- list(
-  token           = token,
-  content         = 'record',
-  format          = 'csv',
-  type            = 'flat'
-)
-
-raw_text <- httr::POST(
-  url             = redcap_uri,
-  body            = post_body,
-  httr::verbose() # Remove this line to suppress the console updates.
-)
-
-raw_text
      +
      redcap_uri <- "https://bbmc.ouhsc.edu/redcap/api/"
+token      <- "9A81268476645C4E5F03428B8AC3AA7B"
+
+post_body <- list(
+  token           = token,
+  content         = 'record',
+  format          = 'csv',
+  type            = 'flat'
+)
+
+raw_text <- httr::POST(
+  url             = redcap_uri,
+  body            = post_body,
+  httr::verbose() # Remove this line to suppress the console updates.
+)
+
+raw_text

      Alternatively, you can try using the RCurl package, which has been mostly replaced by httr in packages developed since 2014.

      -
      raw_text <- RCurl::postForm(
-  uri             = redcap_uri
-  , token         = token
-  , content       = 'record'
-  , format        = 'csv'
-  , type          = 'flat'
-)
      +
      raw_text <- RCurl::postForm(
+  uri             = redcap_uri
+  , token         = token
+  , content       = 'record'
+  , format        = 'csv'
+  , type          = 'flat'
+)

    4. Can you query a subset of your project using httr? This step is like the previous one, but with two differences. First, it’s using your REDCap project (instead of the test project). Second, it pulls fewer records, and a smaller collection of fields. Subsetting can help troubleshoot by avoiding (and thus identifying) cells with problematic values.

      Notice this call now passes values to the records and fields parameters. Also notice each value is a single long string (rather a vector of shorter strings, which is more natural to most R users).

      -
      redcap_uri         <- "https://the.urlofyourinsitution.edu/api/"
-token              <- "your-secret-token"
-
-records_collapsed  <- "1,2,3"                             # Assumes dataset contains ID values of 1-3.
-fields_collapsed   <- "record_id,name_first,name_last"    # Assumes dataset contains these variables.
-
-post_body <- list(
-  token           = token,
-  content         = 'record',
-  format          = 'csv',
-  type            = 'flat',
-  records         = records_collapsed,
-  fields          = fields_collapsed
-)
-
-raw_text <- httr::POST(
-  url             = redcap_uri,
-  body            = post_body,
-  httr::verbose() # Remove this line to suppress the console updates.
-)
-
-raw_text
      +
      redcap_uri         <- "https://the.urlofyourinsitution.edu/api/"
+token              <- "your-secret-token"
+
+records_collapsed  <- "1,2,3"                             # Assumes dataset contains ID values of 1-3.
+fields_collapsed   <- "record_id,name_first,name_last"    # Assumes dataset contains these variables.
+
+post_body <- list(
+  token           = token,
+  content         = 'record',
+  format          = 'csv',
+  type            = 'flat',
+  records         = records_collapsed,
+  fields          = fields_collapsed
+)
+
+raw_text <- httr::POST(
+  url             = redcap_uri,
+  body            = post_body,
+  httr::verbose() # Remove this line to suppress the console updates.
+)
+
+raw_text

    5. Can you query an entire project using httr? There are two advantages of trying a subset of the data. First, small datasets avoid the time-out errors that plague large datasets. Second, it may avoid problematic values being passed through the pipeline. If the current check fails but the previous check succeeds, then experiment with different expanses of records and fields. This should help determine which values are causing the problems, or if there’s simply too much data being pulled in one pass.

      If the desired dataset is too large, consider if you can prune unnecessary records or fields. If not, one solution is to pull smaller, multiple batches using the API, then reassemble them. The redcap_read() function in REDCapR does this automatically, and allows the user to specify a batch_size.

      -
      redcap_uri                  <- "https://the.urlofyourinsitution.edu/api/"
-token                       <- "your-secret-token"
-
-records_collapsed           <- NULL
-fields_collapsed            <- NULL
-
-post_body <- list(
-  token           = token,
-  content         = 'record',
-  format          = 'csv',
-  type            = 'flat',
-  records         = records_collapsed,
-  fields          = fields_collapsed
-)
-
-raw_text <- httr::POST(
-  url             = redcap_uri,
-  body            = post_body,
-  httr::verbose() # Remove this line to suppress the console updates.
-)
-
-raw_text
      +
      redcap_uri                  <- "https://the.urlofyourinsitution.edu/api/"
+token                       <- "your-secret-token"
+
+records_collapsed           <- NULL
+fields_collapsed            <- NULL
+
+post_body <- list(
+  token           = token,
+  content         = 'record',
+  format          = 'csv',
+  type            = 'flat',
+  records         = records_collapsed,
+  fields          = fields_collapsed
+)
+
+raw_text <- httr::POST(
+  url             = redcap_uri,
+  body            = post_body,
+  httr::verbose() # Remove this line to suppress the console updates.
+)
+
+raw_text

    If all these checks pass, proceed to the next section. If not, start by consulting your REDCap administrator.

    @@ -316,81 +298,81 @@

    1. Is the latest version of REDCapR installed on your machine? Currently the easiest way to install REDCapR is with the remotes package. The following code installs remotes, then installs REDCapR. The CRAN version of REDCapR is updated only a few times a year, while the code below will download the latest stable version.

      -
      install.packages("remotes", repos = "https://cran.rstudio.com")
-remotes::install_github(repo = "OuhscBbmc/REDCapR")
      +
      install.packages("remotes", repos = "https://cran.rstudio.com")
+remotes::install_github(repo = "OuhscBbmc/REDCapR")
    2. -

      Does REDCapR load successfully on your machine? If so, running library(REDCapR) should produce the following output if you’re starting with a fresh session of R:

      -
      library(REDCapR)
-# Loading required package: REDCapR
      +

      Does REDCapR load successfully on your machine? If so, running library(REDCapR) should produce the following output if you’re starting with a fresh session of R:

      +
      library(REDCapR)
+# Loading required package: REDCapR

    3. Can you export their data dictionary? Sometimes the problem exists within the metadata/dictionary, instead of the actual data values. Verify the structure and content of this specific project is interpretable by your local environment.

      -
      library(REDCapR) # Load the package into the current R session, if you haven't already.
-redcap_uri       <- "https://the.urlofyourinsitution.edu/api/"
-token            <- "your-secret-token"
-redcap_metadata_read(redcap_uri = uri, token = token)
      -

      If this fails, see “Problems in the project’s metadata/dictionary.” under Gotchas below.

      +
      library(REDCapR) # Load the package into the current R session, if you haven't already.
+redcap_uri       <- "https://the.urlofyourinsitution.edu/api/"
+token            <- "your-secret-token"
+redcap_metadata_read(redcap_uri = uri, token = token)
      +

      If this fails, see “Problems in the project’s metadata/dictionary” under Common Gotchas above. A problematic data dictionary may produce the error Error in inherits(ds, "data.frame") : object 'ds' not found when calling REDCapR::redcap_metadata_read().

    4. Can you export from an example project? This is the same fake data hosted by the OUHSC BBMC as in the previous section.

      -
      library(REDCapR) # Load the package into the current R session.
-uri   <- "https://bbmc.ouhsc.edu/redcap/api/"
-token <- "9A81268476645C4E5F03428B8AC3AA7B"
-redcap_read(redcap_uri = uri, token = token)$data
      +
      library(REDCapR) # Load the package into the current R session.
+uri   <- "https://bbmc.ouhsc.edu/redcap/api/"
+token <- "9A81268476645C4E5F03428B8AC3AA7B"
+redcap_read(redcap_uri = uri, token = token)$data

      The previous code should produce similar output. Notice there are five rows and the columns will wrap around if your console window is too narrow.

      -
      5 records and 1 columns were read from REDCap in 0.41 seconds.
-Starting to read 5 records  at 2014-06-27 17:19:49
-Reading batch 1 of 1, with ids 1 through 5.
-5 records and 16 columns were read from REDCap in 0.42 seconds.
-
-  record_id name_first name_last                                 address      telephone               email
-1         1     Nutmeg  Nutmouse 14 Rose Cottage St.\nKenning UK, 323232 (432) 456-4848     nutty@mouse.com
-2         2     Tumtum  Nutmouse 14 Rose Cottage Blvd.\nKenning UK 34243 (234) 234-2343    tummy@mouse.comm
-3         3     Marcus      Wood          243 Hill St.\nGuthrie OK 73402 (433) 435-9865        mw@mwood.net
-4         4      Trudy       DAG          342 Elm\nDuncanville TX, 75116 (987) 654-3210 peroxide@blonde.com
-5         5   John Lee    Walker      Hotel Suite\nNew Orleans LA, 70115 (333) 333-4444  left@hippocket.com
-
-         dob age ethnicity race sex height weight   bmi
-1 2003-08-30  10         1    2   0   5.00      1 400.0
-2 2003-03-10  10         1    6   1   6.00      1 277.8
-3 1934-04-09  79         0    4   1 180.00     80  24.7
-4 1952-11-02  61         1    4   0 165.00     54  19.8
-5 1955-04-15  58         1    4   1 193.04    104  27.9
-
-                                                                                                     comments
-1                                                                     Character in a book, with some guessing
-2                                                                          A mouse character from a good book
-3                                                                                          completely made up
-4 This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail
-5                 Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache
-
-  demographics_complete
-1                     2
-2                     2
-3                     2
-4                     2
-5                     2
      +
      5 records and 1 columns were read from REDCap in 0.41 seconds.
+Starting to read 5 records  at 2014-06-27 17:19:49
+Reading batch 1 of 1, with ids 1 through 5.
+5 records and 16 columns were read from REDCap in 0.42 seconds.
+
+  record_id name_first name_last                                 address      telephone               email
+1         1     Nutmeg  Nutmouse 14 Rose Cottage St.\nKenning UK, 323232 (432) 456-4848     nutty@mouse.com
+2         2     Tumtum  Nutmouse 14 Rose Cottage Blvd.\nKenning UK 34243 (234) 234-2343    tummy@mouse.comm
+3         3     Marcus      Wood          243 Hill St.\nGuthrie OK 73402 (433) 435-9865        mw@mwood.net
+4         4      Trudy       DAG          342 Elm\nDuncanville TX, 75116 (987) 654-3210 peroxide@blonde.com
+5         5   John Lee    Walker      Hotel Suite\nNew Orleans LA, 70115 (333) 333-4444  left@hippocket.com
+
+         dob age ethnicity race sex height weight   bmi
+1 2003-08-30  10         1    2   0   5.00      1 400.0
+2 2003-03-10  10         1    6   1   6.00      1 277.8
+3 1934-04-09  79         0    4   1 180.00     80  24.7
+4 1952-11-02  61         1    4   0 165.00     54  19.8
+5 1955-04-15  58         1    4   1 193.04    104  27.9
+
+                                                                                                     comments
+1                                                                     Character in a book, with some guessing
+2                                                                          A mouse character from a good book
+3                                                                                          completely made up
+4 This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail
+5                 Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache
+
+  demographics_complete
+1                     2
+2                     2
+3                     2
+4                     2
+5                     2

    5. Can you export from your own project? The code is similar to the previous check, but the uri and token values will need to be modified.

