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expose export_blankforgray_form_status #389

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Aug 14, 2022
Merged

expose export_blankforgray_form_status #389

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499c2ed
updated redcap_read... functions to expose export_blankforgray_form_s…
Mar 9, 2022
2c4ff75
Merge branch 'dev' into dev2
wibeasley Aug 13, 2022
76b1784
adding tests for blank_for_gray
wibeasley Aug 14, 2022
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11 changes: 10 additions & 1 deletion R/redcap-read-oneshot-eav.R
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Expand Up @@ -55,6 +55,12 @@
#' (https://stat.ethz.ch/R-manual/R-devel/library/base/html/as.POSIXlt.html)
#' value.
#' If not specified, REDCap will assume no end time.
#' @param export_blankforgray_form_status A boolean value that specifies whether
#' or not to export blank values for instrument complete status fields that have
#' a gray status icon. All instrument complete status fields having a gray icon
#' can be exported either as a blank value or as "0" (Incomplete). Blank values
#' are recommended in a data export if the data will be re-imported into a
#' REDCap project. Default is `FALSE`.
#'
#' @param verbose A boolean value indicating if `message`s should be printed
#' to the R console during the operation. The verbose output might contain
Expand Down Expand Up @@ -155,6 +161,7 @@ redcap_read_oneshot_eav <- function(
filter_logic = "",
datetime_range_begin = as.POSIXct(NA),
datetime_range_end = as.POSIXct(NA),
export_blankforgray_form_status = FALSE,

# placeholder: guess_type
# placeholder: guess_max
Expand Down Expand Up @@ -183,6 +190,7 @@ redcap_read_oneshot_eav <- function(
checkmate::assert_character(filter_logic , any.missing=FALSE, len=1, pattern="^.{0,}$")
checkmate::assert_posixct( datetime_range_begin , any.missing=TRUE , len=1, null.ok=TRUE)
checkmate::assert_posixct( datetime_range_end , any.missing=TRUE , len=1, null.ok=TRUE)
checkmate::assert_logical(export_blankforgray_form_status , any.missing=FALSE, len=1)

# placeholder: checkmate::assert_logical( guess_type , any.missing=FALSE, len=1)
# placeholder: checkmate::assert_integerish(guess_max , any.missing=FALSE, len=1, lower=1)
Expand Down Expand Up @@ -215,7 +223,8 @@ redcap_read_oneshot_eav <- function(
exportDataAccessGroups = export_data_access_groups,
filterLogic = filter_logic,
dateRangeBegin = datetime_range_begin,
dateRangeEnd = datetime_range_end
dateRangeEnd = datetime_range_end,
exportBlankForGrayFormStatus = export_blankforgray_form_status
# record, fields, forms & events are specified below
)

Expand Down
12 changes: 11 additions & 1 deletion R/redcap-read-oneshot.R
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Expand Up @@ -58,6 +58,13 @@
#' [POSIXct](https://stat.ethz.ch/R-manual/R-devel/library/base/html/as.POSIXlt.html)
#' value.
#' If not specified, REDCap will assume no end time.
#' @param export_blankforgray_form_status A boolean value that specifies whether
#' or not to export blank values for instrument complete status fields that have
#' a gray status icon. All instrument complete status fields having a gray icon
#' can be exported either as a blank value or as "0" (Incomplete). Blank values
#' are recommended in a data export if the data will be re-imported into a
#' REDCap project. Default is `FALSE`.
#'
#' @param col_types A [readr::cols()] object passed internally to
#' [readr::read_csv()]. Optional.
#' @param guess_type A boolean value indicating if all columns should be
Expand Down Expand Up @@ -181,6 +188,7 @@ redcap_read_oneshot <- function(
filter_logic = "",
datetime_range_begin = as.POSIXct(NA),
datetime_range_end = as.POSIXct(NA),
export_blankforgray_form_status = FALSE,