      -
      library(REDCapR) # Load the package into the current R session, if you haven't already.
-redcap_uri       <- "https://the.urlofyourinsitution.edu/api/"
-token            <- "your-secret-token"
-redcap_read(redcap_uri = uri, token = token)$data
      +
      library(REDCapR) # Load the package into the current R session, if you haven't already.
+redcap_uri       <- "https://the.urlofyourinsitution.edu/api/"
+token            <- "your-secret-token"
+redcap_read(redcap_uri = uri, token = token)$data

      Alternatively, a redcap_project object can be declared initially, which makes subsequent calls cleaner when the token and url are required only the when the object is declared.

      -
      library(REDCapR) # Load the package into the current R session, if you haven't already.
-uri               <- "https://bbmc.ouhsc.edu/redcap/api/"
-token             <- "9A81268476645C4E5F03428B8AC3AA7B"
-project           <- redcap_project$new(redcap_uri = uri, token = token)
-
-ds_three_columns  <- project$read(fields = c("record_id", "sex", "age"))$data
-
-ids_of_males      <- ds_three_columns$record_id[ds_three_columns$sex == 1]
-ids_of_minors     <- ds_three_columns$record_id[ds_three_columns$age < 18]
-
-ds_males          <- project$read(records = ids_of_males, batch_size = 2)$data
-ds_minors         <- project$read(records = ids_of_minors)$data
      +
      library(REDCapR) # Load the package into the current R session, if you haven't already.
+uri               <- "https://bbmc.ouhsc.edu/redcap/api/"
+token             <- "9A81268476645C4E5F03428B8AC3AA7B"
+project           <- redcap_project$new(redcap_uri = uri, token = token)
+
+ds_three_columns  <- project$read(fields = c("record_id", "sex", "age"))$data
+
+ids_of_males      <- ds_three_columns$record_id[ds_three_columns$sex == 1]
+ids_of_minors     <- ds_three_columns$record_id[ds_three_columns$age < 18]
+
+ds_males          <- project$read(records = ids_of_males, batch_size = 2)$data
+ds_minors         <- project$read(records = ids_of_minors)$data

    6. Is the export operation still unsuccessful using REDCapR? If so the “Can the user query a entire REDCap project using httr?” check succeeded, but the REDCapR checks did not, consider posting a new GitHub issue to the package developers.

    @@ -405,69 +387,69 @@

    1. Is redcapAPI installed on your machine? Currently, the easiest way to install redcapAPI is from CRAN.

      -
      install.packages("redcapAPI")
      +
      install.packages("redcapAPI")

      Developmental versions may be available on GitHub.

      -
      install.packages("remotes", repos = "http://cran.rstudio.com")
-remotes::install_github(repo = "nutterb/redcapAPI")
      +
      install.packages("remotes", repos = "http://cran.rstudio.com")
+remotes::install_github(repo = "nutterb/redcapAPI")
    2. -

      Does redcapAPI load successfully on your machine? If so, running library(redcapAPI) should produce the following output if you’re starting with a fresh session of R:

      -
      library(redcapAPI)
-# Loading required package: redcapAPI
      +

      Does redcapAPI load successfully on your machine? If so, running library(redcapAPI) should produce the following output if you’re starting with a fresh session of R:

      +
      library(redcapAPI)
+# Loading required package: redcapAPI

    3. Can you export their data dictionary? Sometimes the problem exists within the metadata/dictionary, instead of the actual data values. Verify the structure and content of this specific project is interpretable by your local environment.

      -
      library(redcapAPI) # Load the package into the current R session, if you haven't already.
-redcap_uri       <- "https://the.urlofyourinsitution.edu/api/"
-token            <- "your-secret-token"
-exportMetaData(rcon)
      -

      If this fails, see “Problems in the project’s metadata/dictionary.” under Gotchas below.

      +
      library(redcapAPI) # Load the package into the current R session, if you haven't already.
+redcap_uri       <- "https://the.urlofyourinsitution.edu/api/"
+token            <- "your-secret-token"
+exportMetaData(rcon)
      +

      If this fails, see “Problems in the project’s metadata/dictionary.” under Gotchas above

    4. Can you export from an example project? This is the same fake data hosted by the OUHSC BBMC as in the previous section.

      -
      library(redcapAPI) # Load the package into the current R session.
-rcon <- redcapConnection(
-  url   = "https://bbmc.ouhsc.edu/redcap/api/",
-  token = "9A81268476645C4E5F03428B8AC3AA7B"
-)
-exportRecords(rcon)
      +
      library(redcapAPI) # Load the package into the current R session.
+rcon <- redcapConnection(
+  url   = "https://bbmc.ouhsc.edu/redcap/api/",
+  token = "9A81268476645C4E5F03428B8AC3AA7B"
+)
+exportRecords(rcon)

      The previous code should produce similar output. Notice there are five rows and the columns will wrap around if your console window is too narrow.

      -
      record_id name_first name_last                                 address      telephone               email
-1         1     Nutmeg  Nutmouse 14 Rose Cottage St.\nKenning UK, 323232 (432) 456-4848     nutty@mouse.com
-2         2     Tumtum  Nutmouse 14 Rose Cottage Blvd.\nKenning UK 34243 (234) 234-2343    tummy@mouse.comm
-3         3     Marcus      Wood          243 Hill St.\nGuthrie OK 73402 (433) 435-9865        mw@mwood.net
-4         4      Trudy       DAG          342 Elm\nDuncanville TX, 75116 (987) 654-3210 peroxide@blonde.com
-5         5   John Lee    Walker      Hotel Suite\nNew Orleans LA, 70115 (333) 333-4444  left@hippocket.com
-
-       dob age ethnicity race sex height weight   bmi
-1 2003-08-30  10         1    2   0   5.00      1 400.0
-2 2003-03-10  10         1    6   1   6.00      1 277.8
-3 1934-04-09  79         0    4   1 180.00     80  24.7
-4 1952-11-02  61         1    4   0 165.00     54  19.8
-5 1955-04-15  58         1    4   1 193.04    104  27.9
-
-                                                                                                   comments
-1                                                                     Character in a book, with some guessing
-2                                                                          A mouse character from a good book
-3                                                                                          completely made up
-4 This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail
-5                 Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache
-
-demographics_complete
-1                     2
-2                     2
-3                     2
-4                     2
-5                     2
      +
      record_id name_first name_last                                 address      telephone               email
+1         1     Nutmeg  Nutmouse 14 Rose Cottage St.\nKenning UK, 323232 (432) 456-4848     nutty@mouse.com
+2         2     Tumtum  Nutmouse 14 Rose Cottage Blvd.\nKenning UK 34243 (234) 234-2343    tummy@mouse.comm
+3         3     Marcus      Wood          243 Hill St.\nGuthrie OK 73402 (433) 435-9865        mw@mwood.net
+4         4      Trudy       DAG          342 Elm\nDuncanville TX, 75116 (987) 654-3210 peroxide@blonde.com
+5         5   John Lee    Walker      Hotel Suite\nNew Orleans LA, 70115 (333) 333-4444  left@hippocket.com
+
+       dob age ethnicity race sex height weight   bmi
+1 2003-08-30  10         1    2   0   5.00      1 400.0
+2 2003-03-10  10         1    6   1   6.00      1 277.8
+3 1934-04-09  79         0    4   1 180.00     80  24.7
+4 1952-11-02  61         1    4   0 165.00     54  19.8
+5 1955-04-15  58         1    4   1 193.04    104  27.9
+
+                                                                                                   comments
+1                                                                     Character in a book, with some guessing
+2                                                                          A mouse character from a good book
+3                                                                                          completely made up
+4 This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail
+5                 Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache
+
+demographics_complete
+1                     2
+2                     2
+3                     2
+4                     2
+5                     2

    5. Can you export your own project? The code is similar to the previous check, but the uri and token values will need to be modified.

      -
      library(redcapAPI) # Load the package into the current R session, if you haven't already.
-rcon <- redcapConnection(
-  url   = "https://the.urlofyourinsitution.edu/api/", # Adapt this to your server.
-  token = "your-secret-token"                         # Adapt this to your user's token.
-)
-exportRecords(rcon)
      +
      library(redcapAPI) # Load the package into the current R session, if you haven't already.
+rcon <- redcapConnection(
+  url   = "https://the.urlofyourinsitution.edu/api/", # Adapt this to your server.
+  token = "your-secret-token"                         # Adapt this to your user's token.
+)
+exportRecords(rcon)

    6. Is the export operation still unsuccessful using redcapAPI? If so the “Can the user query a entire REDCap project using httr?” check succeeded, but the redcapAPI checks did not, consider posting a new GitHub issue to the package developers.

    @@ -520,40 +502,11 @@

    - @@ -564,7 +517,7 @@

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/articles/advanced-redcapr-operations.html b/docs/articles/advanced-redcapr-operations.html index 98ef4a33..98d88ac2 100644 --- a/docs/articles/advanced-redcapr-operations.html +++ b/docs/articles/advanced-redcapr-operations.html @@ -12,22 +12,22 @@ - - - - - + + + + + + - - - + + - +
    -

    Advanced REDCapR Operations

    +

    Advanced REDCapR Operations

    -

    2020-03-13

    +

    2020-04-19

    Source: vignettes/advanced-redcapr-operations.Rmd @@ -127,25 +109,25 @@

    Set project-wide values

    There is some information that is specific to a REDCap project, as opposed to an individual operation. This includes the (1) uri of the server, and the (2) token for the user’s project. This is hosted on a machine used in REDCapR’s public test suite, so you can run this example from any computer. Unless tests are running.

    Other than PHI-free demos, we strongly suggest storing tokens securely and avoiding hard-coding them like below. Our recommendation is to store tokens in a database. If that is not feasible for your institution, consider storing them in a secured csv and retrieving with REDCapR::retrieve_credential_local().

    -
    library(REDCapR) #Load the package into the current R session.
-uri                   <- "https://bbmc.ouhsc.edu/redcap/api/"
-token_simple          <- "9A81268476645C4E5F03428B8AC3AA7B"
-token_longitudinal    <- "0434F0E9CF53ED0587847AB6E51DE762"
    +
    library(REDCapR) #Load the package into the current R session.
+uri                   <- "https://bbmc.ouhsc.edu/redcap/api/"
+token_simple          <- "9A81268476645C4E5F03428B8AC3AA7B"
+token_longitudinal    <- "0434F0E9CF53ED0587847AB6E51DE762"

    Converting from tall/long to wide

    Disclaimer: Occasionally we’re asked for a longitudinal dataset to be converted from a “long/tall format” (where typically each row is one observation for a participant) to a “wide format” (where each row is on participant). Usually we advise against it. Besides all the database benefits of a long structure, a wide structure restricts your options with the stat routine. No modern longitudinal analysis procedures (e.g., growth curve models or multilevel/hierarchical models) accept wide. You’re pretty much stuck with repeated measures anova, which is very inflexible for real-world medical-ish analyses. It requires a patient to have a measurement at every time point; otherwise the anova excludes the patient entirely.

    However we like going wide to produce visual tables for publications, and here’s one way to do it in R. First retrieve the dataset from REDCap.

    -
    library(magrittr);
-suppressPackageStartupMessages(requireNamespace("dplyr"))
-suppressPackageStartupMessages(requireNamespace("tidyr"))
-events_to_retain  <- c("dose_1_arm_1", "visit_1_arm_1", "dose_2_arm_1", "visit_2_arm_1")
-
-ds_long <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token_longitudinal)$data
    -
    #> 18 records and 125 columns were read from REDCap in 0.6 seconds.  The http status code was 200.
    -
    ds_long %>%
-  dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4)
    +
    library(magrittr);
+suppressPackageStartupMessages(requireNamespace("dplyr"))
+suppressPackageStartupMessages(requireNamespace("tidyr"))
+events_to_retain  <- c("dose_1_arm_1", "visit_1_arm_1", "dose_2_arm_1", "visit_2_arm_1")
+
+ds_long <- REDCapR::redcap_read_oneshot(redcap_uri = uri, token = token_longitudinal)$data
    +
    #> 18 records and 125 columns were read from REDCap in 0.5 seconds.  The http status code was 200.
    +
    ds_long %>%
+  dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4)
    #>    study_id        redcap_event_name pmq1 pmq2 pmq3 pmq4
 #> 1       100         enrollment_arm_1   NA   NA   NA   NA
 #> 2       100             dose_1_arm_1    2    2    1    1
@@ -166,44 +148,44 @@ 
    
 #> 17      304        final_visit_arm_2   NA   NA   NA   NA
 #> 18      304 deadline_to_return_arm_2   NA   NA   NA   NA

    When widening only one variable (e.g., pmq1), the code’s pretty simple:

    -
    ds_wide <-
-  ds_long %>%
-  dplyr::select(study_id, redcap_event_name, pmq1) %>%
-  dplyr::filter(redcap_event_name %in% events_to_retain) %>%
-  tidyr::pivot_wider(
-    id_cols     = study_id,
-    names_from  = redcap_event_name,
-    values_from = pmq1
-  )
-  # For old versions of tidyr that predate `pivot_wider()`:
-  # tidyr::spread(key=redcap_event_name, value=pmq1)
-ds_wide
    +
    ds_wide <-
+  ds_long %>%
+  dplyr::select(study_id, redcap_event_name, pmq1) %>%
+  dplyr::filter(redcap_event_name %in% events_to_retain) %>%
+  tidyr::pivot_wider(
+    id_cols     = study_id,
+    names_from  = redcap_event_name,
+    values_from = pmq1
+  )
+  # For old versions of tidyr that predate `pivot_wider()`:
+  # tidyr::spread(key=redcap_event_name, value=pmq1)
+ds_wide
    #> # A tibble: 2 x 5
 #>   study_id dose_1_arm_1 visit_1_arm_1 dose_2_arm_1 visit_2_arm_1
 #>      <dbl>        <dbl>         <dbl>        <dbl>         <dbl>
 #> 1      100            2             1            3             0
 #> 2      220            0             0            1             3

    In some scenarios, multiple variables (e.g., pmq1 - pmq4) can be widened in a single tidyr::pivot_wider() operation. This example contains the additional wrinkle that the REDCap event names “first_dose” and “first_visit” are renamed “dose_1” and “visit_1”, which will help all the values be dose and visit values be proper numbers.

    -
    pattern <- "^(\\w+?)_arm_(\\d)$"
-ds_wide <-
-  ds_long %>%
-  dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4) %>%
-  dplyr::mutate(
-    event = sub(pattern, "\\1", redcap_event_name),
-    event = dplyr::recode(event, "first_dose"="dose_1", "first_visit"="visit_1"),
-    arm   = as.integer(sub(pattern, "\\2", redcap_event_name))
-  ) %>%
-  dplyr::select(study_id, event, arm, pmq1, pmq2, pmq3, pmq4) %>%
-  dplyr::filter(!(event %in% c(
-    "enrollment", "final_visit", "deadline_to_return", "deadline_to_opt_ou")
-  )) %>%
-  tidyr::pivot_wider(
-    id_cols     = c(study_id, arm),
-    names_from  = event,
-    values_from = c(pmq1, pmq2, pmq3, pmq4)
-  )
-
-ds_wide
    +
    pattern <- "^(\\w+?)_arm_(\\d)$"
+ds_wide <-
+  ds_long %>%
+  dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4) %>%
+  dplyr::mutate(
+    event = sub(pattern, "\\1", redcap_event_name),
+    event = dplyr::recode(event, "first_dose"="dose_1", "first_visit"="visit_1"),
+    arm   = as.integer(sub(pattern, "\\2", redcap_event_name))
+  ) %>%
+  dplyr::select(study_id, event, arm, pmq1, pmq2, pmq3, pmq4) %>%
+  dplyr::filter(!(event %in% c(
+    "enrollment", "final_visit", "deadline_to_return", "deadline_to_opt_ou")
+  )) %>%
+  tidyr::pivot_wider(
+    id_cols     = c(study_id, arm),
+    names_from  = event,
+    values_from = c(pmq1, pmq2, pmq3, pmq4)
+  )
+
+ds_wide
    #> # A tibble: 3 x 18
 #>   study_id   arm pmq1_dose_1 pmq1_visit_1 pmq1_dose_2 pmq1_visit_2 pmq2_dose_1
 #>      <dbl> <int>       <dbl>        <dbl>       <dbl>        <dbl>       <dbl>
@@ -215,33 +197,33 @@ 
    
 #> #   pmq3_dose_2 <dbl>, pmq3_visit_2 <dbl>, pmq4_dose_1 <dbl>,
 #> #   pmq4_visit_1 <dbl>, pmq4_dose_2 <dbl>, pmq4_visit_2 <dbl>

    However, in other widening scenarios, it can be easier to go even longer/taller (e.g., ds_eav) before reversing direction and going wide.

    -
    ds_eav <-
-  ds_long %>%
-  dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4) %>%
-  dplyr::mutate(
-    event = sub(pattern, "\\1", redcap_event_name),
-    event = dplyr::recode(event, "first_dose"="dose_1", "first_visit"="visit_1"),
-    arm   = as.integer(sub(pattern, "\\2", redcap_event_name))
-  ) %>%
-  dplyr::select(study_id, event, arm, pmq1, pmq2, pmq3, pmq4) %>%
-  tidyr::pivot_longer(
-    cols      = c(pmq1, pmq2, pmq3, pmq4),
-    names_to  = "key",
-    values_to = "value"
-  ) %>%
-  # For old versions of tidyr that predate `pivot_wider()`:
-  # tidyr::gather(key=key, value=value, pmq1, pmq2, pmq3, pmq4) %>%
-  dplyr::filter(!(event %in% c(
-    "enrollment", "final_visit", "deadline_to_return", "deadline_to_opt_ou")
-  )) %>%
-  dplyr::mutate( # Simulate correcting for mismatched names across arms:
-    key = paste0(key, "_", event)
-  ) %>%
-  dplyr::select(-event)
-
-# Show the first 10 rows of the EAV table.
-ds_eav %>%
-  head(10)
    +
    ds_eav <-
+  ds_long %>%
+  dplyr::select(study_id, redcap_event_name, pmq1, pmq2, pmq3, pmq4) %>%
+  dplyr::mutate(
+    event = sub(pattern, "\\1", redcap_event_name),
+    event = dplyr::recode(event, "first_dose" = "dose_1", "first_visit" = "visit_1"),
+    arm   = as.integer(sub(pattern, "\\2", redcap_event_name))
+  ) %>%
+  dplyr::select(study_id, event, arm, pmq1, pmq2, pmq3, pmq4) %>%
+  tidyr::pivot_longer(
+    cols      = c(pmq1, pmq2, pmq3, pmq4),
+    names_to  = "key",
+    values_to = "value"
+  ) %>%
+  # For old versions of tidyr that predate `pivot_wider()`:
+  # tidyr::gather(key=key, value=value, pmq1, pmq2, pmq3, pmq4) %>%
+  dplyr::filter(!(event %in% c(
+    "enrollment", "final_visit", "deadline_to_return", "deadline_to_opt_ou")
+  )) %>%
+  dplyr::mutate( # Simulate correcting for mismatched names across arms:
+    key = paste0(key, "_", event)
+  ) %>%
+  dplyr::select(-event)
+
+# Show the first 10 rows of the EAV table.
+ds_eav %>%
+  head(10)
    #> # A tibble: 10 x 4
 #>    study_id   arm key          value
 #>       <dbl> <int> <chr>        <dbl>
@@ -255,17 +237,17 @@ 
    
 #>  8      100     1 pmq4_visit_1     0
 #>  9      100     1 pmq1_dose_2      3
 #> 10      100     1 pmq2_dose_2      1
    -
    # Spread the EAV to wide.
-ds_wide_2 <-
-  ds_eav %>%
-  tidyr::pivot_wider(
-    id_cols     = c(study_id, arm),
-    names_from  = key,
-    values_from = value
-  )
-  # For old versions of tidyr that predate `pivot_wider()`:
-  # tidyr::spread(key=key, value=value)
-ds_wide_2
    +
    # Spread the EAV to wide.
+ds_wide_2 <-
+  ds_eav %>%
+  tidyr::pivot_wider(
+    id_cols     = c(study_id, arm),
+    names_from  = key,
+    values_from = value
+  )
+  # For old versions of tidyr that predate `pivot_wider()`:
+  # tidyr::spread(key=key, value=value)
+ds_wide_2
    #> # A tibble: 3 x 18
 #>   study_id   arm pmq1_dose_1 pmq2_dose_1 pmq3_dose_1 pmq4_dose_1 pmq1_visit_1
 #>      <dbl> <int>       <dbl>       <dbl>       <dbl>       <dbl>        <dbl>
@@ -278,35 +260,64 @@ 
    
 #> #   pmq2_visit_2 <dbl>, pmq3_visit_2 <dbl>, pmq4_visit_2 <dbl>

    Lots of packages and documentation exist. Our current preference is the tidyverse approach to pivoting, but the data.table approach is worth considering if you’re comfortable with that package. This Stack Overflow post describes several ways. We recommend against the reshape and reshape2 packages, because their developers have replaced them with the tidyr functions described above.