col_types = NULL,
guess_type = TRUE,
Expand Down Expand Up @@ -212,6 +220,7 @@ redcap_read_oneshot <- function(
checkmate::assert_character(filter_logic , any.missing=FALSE, len=1, pattern="^.{0,}$")
checkmate::assert_posixct( datetime_range_begin , any.missing=TRUE , len=1, null.ok=TRUE)
checkmate::assert_posixct( datetime_range_end , any.missing=TRUE , len=1, null.ok=TRUE)
checkmate::assert_logical(export_blankforgray_form_status , any.missing=FALSE, len=1)

checkmate::assert_logical( guess_type , any.missing=FALSE, len=1)
checkmate::assert_integerish(guess_max , any.missing=FALSE, len=1, lower=1)
Expand Down Expand Up @@ -249,7 +258,8 @@ redcap_read_oneshot <- function(
exportDataAccessGroups = tolower(as.character(export_data_access_groups)),
filterLogic = filter_logic,
dateRangeBegin = datetime_range_begin,
dateRangeEnd = datetime_range_end
dateRangeEnd = datetime_range_end,
exportBlankForGrayFormStatus = export_blankforgray_form_status
# record, fields, forms & events are specified below
)

Expand Down
11 changes: 11 additions & 0 deletions R/redcap-read.R
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Expand Up @@ -71,6 +71,13 @@
#' [POSIXct](https://stat.ethz.ch/R-manual/R-devel/library/base/html/as.POSIXlt.html)
#' value.
#' If not specified, REDCap will assume no end time.
#' @param export_blankforgray_form_status A boolean value that specifies whether
#' or not to export blank values for instrument complete status fields that have
#' a gray status icon. All instrument complete status fields having a gray icon
#' can be exported either as a blank value or as "0" (Incomplete). Blank values
#' are recommended in a data export if the data will be re-imported into a
#' REDCap project. Default is `FALSE`.
#'
#' @param col_types A [readr::cols()] object passed internally to
#' [readr::read_csv()]. Optional.
#' @param guess_type A boolean value indicating if all columns should be
Expand Down Expand Up @@ -196,6 +203,7 @@ redcap_read <- function(
filter_logic = "",
datetime_range_begin = as.POSIXct(NA),
datetime_range_end = as.POSIXct(NA),
export_blankforgray_form_status = FALSE,

col_types = NULL,
guess_type = TRUE,
Expand Down Expand Up @@ -227,6 +235,7 @@ redcap_read <- function(
checkmate::assert_logical( export_data_access_groups , any.missing=FALSE, len=1)
checkmate::assert_posixct( datetime_range_begin , any.missing=TRUE , len=1, null.ok=TRUE)
checkmate::assert_posixct( datetime_range_end , any.missing=TRUE , len=1, null.ok=TRUE)
checkmate::assert_logical(export_blankforgray_form_status , any.missing=FALSE, len=1)

checkmate::assert_logical( guess_type , any.missing=FALSE, len=1)
if (!is.null(guess_max)) warning("The `guess_max` parameter in `REDCapR::redcap_read()` is deprecated.")
Expand Down Expand Up @@ -278,6 +287,7 @@ redcap_read <- function(
filter_logic = filter_logic,
datetime_range_begin = datetime_range_begin,
datetime_range_end = datetime_range_end,
export_blankforgray_form_status = export_blankforgray_form_status,
guess_type = guess_type,
http_response_encoding = http_response_encoding,
locale = locale,
Expand Down Expand Up @@ -352,6 +362,7 @@ redcap_read <- function(
filter_logic = filter_logic,
datetime_range_begin = datetime_range_begin,
datetime_range_end = datetime_range_end,
export_blankforgray_form_status = export_blankforgray_form_status,