    +
    +

    +Query the Underlying MySQL Database

    +

    If you require a feature that is not available from your instance’s API, first upgrade your institution’s REDcap instance and see if the feature has been added recently. Second, check if someone has released the desired API-like features as an REDCap External Module.

    +

    Third, you may need to query the database underneath REDCap’s web server. The Transfer Credentials section of the Security Database Vignette provides a complete example of using R to query the MySQL database through odbc.

    +

    We find it’s best to develop the query in MySQL Workbench, then copy the code to R (or alternatively, use OuhscMunge::execute_sql_file()).

    +

    Here is an example that retrieves the first_submit_time, which is helpful if you need a timestamp from surveys that were not marked as completed. Replace ‘444’ with your pid, and 1001 through 1003 with the desired events.

    +
    SELECT 
+  p.participant_id      as participant_survey_id
+  ,r.record             as record_id
+  ,p.event_id
+  ,e.descrip            as event_name
+  ,r.first_submit_time
+  ,r.completion_time
+  
+  -- ,p.*
+  -- ,r.*
+FROM redcapv3.redcap_surveys_participants     as p
+  left  join redcapv3.redcap_surveys_response as r on p.participant_id = r.participant_id
+  left  join redcapv3.redcap_events_metadata  as e on p.event_id       = e.event_id
+where 
+  p.survey_id = 444
+  and
+  p.event_id in (
+    1001, -- start of the year
+    1002, -- mid term
+    1003  -- end of year
+  )
    +

    SSL Options

    The official cURL site discusses the process of using SSL to verify the server being connected to.

    Use the SSL cert file that come with the openssl package.

    -
    cert_location <- system.file("cacert.pem", package="openssl")
-if( file.exists(cert_location) ) {
-  config_options         <- list(cainfo=cert_location)
-  ds_different_cert_file <- redcap_read_oneshot(
-    redcap_uri     = uri,
-    token          = token_simple,
-    config_options = config_options
-  )$data
-}
    +
    cert_location <- system.file("cacert.pem", package = "openssl")
+if (file.exists(cert_location)) {
+  config_options         <- list(cainfo = cert_location)
+  ds_different_cert_file <- redcap_read_oneshot(
+    redcap_uri     = uri,
+    token          = token_simple,
+    config_options = config_options
+  )$data
+}
    #> 5 records and 24 columns were read from REDCap in 0.2 seconds.  The http status code was 200.

    Force the connection to use SSL=3 (which is not preferred, and possibly insecure).

    -
    config_options <- list(sslversion=3)
-ds_ssl_3 <- redcap_read_oneshot(
-  redcap_uri     = uri,
-  token          = token_simple,
-  config_options = config_options
-)$data
    -
    #> 5 records and 24 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
    -
    config_options <- list(ssl.verifypeer=FALSE)
-ds_no_ssl <- redcap_read_oneshot(
-   redcap_uri     = uri,
-   token          = token_simple,
-   config_options = config_options
-)$data
    +
    config_options <- list(sslversion = 3)
+ds_ssl_3 <- redcap_read_oneshot(
+  redcap_uri     = uri,
+  token          = token_simple,
+  config_options = config_options
+)$data
    +
    #> 5 records and 24 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    +
    config_options <- list(ssl.verifypeer = FALSE)
+ds_no_ssl <- redcap_read_oneshot(
+  redcap_uri     = uri,
+  token          = token_simple,
+  config_options = config_options
+)$data
    #> 5 records and 24 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
    @@ -325,35 +336,6 @@

    SEX 0, Male | 1, Female LANGUAGE 1, English | 2, Spanish | 3, Other | 6, Unknown

    -
    -

    -Query the Underlying MySQL Database

    -

    If you require a feature that is not available from your instance’s API, first upgrade your institution’s REDcap instance and see if the feature has been added recently. Second, check if someone has released the desired API-like features as an REDCap External Module.

    -

    Third, you may need to query the database underneath REDCap’s web server. The Transfer Credentials section of the Security Database Vignette provides a complete example of using R to query the MySQL database through odbc.

    -

    We find it’s best to develop the query in MySQL Workbench, then copy the code to R (or alternatively, use OuhscMunge::execute_sql_file()).

    -

    Here is an example that retrieves the first_submit_time, which is helpful if you need a timestamp from surveys that were not marked as completed. Replace ‘444’ with your pid, and 1001 through 1003 with the desired events.

    -
    SELECT 
-  p.participant_id      as participant_survey_id
-  ,r.record             as record_id
-  ,p.event_id
-  ,e.descrip            as event_name
-  ,r.first_submit_time
-  ,r.completion_time
-  
-  -- ,p.*
-  -- ,r.*
-FROM redcapv3.redcap_surveys_participants     as p
-  left  join redcapv3.redcap_surveys_response as r on p.participant_id = r.participant_id
-  left  join redcapv3.redcap_events_metadata  as e on p.event_id       = e.event_id
-where 
-  p.survey_id = 444
-  and
-  p.event_id in (
-    1001, -- start of the year
-    1002, -- mid term
-    1003  -- end of year
-  )
    -

    Session Information

    @@ -369,27 +351,25 @@

    #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz America/Chicago -#> date 2020-03-13 +#> date 2020-04-19 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date lib source #> assertthat 0.2.1 2019-03-21 [2] CRAN (R 3.6.1) -#> backports 1.1.5 2019-10-02 [2] CRAN (R 3.6.1) -#> callr 3.4.2 2020-02-12 [2] CRAN (R 3.6.2) +#> backports 1.1.6 2020-04-05 [2] CRAN (R 3.6.3) #> checkmate 2.0.0 2019-12-03 [2] local #> cli 2.0.2 2020-02-28 [2] CRAN (R 3.6.2) #> colorspace 1.4-1 2019-03-18 [2] CRAN (R 3.6.1) #> crayon 1.3.4 2017-09-16 [2] CRAN (R 3.6.1) #> curl 4.3 2019-12-02 [2] CRAN (R 3.6.1) #> desc 1.2.0 2018-05-01 [2] CRAN (R 3.6.1) -#> devtools 2.2.2 2020-02-17 [2] CRAN (R 3.6.2) #> digest 0.6.25 2020-02-23 [2] CRAN (R 3.6.2) #> dplyr 0.8.5 2020-03-07 [2] CRAN (R 3.6.3) #> ellipsis 0.3.0 2019-09-20 [2] CRAN (R 3.6.1) #> evaluate 0.14 2019-05-28 [2] CRAN (R 3.6.1) #> fansi 0.4.1 2020-01-08 [2] CRAN (R 3.6.1) -#> fs 1.3.2 2020-03-05 [2] CRAN (R 3.6.3) -#> glue 1.3.2 2020-03-12 [2] CRAN (R 3.6.3) +#> fs 1.4.1 2020-04-04 [2] CRAN (R 3.6.3) +#> glue 1.4.0 2020-04-03 [2] CRAN (R 3.6.3) #> hms 0.5.3 2020-01-08 [2] CRAN (R 3.6.1) #> htmltools 0.4.0 2019-10-04 [2] CRAN (R 3.6.1) #> httr 1.4.1 2019-08-05 [2] CRAN (R 3.6.1) @@ -401,19 +381,13 @@

    #> memoise 1.1.0 2017-04-21 [2] CRAN (R 3.6.1) #> munsell 0.5.0 2018-06-12 [2] CRAN (R 3.6.1) #> pillar 1.4.3 2019-12-20 [2] CRAN (R 3.6.1) -#> pkgbuild 1.0.6 2019-10-09 [2] CRAN (R 3.6.1) #> pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 3.6.1) -#> pkgdown 1.4.1 2019-09-15 [2] CRAN (R 3.6.1) -#> pkgload 1.0.2 2018-10-29 [2] CRAN (R 3.6.1) -#> prettyunits 1.1.1 2020-01-24 [2] CRAN (R 3.6.2) -#> processx 3.4.2 2020-02-09 [2] CRAN (R 3.6.2) -#> ps 1.3.2 2020-02-13 [2] CRAN (R 3.6.2) +#> pkgdown 1.5.0 2020-03-25 [2] CRAN (R 3.6.3) #> purrr 0.3.3 2019-10-18 [2] CRAN (R 3.6.1) #> R6 2.4.1 2019-11-12 [2] CRAN (R 3.6.1) -#> Rcpp 1.0.3 2019-11-08 [2] CRAN (R 3.6.1) +#> Rcpp 1.0.4 2020-03-17 [2] CRAN (R 3.6.3) #> readr 1.3.1 2018-12-21 [2] CRAN (R 3.6.1) -#> REDCapR * 0.10.2.9005 2020-03-14 [1] local -#> remotes 2.1.1 2020-02-15 [2] CRAN (R 3.6.2) +#> REDCapR * 0.10.2.9006 2020-04-19 [1] local #> rlang 0.4.5 2020-03-01 [2] CRAN (R 3.6.2) #> rmarkdown 2.1 2020-01-20 [2] CRAN (R 3.6.2) #> rprojroot 1.3-2 2018-01-03 [2] CRAN (R 3.6.1) @@ -423,45 +397,32 @@