col_types = col_types,
guess_type = FALSE,
Expand Down
1 change: 1 addition & 0 deletions inst/misc/example.credentials
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Expand Up @@ -32,3 +32,4 @@ redcap_uri,username,project_id,token,comment
"https://bbmc.ouhsc.edu/redcap/api/","myusername","2631","D2A6FF48D266C0CFAAED8842CDCC7CED","decimal comma"
"https://bbmc.ouhsc.edu/redcap/api/","myusername","2632","D7DDE242E717619E17F7DF0D3CE582B1","decimal dot"
"https://bbmc.ouhsc.edu/redcap/api/","myusername","2634","8F5313CAA266789F560D79EFCEE2E2F1","Validation Types"
"https://bbmc.ouhsc.edu/redcap/api/","myusername","3003","1F2EC7059AC339DFDCD5800225DC7A95","Blank for Gray Status"
25 changes: 25 additions & 0 deletions inst/test-data/specific-redcapr/read-batch-simple/blank-for-gray-false.R
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structure(list(record_id = c(1, 2, 3, 4, 5, 6), name_first = c("Nutmeg",
"Tumtum", "Marcus", "Trudy", "John Lee", "blank-for-gray"), name_last = c("Nutmouse",
"Nutmouse", "Wood", "DAG", "Walker", "blank-for-gray"), address = c("14 Rose Cottage St.\nKenning UK, 323232",
"14 Rose Cottage Blvd.\nKenning UK 34243", "243 Hill St.\nGuthrie OK 73402",
"342 Elm\nDuncanville TX, 75116", "Hotel Suite\nNew Orleans LA, 70115",
NA), telephone = c("(405) 321-1111", "(405) 321-2222", "(405) 321-3333",
"(405) 321-4444", "(405) 321-5555", NA), email = c("[email protected]",
"[email protected]", "[email protected]", "[email protected]", "[email protected]",
NA), dob = structure(c(12294, 12121, -13051, -6269, -5375, NA
), class = "Date"), age = c(11, 11, 80, 61, 59, NA), sex = c(0,
1, 1, 0, 1, NA), demographics_complete = c(2, 2, 2, 2, 2, 0),
height = c(7, 6, 180, 165, 193.04, NA), weight = c(1, 1,
80, 54, 104, NA), bmi = c(204.1, 277.8, 24.7, 19.8, 27.9,
NA), comments = c("Character in a book, with some guessing",
"A mouse character from a good book", "completely made up",
"This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail",
"Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache",
NA), mugshot = c("mugshot-1.jpg", "mugshot-2.jpg", "mugshot-3.jpg",
"mugshot-4.jpg", "mugshot-5.jpg", NA), health_complete = c(1,
0, 2, 2, 0, 0), race___1 = c(0, 0, 0, 0, 1, 0), race___2 = c(0,
0, 0, 1, 0, 0), race___3 = c(0, 1, 0, 0, 0, 0), race___4 = c(0,
0, 1, 0, 0, 0), race___5 = c(1, 1, 1, 1, 0, 0), race___6 = c(0,
0, 0, 0, 1, 0), ethnicity = c(1, 1, 0, 1, 2, NA), interpreter_needed = c(0,
0, 1, NA, 0, NA), race_and_ethnicity_complete = c(2, 0, 2,
2, 2, 0)), row.names = c(NA, -6L), class = "data.frame")
25 changes: 25 additions & 0 deletions inst/test-data/specific-redcapr/read-batch-simple/blank-for-gray-true.R
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structure(list(record_id = c(1, 2, 3, 4, 5, 6), name_first = c("Nutmeg",
"Tumtum", "Marcus", "Trudy", "John Lee", "blank-for-gray"), name_last = c("Nutmouse",
"Nutmouse", "Wood", "DAG", "Walker", "blank-for-gray"), address = c("14 Rose Cottage St.\nKenning UK, 323232",
"14 Rose Cottage Blvd.\nKenning UK 34243", "243 Hill St.\nGuthrie OK 73402",
"342 Elm\nDuncanville TX, 75116", "Hotel Suite\nNew Orleans LA, 70115",