    #> sessioninfo 1.1.1 2018-11-05 [2] CRAN (R 3.6.1) #> stringi 1.4.6 2020-02-17 [2] CRAN (R 3.6.2) #> stringr 1.4.0 2019-02-10 [2] CRAN (R 3.6.1) -#> testthat 2.3.2 2020-03-02 [2] CRAN (R 3.6.3) -#> tibble 2.1.3 2019-06-06 [2] CRAN (R 3.6.1) +#> tibble 3.0.0 2020-03-30 [2] CRAN (R 3.6.3) #> tidyr 1.0.2 2020-01-24 [2] CRAN (R 3.6.2) #> tidyselect 1.0.0 2020-01-27 [2] CRAN (R 3.6.2) -#> usethis 1.5.1 2019-07-04 [2] CRAN (R 3.6.1) #> utf8 1.1.4 2018-05-24 [2] CRAN (R 3.6.1) #> vctrs 0.2.4 2020-03-10 [2] CRAN (R 3.6.3) #> viridisLite 0.3.0 2018-02-01 [2] CRAN (R 3.6.1) #> webshot 0.5.2 2019-11-22 [2] CRAN (R 3.6.1) #> withr 2.1.2 2018-03-15 [2] CRAN (R 3.6.1) #> xfun 0.12 2020-01-13 [2] CRAN (R 3.6.1) -#> xml2 1.2.5 2020-03-11 [2] CRAN (R 3.6.3) +#> xml2 1.3.0 2020-04-01 [2] CRAN (R 3.6.3) #> yaml 2.2.1 2020-02-01 [2] CRAN (R 3.6.2) #> -#> [1] /tmp/Rtmp830zQN/temp_libpath1f7158fa5947 +#> [1] /tmp/Rtmp5avAp4/temp_libpath4e6a183ad817 #> [2] /home/wibeasley/R/x86_64-pc-linux-gnu-library/3.6 #> [3] /usr/local/lib/R/site-library #> [4] /usr/lib/R/site-library #> [5] /usr/lib/R/library -

    Report rendered by wibeasley at 2020-03-13, 20:40 -0500 in 4 seconds.

    +

    Report rendered by wibeasley at 2020-04-19, 13:32 -0500 in 7 seconds.

    - @@ -472,7 +433,7 @@

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/articles/index.html b/docs/articles/index.html index 97bec46b..87448b36 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,15 +46,14 @@ - + - - + @@ -68,7 +71,7 @@ - +
    @@ -97,26 +100,8 @@
  • Reference
    • -
  • - - +
  • + Articles
  • Changelog @@ -124,7 +109,7 @@
    • @@ -172,7 +161,7 @@

    Getting Started

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/authors.html b/docs/authors.html index 3364d87c..32ba9174 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,15 +46,14 @@ - + - - + @@ -68,7 +71,7 @@ - +
    @@ -97,26 +100,8 @@
  • Reference
    • -
  • - - +
  • + Articles
  • Changelog @@ -124,7 +109,7 @@
    • - + @@ -153,7 +138,7 @@

      Authors

      • -

        Will Beasley. Author, maintainer. ORCID +

        Will Beasley. Author, maintainer.

      • @@ -181,13 +166,17 @@

        Authors

      • -

        Hao Zhu. Contributor. ORCID +

        Hao Zhu. Contributor.

      • Felix Torres. Contributor.

        • +
      • +

        Philip Chase. Contributor. +

        +
    • @@ -202,7 +191,7 @@

    Authors

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.5.0.

    diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 00000000..5a859415 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 00000000..1cdd573b --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('
      '); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
    • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

      `, then `

      `, etc.) that has more than one element. Defaults to 1 (for `

      `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/docsearch.json b/docs/docsearch.json index 3df6fce9..cdc94736 100644 --- a/docs/docsearch.json +++ b/docs/docsearch.json @@ -74,7 +74,7 @@ "selector": ".contents h2, .contents h3", "default_value": "Context" }, - "text": ".contents p, .contents li, .tempate-article .contents .pre" + "text": ".contents p, .contents li" } }, "selectors_exclude": [ diff --git a/docs/favicon-16x16.png b/docs/favicon-16x16.png new file mode 100644 index 0000000000000000000000000000000000000000..20d5957754577f371ae4ba3bf6b8a1d22a8042de GIT binary patch literal 1570 zcma)6X;4#V6#bHrog^#a1cM|7vJfhutm1}MK?s(LiWsZXR^!rEwAR+G z*dl5zo8p3?vWN&oWC<#2tz9*xbUIE)XXp<*)~UUjXlMGPGktUOzW3fe_ndR@m-ni& zGiNbq;WUI0BQ4dD3oGXTQ3!BWMYHC@612jWVMC~8Fa3ET5$>f$sks>lRVom2??C7o zJaYev(0VOGj|vbnRU;HuUelRlMhJf)drn@;077>V8m3TgA~YBrd;_5oGPy@6^l&(% za80GUD=WLEP8~zYOCk-?=^c@g15D->k?68S(kYV-2?T=-Mq55$;rKZ{uQwpsZ<~V-2m(wn|+k|i;0$1ZK@4CR^fF2y 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      -
      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/collapse_vector.html b/docs/reference/collapse_vector.html index b6814cef..4938672f 100644 --- a/docs/reference/collapse_vector.html +++ b/docs/reference/collapse_vector.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -54,8 +58,7 @@ In the R world, it's easier to keep these values as separate elements in a vector. This functions squashes them together in a single character element (presumably right before the return value is passed to the API)" /> - - + @@ -73,7 +76,7 @@ - +
      @@ -102,26 +105,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -129,7 +114,7 @@
      • - + @@ -189,18 +174,12 @@

        Value

        Examples

        library(REDCapR) #Load the package into the current R session.
-REDCapR:::collapse_vector(elements=NULL, collapsed=NULL)
        #> [1] ""
        REDCapR:::collapse_vector(elements=letters, collapsed=NULL)
        #> [1] "a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z"
        REDCapR:::collapse_vector(elements=NULL, collapsed="4,5,6")
        #> [1] "4,5,6"
        +REDCapR:::collapse_vector(elements=NULL, collapsed=NULL)
      • #> [1] ""
      REDCapR:::collapse_vector(elements=letters, collapsed=NULL)
      #> [1] "a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z"
      REDCapR:::collapse_vector(elements=NULL, collapsed="4,5,6")
      #> [1] "4,5,6"
      - @@ -211,7 +190,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/constant.html b/docs/reference/constant.html index 9cb46b71..4682ba7d 100644 --- a/docs/reference/constant.html +++ b/docs/reference/constant.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -212,15 +197,15 @@

        Details in the GitHub documentation.

        Examples

        - 
        REDCapR::constant("form_incomplete")  # Returns 0L
        #> [1] 0
        REDCapR::constant("form_unverified")  # Returns 1L
        #> [1] 1
        REDCapR::constant("form_complete"  )  # Returns 2L
        #> [1] 2
        
-REDCapR::constant("data_export_rights_no_access"   )  # Returns 0L
        #> [1] 0
        REDCapR::constant("data_export_rights_deidentified")  # Returns 1L
        #> [1] 1
        REDCapR::constant("data_export_rights_full"        )  # Returns 2L
        #> [1] 2
        
-REDCapR::constant("form_rights_no_access")   # Returns 0L
        #> [1] 0
        REDCapR::constant("form_rights_readonly" )   # Returns 2L --Notice the order
        #> [1] 2
        REDCapR::constant("form_rights_edit_form")   # Returns 1L
        #> [1] 1
        REDCapR::constant("form_rights_edit_survey") # Returns 3L
        #> [1] 3
        
-REDCapR::constant("access_no" )  # Returns 0L
        #> [1] 0
        REDCapR::constant("access_yes")  # Returns 1L
        #> [1] 1
        
-REDCapR::constant(c(
+    
        REDCapR::constant("form_incomplete")  # Returns 0L
        #> [1] 0
        REDCapR::constant("form_unverified")  # Returns 1L
        #> [1] 1
        REDCapR::constant("form_complete"  )  # Returns 2L
        #> [1] 2
        
+REDCapR::constant("data_export_rights_no_access"   )  # Returns 0L
        #> [1] 0
        REDCapR::constant("data_export_rights_deidentified")  # Returns 1L
        #> [1] 1
        REDCapR::constant("data_export_rights_full"        )  # Returns 2L
        #> [1] 2
        
+REDCapR::constant("form_rights_no_access")   # Returns 0L
        #> [1] 0
        REDCapR::constant("form_rights_readonly" )   # Returns 2L --Notice the order
        #> [1] 2
        REDCapR::constant("form_rights_edit_form")   # Returns 1L
        #> [1] 1
        REDCapR::constant("form_rights_edit_survey") # Returns 3L
        #> [1] 3
        
+REDCapR::constant("access_no" )  # Returns 0L
        #> [1] 0
        REDCapR::constant("access_yes")  # Returns 1L
        #> [1] 1
        
+REDCapR::constant(c(
   "form_complete",
   "form_complete",
   "form_incomplete"
-)) # Returns c(2L, 2L, 0L)
        #> [1] 2 2 0
        REDCapR::constant(c(
+)) # Returns c(2L, 2L, 0L)
        #> [1] 2 2 0
        REDCapR::constant(c(
   "form_rights_no_access",
   "form_rights_readonly",
   "form_rights_edit_form",
@@ -238,22 +223,15 @@ 
        Examp
 #     {'form_complete','form_incomplete','form_unverified'},
 #     but is {'bad-name'}.
 
-REDCapR::constant("bad-name")    # Returns an error
+REDCapR::constant("bad-name")    # Returns an error
 
-REDCapR::constant(c("form_complete", "bad-name")) # Returns an error
+REDCapR::constant(c("form_complete", "bad-name")) # Returns an error
 }
        
   
        
-  
 
@@ -264,7 +242,7 @@ 
        Author
      • -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/create_batch_glossary.html b/docs/reference/create_batch_glossary.html index a170181f..ed2b7a9b 100644 --- a/docs/reference/create_batch_glossary.html +++ b/docs/reference/create_batch_glossary.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -56,8 +60,7 @@ multiple, smaller REDCap calls. The goal is to (1) reduce the chance of time-outs, and (2) introduce little breaks between batches so that the server isn't continually tied up." /> - - + @@ -75,7 +78,7 @@ - +
      @@ -104,26 +107,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -131,7 +116,7 @@
      • - + @@ -211,12 +196,12 @@

        See a

        See redcap_read() for a function that uses create_batch_gloassary.

        Examples

        - 
        REDCapR::create_batch_glossary(100, 50)
        #>   id start_index stop_index index_pretty start_index_pretty stop_index_pretty
+    
        REDCapR::create_batch_glossary(100, 50)
        #>   id start_index stop_index index_pretty start_index_pretty stop_index_pretty
 #> 1  1           1         50            1                001               050
 #> 2  2          51        100            2                051               100
 #>       label
 #> 1 1_001_050
-#> 2 2_051_100
        REDCapR::create_batch_glossary(100, 25)
        #>   id start_index stop_index index_pretty start_index_pretty stop_index_pretty
+#> 2 2_051_100
        REDCapR::create_batch_glossary(100, 25)
        #>   id start_index stop_index index_pretty start_index_pretty stop_index_pretty
 #> 1  1           1         25            1                001               025
 #> 2  2          26         50            2                026               050
 #> 3  3          51         75            3                051               075
@@ -225,7 +210,7 @@ 
        Examp
 #> 1 1_001_025
 #> 2 2_026_050
 #> 3 3_051_075
-#> 4 4_076_100
        REDCapR::create_batch_glossary(100, 3)
        #>    id start_index stop_index index_pretty start_index_pretty stop_index_pretty
+#> 4 4_076_100
        REDCapR::create_batch_glossary(100, 3)
        #>    id start_index stop_index index_pretty start_index_pretty stop_index_pretty
 #> 1   1           1          3           01                001               003
 #> 2   2           4          6           02                004               006
 #> 3   3           7          9           03                007               009
@@ -299,7 +284,7 @@ 
        Examp
   iv        = sample(x=4, size=100, replace=TRUE),
   dv        = rnorm(n=100)
 )
-REDCapR::create_batch_glossary(nrow(d), batch_size=40)
        #>   id start_index stop_index index_pretty start_index_pretty stop_index_pretty
+REDCapR::create_batch_glossary(nrow(d), batch_size=40)
        #>   id start_index stop_index index_pretty start_index_pretty stop_index_pretty
 #> 1  1           1         40            1                001               040
 #> 2  2          41         80            2                041               080
 #> 3  3          81        100            3                081               100
@@ -308,18 +293,10 @@ 
        Examp
 #> 2 2_041_080
 #> 3 3_081_100
        
   
        
-  
 
@@ -330,7 +307,7 @@ 
        Author
      • -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/index.html b/docs/reference/index.html index 95576147..b561a209 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,15 +46,14 @@ - + - - + @@ -68,7 +71,7 @@ - +
      @@ -97,26 +100,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -124,7 +109,7 @@
      • - @@ -383,7 +394,7 @@

      Contents

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/kernel_api.html b/docs/reference/kernel_api.html index 58d2d5b8..4f195924 100644 --- a/docs/reference/kernel_api.html +++ b/docs/reference/kernel_api.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,8 +55,7 @@ - - + @@ -70,7 +73,7 @@ - +
      @@ -99,26 +102,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -126,7 +111,7 @@
      • - + @@ -216,11 +201,11 @@

        Examp content = 'project', format = 'csv' ) -kernel <- REDCapR:::kernel_api(uri, post_body, config_options) +kernel <- REDCapR:::kernel_api(uri, post_body, config_options) # Consume the results in a few different ways. kernel$result

      • #> Response [https://bbmc.ouhsc.edu/redcap/api/] -#> Date: 2020-02-18 16:35 +#> Date: 2020-04-19 18:31 #> Status: 200 #> Content-Type: text/csv; charset=utf-8 #> Size: 557 B @@ -312,15 +297,10 @@

      Examp #> [1] 0 #>

      - @@ -331,7 +311,7 @@

      Contents

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/metadata_utilities.html b/docs/reference/metadata_utilities.html index 235650b2..d0081f5a 100644 --- a/docs/reference/metadata_utilities.html +++ b/docs/reference/metadata_utilities.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,8 +55,7 @@ - - + @@ -70,7 +73,7 @@ - +
      @@ -99,26 +102,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -126,7 +111,7 @@
      • - + @@ -226,7 +211,7 @@

        Examp "6, Unknown / Not Reported") # This calls the general function, and requires the correct regex pattern. -REDCapR::regex_named_captures(pattern=pattern_boxes, text=choices_1)

      • #> id label +REDCapR::regex_named_captures(pattern=pattern_boxes, text=choices_1)
      #> id label #> 1 1 American Indian/Alaska Native #> 2 2 Asian #> 3 3 Native Hawaiian or Other Pacific Islander @@ -234,7 +219,7 @@

      Examp #> 5 5 White #> 6 6 Unknown / Not Reported

      # This function is designed specifically for the checkbox values. -REDCapR::checkbox_choices(select_choices=choices_1)
      #> id label +REDCapR::checkbox_choices(select_choices=choices_1)
      #> id label #> 1 1 American Indian/Alaska Native #> 2 2 Asian #> 3 3 Native Hawaiian or Other Pacific Islander @@ -248,13 +233,13 @@

      Examp ds_metadata <- redcap_metadata_read(redcap_uri=uri, token=token)$data choices_2 <- ds_metadata[ds_metadata$field_name=="race", "select_choices_or_calculations"] -REDCapR::regex_named_captures(pattern=pattern_boxes, text=choices_2) +REDCapR::regex_named_captures(pattern=pattern_boxes, text=choices_2) } path_3 <- system.file(package="REDCapR", "test-data/project-simple/simple-metadata.csv") ds_metadata_3 <- read.csv(path_3, stringsAsFactors=FALSE) choices_3 <- ds_metadata_3[ds_metadata_3$field_name=="race", "select_choices_or_calculations"] -REDCapR::regex_named_captures(pattern=pattern_boxes, text=choices_3)

      #> id label +REDCapR::regex_named_captures(pattern=pattern_boxes, text=choices_3)
      #> id label #> 1 1 American Indian/Alaska Native #> 2 2 Asian #> 3 3 Native Hawaiian or Other Pacific Islander @@ -262,18 +247,10 @@

      Examp #> 5 5 White #> 6 6 Unknown / Not Reported

      - @@ -284,7 +261,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_column_sanitize.html b/docs/reference/redcap_column_sanitize.html index f295d152..8001f4d5 100644 --- a/docs/reference/redcap_column_sanitize.html +++ b/docs/reference/redcap_column_sanitize.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,8 +55,7 @@ - - + @@ -70,7 +73,7 @@ - +
      @@ -99,26 +102,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -126,7 +111,7 @@
      • - + @@ -213,22 +198,15 @@

        Examp names = c("Ekstr\xf8m", "J\xf6reskog", "bi\xdfchen Z\xfcrcher") ) -REDCapR::redcap_column_sanitize(dirty)

      • #> id names +REDCapR::redcap_column_sanitize(dirty)
      #> id names #> 1 1 Ekstrom #> 2 2 Joreskog #> 3 3 bisschen Zurcher
      - @@ -239,7 +217,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_download_file_oneshot.html b/docs/reference/redcap_download_file_oneshot.html index f06e2360..f8776549 100644 --- a/docs/reference/redcap_download_file_oneshot.html +++ b/docs/reference/redcap_download_file_oneshot.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -167,6 +152,8 @@

        Download a file from a REDCap project record

        record, field, event = "", + repeat_instrument = NULL, + repeat_instance = NULL, verbose = TRUE, config_options = NULL ) @@ -212,6 +199,19 @@

        Arg event

        The name of the event where the file is saved in REDCap. +Optional

        + + + repeat_instrument +

        The name of the instrument that is repeating +for a given event. +Optional

        + + + repeat_instance +

        (only for projects with repeating instruments/events) +The repeat instance number of the repeating event (if longitudinal) or the +repeating instrument (if classic or longitudinal). Default value is '1'. Optional

        @@ -268,7 +268,7 @@

        Examp field <- "mugshot" # event <- "" # only for longitudinal projects -result_1 <- REDCapR::redcap_download_file_oneshot( +result_1 <- REDCapR::redcap_download_file_oneshot( record = record, field = field, redcap_uri = uri, @@ -277,7 +277,7 @@

        Examp base::unlink("mugshot-1.jpg") (full_name <- base::tempfile(pattern="mugshot", fileext=".jpg")) -result_2 <- REDCapR::redcap_download_file_oneshot( +result_2 <- REDCapR::redcap_download_file_oneshot( file_name = full_name, record = record, field = field, @@ -287,7 +287,7 @@

        Examp base::unlink(full_name) (relative_name <- "ssss.jpg") -result_3 <- REDCapR::redcap_download_file_oneshot( +result_3 <- REDCapR::redcap_download_file_oneshot( file_name = relative_name, record = record, field = field, @@ -297,18 +297,10 @@

        Examp base::unlink(relative_name) }

      • - @@ -319,7 +311,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_download_instrument.html b/docs/reference/redcap_download_instrument.html index 2e041fd2..2b854bc8 100644 --- a/docs/reference/redcap_download_instrument.html +++ b/docs/reference/redcap_download_instrument.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -268,7 +253,7 @@

        Examp # event <- "" # only for longitudinal projects (full_name <- base::temp(pattern="instruments-all-records-all", fileext=".pdf")) -result_1 <- REDCapR::redcap_download_instrument( +result_1 <- REDCapR::redcap_download_instrument( file_name = full_name, redcap_uri = uri, token = token @@ -276,7 +261,7 @@

        Examp base::unlink(full_name) (full_name <- base::tempfile(pattern="instruments-all-record-1-", fileext=".pdf")) -result_2 <- REDCapR::redcap_download_instrument( +result_2 <- REDCapR::redcap_download_instrument( record = 5, file_name = full_name, redcap_uri = uri, @@ -284,7 +269,7 @@

        Examp ) base::unlink(full_name) (full_name <- base::tempfile(pattern="instrument-1-record-1-", fileext=".pdf")) -result_3 <- REDCapR::redcap_download_instrument( +result_3 <- REDCapR::redcap_download_instrument( record = 5, instrument = "health", file_name = full_name, @@ -294,18 +279,10 @@

        Examp base::unlink(full_name) }

      • - @@ -316,7 +293,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_metadata_read.html b/docs/reference/redcap_metadata_read.html index 15d9406a..d03c3248 100644 --- a/docs/reference/redcap_metadata_read.html +++ b/docs/reference/redcap_metadata_read.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,8 +56,7 @@ - - + @@ -71,7 +74,7 @@ - +
      @@ -100,26 +103,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -127,7 +112,7 @@
      • - + @@ -262,21 +247,13 @@

        Examp 
        if (FALSE) {
 uri   <- "https://bbmc.ouhsc.edu/redcap/api/"
 token <- "9A81268476645C4E5F03428B8AC3AA7B"
-REDCapR::redcap_metadata_read(redcap_uri=uri, token=token)
+REDCapR::redcap_metadata_read(redcap_uri=uri, token=token)
 }