NA), telephone = c("(405) 321-1111", "(405) 321-2222", "(405) 321-3333",
"(405) 321-4444", "(405) 321-5555", NA), email = c("[email protected]",
"[email protected]", "[email protected]", "[email protected]", "[email protected]",
NA), dob = structure(c(12294, 12121, -13051, -6269, -5375, NA
), class = "Date"), age = c(11, 11, 80, 61, 59, NA), sex = c(0,
1, 1, 0, 1, NA), demographics_complete = c(2, 2, 2, 2, 2, 0),
height = c(7, 6, 180, 165, 193.04, NA), weight = c(1, 1,
80, 54, 104, NA), bmi = c(204.1, 277.8, 24.7, 19.8, 27.9,
NA), comments = c("Character in a book, with some guessing",
"A mouse character from a good book", "completely made up",
"This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail",
"Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache",
NA), mugshot = c("mugshot-1.jpg", "mugshot-2.jpg", "mugshot-3.jpg",
"mugshot-4.jpg", "mugshot-5.jpg", NA), health_complete = c(1,
0, 2, 2, 0, NA), race___1 = c(0, 0, 0, 0, 1, 0), race___2 = c(0,
0, 0, 1, 0, 0), race___3 = c(0, 1, 0, 0, 0, 0), race___4 = c(0,
0, 1, 0, 0, 0), race___5 = c(1, 1, 1, 1, 0, 0), race___6 = c(0,
0, 0, 0, 1, 0), ethnicity = c(1, 1, 0, 1, 2, NA), interpreter_needed = c(0,
0, 1, NA, 0, NA), race_and_ethnicity_complete = c(2, 0, 2,
2, 2, NA)), row.names = c(NA, -6L), class = "data.frame")
28 changes: 28 additions & 0 deletions inst/test-data/specific-redcapr/read-oneshot-eav/blank-for-gray-false.R
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structure(list(record_id = 1:6, name_first = c("Nutmeg", "Tumtum",
"Marcus", "Trudy", "John Lee", "blank-for-gray"), name_last = c("Nutmouse",
"Nutmouse", "Wood", "DAG", "Walker", "blank-for-gray"), address = c("14 Rose Cottage St.\nKenning UK, 323232",
"14 Rose Cottage Blvd.\nKenning UK 34243", "243 Hill St.\nGuthrie OK 73402",
"342 Elm\nDuncanville TX, 75116", "Hotel Suite\nNew Orleans LA, 70115",
NA), telephone = c("(405) 321-1111", "(405) 321-2222", "(405) 321-3333",
"(405) 321-4444", "(405) 321-5555", NA), email = c("[email protected]",
"[email protected]", "[email protected]", "[email protected]", "[email protected]",
NA), dob = c("2003-08-30", "2003-03-10", "1934-04-09", "1952-11-02",
"1955-04-15", NA), age = c(11L, 11L, 80L, 61L, 59L, NA), sex = c(0L,
1L, 1L, 0L, 1L, NA), height = c(7, 6, 180, 165, 193.04, NA),
weight = c(1L, 1L, 80L, 54L, 104L, NA), bmi = c(204.1, 277.8,
24.7, 19.8, 27.9, NA), comments = c("Character in a book, with some guessing",
"A mouse character from a good book", "completely made up",
"This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail",
"Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache",
NA), mugshot = c(324901L, 324902L, 324903L, 324904L, 324905L,
NA), race___1 = c(FALSE, FALSE, FALSE, FALSE, TRUE, FALSE
), race___2 = c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE),
race___3 = c(FALSE, TRUE, FALSE, FALSE, FALSE, FALSE), race___4 = c(FALSE,
FALSE, TRUE, FALSE, FALSE, FALSE), race___5 = c(TRUE, TRUE,
TRUE, TRUE, FALSE, FALSE), race___6 = c(FALSE, FALSE, FALSE,
FALSE, TRUE, FALSE), ethnicity = c(1L, 1L, 0L, 1L, 2L, NA
), interpreter_needed = c(0L, 0L, 1L, NA, 0L, NA), demographics_complete = c(2L,