      • - @@ -287,7 +264,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_metadata_write.html b/docs/reference/redcap_metadata_write.html index 638098b6..50dc1b30 100644 --- a/docs/reference/redcap_metadata_write.html +++ b/docs/reference/redcap_metadata_write.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,8 +56,7 @@ - - + @@ -71,7 +74,7 @@ - +
      @@ -100,26 +103,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -127,7 +112,7 @@
      • - + @@ -245,24 +230,17 @@

        Examp ds_to_write # Import the dictionary into the REDCap project -REDCapR::redcap_metadata_write( +REDCapR::redcap_metadata_write( ds = ds_to_write, redcap_uri = uri, token = token ) }

      • - @@ -273,7 +251,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_next_free_record_name.html b/docs/reference/redcap_next_free_record_name.html index 34a2742e..5d146e09 100644 --- a/docs/reference/redcap_next_free_record_name.html +++ b/docs/reference/redcap_next_free_record_name.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -233,18 +218,12 @@

        Examp 
        uri      <- "https://bbmc.ouhsc.edu/redcap/api/"
 token    <- "9A81268476645C4E5F03428B8AC3AA7B"
 # Returns 6
-REDCapR::redcap_next_free_record_name(redcap_uri = uri, token = token)
        #> The next free record name in REDCap was successfully determined in 0.2 seconds.  The http status code was 200.  Is is 6.
        #> [1] "6"
        +REDCapR::redcap_next_free_record_name(redcap_uri = uri, token = token)

      • #> The next free record name in REDCap was successfully determined in 0.2 seconds. The http status code was 200. Is is 6.
      #> [1] "6"
      - @@ -255,7 +234,7 @@

      Contents

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_project.html b/docs/reference/redcap_project.html index b11cb20b..1d59fbe5 100644 --- a/docs/reference/redcap_project.html +++ b/docs/reference/redcap_project.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,8 +57,7 @@ Once some values are set that are specific to a REDCap project (such as the URI and token), later calls are less verbose (such as reading and writing data)." /> - - + @@ -72,7 +75,7 @@ - +
      @@ -101,26 +104,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -128,7 +113,7 @@
      • - + @@ -170,7 +155,7 @@

        Fields +
        redcap_uri

        The URI (uniform resource identifier) of the REDCap project. Required.

        @@ -182,7 +167,7 @@

        Methods -
        +
        read( batch_size = 100L, interbatch_delay = 0, @@ -221,7 +206,7 @@

        Examp 
        uri     <- "https://bbmc.ouhsc.edu/redcap/api/"
 token   <- "D70F9ACD1EDD6F151C6EA78683944E98"
 if (FALSE) {
-project <- REDCapR::redcap_project$new(redcap_uri=uri, token=token)
+project <- REDCapR::redcap_project$new(redcap_uri=uri, token=token)
 ds_all  <- project$read()
 
 # Demonstrate how repeated calls are more concise when the token and
@@ -244,14 +229,10 @@ 
        Examp
 project$write(ds_skinny)
 }

      • - @@ -262,7 +243,7 @@

      Contents

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_read.html b/docs/reference/redcap_read.html index 99dcf3bd..5d10d3c5 100644 --- a/docs/reference/redcap_read.html +++ b/docs/reference/redcap_read.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -57,8 +61,7 @@ (among other objects) a single base::data.frame(). This function can be more appropriate than redcap_read_oneshot() when returning large datasets that could tie up the server." /> - - + @@ -76,7 +79,7 @@ - +
      @@ -105,26 +108,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -132,7 +117,7 @@
      • - + @@ -403,7 +388,7 @@

        Examp 
        if (FALSE) {
 uri     <- "https://bbmc.ouhsc.edu/redcap/api/"
 token   <- "9A81268476645C4E5F03428B8AC3AA7B"
-REDCapR::redcap_read(batch_size=2, redcap_uri=uri, token=token)$data
+REDCapR::redcap_read(batch_size=2, redcap_uri=uri, token=token)$data
 
 # Specify the column types.
 col_types <- readr::cols(
@@ -415,7 +400,7 @@ 
        Examp
   race___5   = readr::col_logical(),
   race___6   = readr::col_logical()
 )
-REDCapR::redcap_read(
+REDCapR::redcap_read(
   redcap_uri = uri,
   token      = token,
   col_types  = col_types,
@@ -424,18 +409,10 @@ 
        Examp
 
 }

      • - @@ -446,7 +423,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_read_oneshot.html b/docs/reference/redcap_read_oneshot.html index 27a79d1c..4506be18 100644 --- a/docs/reference/redcap_read_oneshot.html +++ b/docs/reference/redcap_read_oneshot.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -350,11 +335,11 @@

        Examp token <- "9A81268476645C4E5F03428B8AC3AA7B" #Return all records and all variables. -ds <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token)$data +ds <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token)$data #Return only records with IDs of 1 and 3 desired_records_v1 <- c(1, 3) -ds_some_rows_v1 <- REDCapR::redcap_read_oneshot( +ds_some_rows_v1 <- REDCapR::redcap_read_oneshot( redcap_uri = uri, token = token, records = desired_records_v1 @@ -362,7 +347,7 @@

        Examp #Return only the fields record_id, name_first, and age desired_fields_v1 <- c("record_id", "name_first", "age") -ds_some_fields_v1 <- REDCapR::redcap_read_oneshot( +ds_some_fields_v1 <- REDCapR::redcap_read_oneshot( redcap_uri = uri, token = token, fields = desired_fields_v1 @@ -379,7 +364,7 @@

        Examp race___5 = readr::col_logical(), race___6 = readr::col_logical() ) -ds_col_types <- REDCapR::redcap_read_oneshot( +ds_col_types <- REDCapR::redcap_read_oneshot( redcap_uri = uri, token = token, col_types = col_types @@ -387,18 +372,10 @@

        Examp }

      • - @@ -409,7 +386,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_read_oneshot_eav.html b/docs/reference/redcap_read_oneshot_eav.html index d17dcf8c..80b46918 100644 --- a/docs/reference/redcap_read_oneshot_eav.html +++ b/docs/reference/redcap_read_oneshot_eav.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,8 +55,7 @@ - - + @@ -70,7 +73,7 @@ - +
      @@ -99,26 +102,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -126,7 +111,7 @@
      • - + @@ -322,11 +307,11 @@

        Examp token <- "9A81268476645C4E5F03428B8AC3AA7B" #Return all records and all variables. -ds <- REDCapR:::redcap_read_oneshot_eav(redcap_uri=uri, token=token)$data +ds <- REDCapR:::redcap_read_oneshot_eav(redcap_uri=uri, token=token)$data #Return only records with IDs of 1 and 3 desired_records_v1 <- c(1, 3) -ds_some_rows_v1 <- REDCapR::redcap_read_oneshot_eav( +ds_some_rows_v1 <- REDCapR::redcap_read_oneshot_eav( redcap_uri = uri, token = token, records = desired_records_v1 @@ -341,18 +326,10 @@

        Examp )$data }

      • - @@ -363,7 +340,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_survey_link_export_oneshot.html b/docs/reference/redcap_survey_link_export_oneshot.html index 05148c80..728d1100 100644 --- a/docs/reference/redcap_survey_link_export_oneshot.html +++ b/docs/reference/redcap_survey_link_export_oneshot.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -252,7 +237,7 @@

        Examp instrument <- "participant_morale_questionnaire" # event <- "" # only for longitudinal projects -result <- REDCapR::redcap_survey_link_export_oneshot( +result <- REDCapR::redcap_survey_link_export_oneshot( record = record, instrument = instrument, redcap_uri = uri, @@ -261,18 +246,10 @@

        Examp result$survey_link }

      • - @@ -283,7 +260,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_upload_file_oneshot.html b/docs/reference/redcap_upload_file_oneshot.html index 56fcc80b..8e6b6ebc 100644 --- a/docs/reference/redcap_upload_file_oneshot.html +++ b/docs/reference/redcap_upload_file_oneshot.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -257,7 +242,7 @@

        Examp record <- 1 file_path <- system.file("test-data/mugshot-1.jpg", package="REDCapR") -REDCapR::redcap_upload_file_oneshot( +REDCapR::redcap_upload_file_oneshot( file_name = file_path, record = record, field = field, @@ -275,7 +260,7 @@

        Examp for (i in seq_along(records)) { record <- records[i] file_path <- file_paths[i] - REDCapR::redcap_upload_file_oneshot( + REDCapR::redcap_upload_file_oneshot( file_name = file_path, record = record, field = field, @@ -285,18 +270,10 @@

        Examp } }

      • - @@ -307,7 +284,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_users_export.html b/docs/reference/redcap_users_export.html index bf1520d2..0275268a 100644 --- a/docs/reference/redcap_users_export.html +++ b/docs/reference/redcap_users_export.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -204,34 +189,29 @@

        Note

        Examples

        uri      <- "https://bbmc.ouhsc.edu/redcap/api/"
 token    <- "06DEFB601F9B46847DAA9DF0CFA951B4"
-result   <- REDCapR::redcap_users_export(redcap_uri=uri, token=token)
        #> The REDCap users were successfully exported in 0.3 seconds.  The http status code was 200.
        result$data_user
        #> # A tibble: 2 x 31
+result   <- REDCapR::redcap_users_export(redcap_uri=uri, token=token)
        #> The REDCap users were successfully exported in 0.2 seconds.  The http status code was 200.
        result$data_user
        #> # A tibble: 2 x 31
 #>   username email firstname lastname expiration data_access_gro… data_access_gro…
 #>   <chr>    <chr> <chr>     <chr>    <date>     <chr>            <chr>           
 #> 1 unittes… wibe… Unit Test PHI Free NA         daga             331             
 #> 2 wbeasle… will… Will      Beasley… NA         NA               NA              
-#> # … with 24 more variables: design <lgl>, user_rights <lgl>,
-#> #   data_access_groups <lgl>, data_export <chr>, reports <lgl>,
-#> #   stats_and_charts <lgl>, manage_survey_participants <lgl>, calendar <lgl>,
-#> #   data_import_tool <lgl>, data_comparison_tool <lgl>, logging <lgl>,
-#> #   file_repository <lgl>, data_quality_create <lgl>,
-#> #   data_quality_execute <lgl>, api_export <lgl>, api_import <lgl>,
-#> #   mobile_app <lgl>, mobile_app_download_data <lgl>, record_create <lgl>,
-#> #   record_rename <lgl>, record_delete <lgl>, lock_records_all_forms <lgl>,
-#> #   lock_records <lgl>, lock_records_customization <lgl>
        result$data_user_form
        #> # A tibble: 2 x 4
+#> # … with 24 more variables: design <lgl>, user_rights <lgl>,
+#> #   data_access_groups <lgl>, data_export <chr>, reports <lgl>,
+#> #   stats_and_charts <lgl>, manage_survey_participants <lgl>, calendar <lgl>,
+#> #   data_import_tool <lgl>, data_comparison_tool <lgl>, logging <lgl>,
+#> #   file_repository <lgl>, data_quality_create <lgl>,
+#> #   data_quality_execute <lgl>, api_export <lgl>, api_import <lgl>,
+#> #   mobile_app <lgl>, mobile_app_download_data <lgl>, record_create <lgl>,
+#> #   record_rename <lgl>, record_delete <lgl>, lock_records_all_forms <lgl>,
+#> #   lock_records <lgl>, lock_records_customization <lgl>
        result$data_user_form
        #> # A tibble: 2 x 4
 #>   username        form_name    permission_id permission
 #>   <chr>           <chr>                <int> <fct>     
 #> 1 unittestphifree demographics             1 edit_form 
 #> 2 wbeasleya       demographics             1 edit_form
      • - @@ -242,7 +222,7 @@

      Contents

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_variables.html b/docs/reference/redcap_variables.html index 91da6971..94c9b1d9 100644 --- a/docs/reference/redcap_variables.html +++ b/docs/reference/redcap_variables.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -51,8 +55,7 @@ - - + @@ -70,7 +73,7 @@ - +
      @@ -99,26 +102,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -126,7 +111,7 @@
      • - + @@ -228,21 +213,13 @@

        Examp 
        if (FALSE) {
 uri         <- "https://bbmc.ouhsc.edu/redcap/api/"
 token       <- "9A81268476645C4E5F03428B8AC3AA7B"
-ds_variable <- REDCapR::redcap_variables(redcap_uri=uri, token=token)$data
+ds_variable <- REDCapR::redcap_variables(redcap_uri=uri, token=token)$data
 }

      • - @@ -253,7 +230,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_version.html b/docs/reference/redcap_version.html index 8c370e06..4aea7636 100644 --- a/docs/reference/redcap_version.html +++ b/docs/reference/redcap_version.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -201,17 +186,12 @@

        Details

        Examples

        uri      <- "https://bbmc.ouhsc.edu/redcap/api/"
 token    <- "9A81268476645C4E5F03428B8AC3AA7B"
-REDCapR::redcap_version(redcap_uri = uri, token = token)
        #> The REDCap version was successfully determined in 0.3 seconds. The http status code was 200.  Is is 9.0.0.
        #> [1] ‘9.0.0’
        +REDCapR::redcap_version(redcap_uri = uri, token = token)
      • #> The REDCap version was successfully determined in 0.2 seconds. The http status code was 200. Is is 9.0.0.
      #> [1] ‘9.0.0’
      - @@ -222,7 +202,7 @@

      Contents

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_write.html b/docs/reference/redcap_write.html index 979b7212..9a452dcb 100644 --- a/docs/reference/redcap_write.html +++ b/docs/reference/redcap_write.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -263,7 +248,7 @@

        Examp token <- "D70F9ACD1EDD6F151C6EA78683944E98" # Read the dataset for the first time. -result_read1 <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token) +result_read1 <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token) ds1 <- result_read1$data ds1$telephone @@ -272,10 +257,10 @@

        Examp ds1 <- ds1[1:3, ] ds1$age <- NULL; ds1$bmi <- NULL #Drop the calculated fields before writing. -result_write <- REDCapR::redcap_write(ds=ds1, redcap_uri=uri, token=token) +result_write <- REDCapR::redcap_write(ds=ds1, redcap_uri=uri, token=token) # Read the dataset for the second time. -result_read2 <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token) +result_read2 <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token) ds2 <- result_read2$data ds2$telephone @@ -283,22 +268,14 @@

        Examp ds1$telephone <- paste0("(405) 321-000", seq_len(nrow(ds1))) # This next line will throw an error. -result_write <- REDCapR::redcap_write(ds=ds1, redcap_uri=uri, token=token) +result_write <- REDCapR::redcap_write(ds=ds1, redcap_uri=uri, token=token) result_write$raw_text }

      • - @@ -309,7 +286,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/redcap_write_oneshot.html b/docs/reference/redcap_write_oneshot.html index 6bf5503f..4f96faa1 100644 --- a/docs/reference/redcap_write_oneshot.html +++ b/docs/reference/redcap_write_oneshot.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -50,8 +54,7 @@ - - + @@ -69,7 +72,7 @@ - +
      @@ -98,26 +101,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -125,7 +110,7 @@
      • - + @@ -237,7 +222,7 @@

        Examp token <- "D70F9ACD1EDD6F151C6EA78683944E98" # Read the dataset for the first time. -result_read1 <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token) +result_read1 <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token) ds1 <- result_read1$data ds1$telephone @@ -246,10 +231,10 @@

        Examp ds1 <- ds1[1:3, ] ds1$age <- NULL; ds1$bmi <- NULL #Drop the calculated fields before writing. -result_write <- REDCapR::redcap_write_oneshot(ds=ds1, redcap_uri=uri, token=token) +result_write <- REDCapR::redcap_write_oneshot(ds=ds1, redcap_uri=uri, token=token) # Read the dataset for the second time. -result_read2 <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token) +result_read2 <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token) ds2 <- result_read2$data ds2$telephone @@ -257,22 +242,14 @@

        Examp ds1$telephone <- paste0("(405) 321-000", seq_len(nrow(ds1))) # This next line will throw an error. -result_write <- REDCapR::redcap_write_oneshot(ds=ds1, redcap_uri=uri, token=token) +result_write <- REDCapR::redcap_write_oneshot(ds=ds1, redcap_uri=uri, token=token) result_write$raw_text }

      • - @@ -283,7 +260,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/replace_nas_with_explicit.html b/docs/reference/replace_nas_with_explicit.html index b1fbc08e..68fd9dab 100644 --- a/docs/reference/replace_nas_with_explicit.html +++ b/docs/reference/replace_nas_with_explicit.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -53,8 +57,7 @@ This explicit assignment can reduce the chances that missing values are inadvertently ignored. It also allows the presence of a missing to become a predictor in models." /> - - + @@ -72,7 +75,7 @@ - +
      @@ -101,26 +104,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -128,7 +113,7 @@
      • - + @@ -210,17 +195,10 @@

        Note

        Examples

        library(REDCapR) #Load the package into the current R session.
      • - @@ -231,7 +209,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/retrieve_credential.html b/docs/reference/retrieve_credential.html index 5b6abb9a..62495a60 100644 --- a/docs/reference/retrieve_credential.html +++ b/docs/reference/retrieve_credential.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -53,8 +57,7 @@ database or file — retrieve_credential" /> - - + @@ -72,7 +75,7 @@ - +
      @@ -101,26 +104,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -128,7 +113,7 @@
      • - + @@ -252,7 +237,7 @@

        Note

        Examples

        # ---- Local File Example ----------------------------
 path <- system.file("misc/example.credentials", package = "REDCapR")
-(p1  <- REDCapR::retrieve_credential_local(path, 153L))
        #> $redcap_uri
+(p1  <- REDCapR::retrieve_credential_local(path, 153L))
        #> $redcap_uri
 #> [1] "https://bbmc.ouhsc.edu/redcap/api/"
 #> 
 #> $username
@@ -266,7 +251,7 @@ 
        Examp
 #> 
 #> $comment
 #> [1] "simple static (read-only) test project"
-#> 
        (p2  <- REDCapR::retrieve_credential_local(path, 212L))
        #> $redcap_uri
+#> 
        (p2  <- REDCapR::retrieve_credential_local(path, 212L))
        #> $redcap_uri
 #> [1] "https://bbmc.ouhsc.edu/redcap/api/"
 #> 
 #> $username
@@ -282,18 +267,10 @@ 
        Examp
 #> [1] "longitudinal (read-only) ARM test project"
 #>
      • - @@ -304,7 +281,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/sanitize_token.html b/docs/reference/sanitize_token.html index cab9374f..c3744d7b 100644 --- a/docs/reference/sanitize_token.html +++ b/docs/reference/sanitize_token.html @@ -17,23 +17,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,7 @@ - + @@ -52,8 +56,7 @@ - - + @@ -71,7 +74,7 @@ - +
      @@ -100,26 +103,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -127,7 +112,7 @@
      • - + @@ -184,19 +169,12 @@

        Note

        Examples

        secret_token_1 <- "12345678901234567890123456ABCDEF"
 secret_token_2 <- "12345678901234567890123456ABCDEF\n"
-REDCapR::sanitize_token(secret_token_1)
        #> [1] "12345678901234567890123456ABCDEF"
        REDCapR::sanitize_token(secret_token_2)
        #> [1] "12345678901234567890123456ABCDEF"
        +REDCapR::sanitize_token(secret_token_1)
      • #> [1] "12345678901234567890123456ABCDEF"
      REDCapR::sanitize_token(secret_token_2)
      #> [1] "12345678901234567890123456ABCDEF"
      - @@ -207,7 +185,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.

      diff --git a/docs/reference/validate.html b/docs/reference/validate.html index bc972298..98e30b5b 100644 --- a/docs/reference/validate.html +++ b/docs/reference/validate.html @@ -18,23 +18,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,7 @@ - + @@ -53,8 +57,7 @@ writing to a REDCap project — validate" /> - - + @@ -72,7 +75,7 @@ - +
      @@ -101,26 +104,8 @@
    • Reference
      • -
    • - - +
    • + Articles
    • Changelog @@ -128,7 +113,7 @@
      • - + @@ -249,24 +234,16 @@

        Examp flag_logical = c(TRUE, TRUE, FALSE, TRUE), flag_Uppercase = c(4, 6, 8, 2) ) -REDCapR::validate_for_write(d = d)

      • #> # A tibble: 2 x 4 +REDCapR::validate_for_write(d = d)
      #> # A tibble: 2 x 4 #> field_name field_index concern suggestion #> <chr> <int> <chr> <chr> #> 1 flag_logical 2 The REDCap API does not … Convert the variable with … #> 2 flag_Upperc… 3 A REDCap project does no… Change the uppercase lette…
      - @@ -277,7 +254,7 @@

      Author

      -

      Site built with pkgdown 1.4.1.

      +

      Site built with pkgdown 1.5.0.