2L, 2L, 2L, 2L, 0L), health_complete = c(1L, 0L, 2L, 2L,
0L, NA), race_and_ethnicity_complete = c(2L, 0L, 2L, 2L,
2L, NA)), row.names = c(NA, -6L), class = c("tbl_df", "tbl",
"data.frame"))
28 changes: 28 additions & 0 deletions inst/test-data/specific-redcapr/read-oneshot-eav/blank-for-gray-true.R
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structure(list(record_id = 1:6, name_first = c("Nutmeg", "Tumtum",
"Marcus", "Trudy", "John Lee", "blank-for-gray"), name_last = c("Nutmouse",
"Nutmouse", "Wood", "DAG", "Walker", "blank-for-gray"), address = c("14 Rose Cottage St.\nKenning UK, 323232",
"14 Rose Cottage Blvd.\nKenning UK 34243", "243 Hill St.\nGuthrie OK 73402",
"342 Elm\nDuncanville TX, 75116", "Hotel Suite\nNew Orleans LA, 70115",
NA), telephone = c("(405) 321-1111", "(405) 321-2222", "(405) 321-3333",
"(405) 321-4444", "(405) 321-5555", NA), email = c("[email protected]",
"[email protected]", "[email protected]", "[email protected]", "[email protected]",
NA), dob = c("2003-08-30", "2003-03-10", "1934-04-09", "1952-11-02",
"1955-04-15", NA), age = c(11L, 11L, 80L, 61L, 59L, NA), sex = c(0L,
1L, 1L, 0L, 1L, NA), height = c(7, 6, 180, 165, 193.04, NA),
weight = c(1L, 1L, 80L, 54L, 104L, NA), bmi = c(204.1, 277.8,
24.7, 19.8, 27.9, NA), comments = c("Character in a book, with some guessing",
"A mouse character from a good book", "completely made up",
"This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail",
"Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache",
NA), mugshot = c(324901L, 324902L, 324903L, 324904L, 324905L,
NA), race___1 = c(FALSE, FALSE, FALSE, FALSE, TRUE, FALSE
), race___2 = c(FALSE, FALSE, FALSE, TRUE, FALSE, FALSE),
race___3 = c(FALSE, TRUE, FALSE, FALSE, FALSE, FALSE), race___4 = c(FALSE,
FALSE, TRUE, FALSE, FALSE, FALSE), race___5 = c(TRUE, TRUE,
TRUE, TRUE, FALSE, FALSE), race___6 = c(FALSE, FALSE, FALSE,
FALSE, TRUE, FALSE), ethnicity = c(1L, 1L, 0L, 1L, 2L, NA
), interpreter_needed = c(0L, 0L, 1L, NA, 0L, NA), demographics_complete = c(2L,
2L, 2L, 2L, 2L, 0L), health_complete = c(1L, 0L, 2L, 2L,
0L, NA), race_and_ethnicity_complete = c(2L, 0L, 2L, 2L,
2L, NA)), row.names = c(NA, -6L), class = c("tbl_df", "tbl",
"data.frame"))
25 changes: 25 additions & 0 deletions inst/test-data/specific-redcapr/read-oneshot/blank-for-gray-false.R
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structure(list(record_id = c(1, 2, 3, 4, 5, 6), name_first = c("Nutmeg",
"Tumtum", "Marcus", "Trudy", "John Lee", "blank-for-gray"), name_last = c("Nutmouse",
"Nutmouse", "Wood", "DAG", "Walker", "blank-for-gray"), address = c("14 Rose Cottage St.\nKenning UK, 323232",
"14 Rose Cottage Blvd.\nKenning UK 34243", "243 Hill St.\nGuthrie OK 73402",
"342 Elm\nDuncanville TX, 75116", "Hotel Suite\nNew Orleans LA, 70115",
NA), telephone = c("(405) 321-1111", "(405) 321-2222", "(405) 321-3333",
"(405) 321-4444", "(405) 321-5555", NA), email = c("[email protected]",
"[email protected]", "[email protected]", "[email protected]", "[email protected]",
NA), dob = structure(c(12294, 12121, -13051, -6269, -5375, NA
), class = "Date"), age = c(11, 11, 80, 61, 59, NA), sex = c(0,
1, 1, 0, 1, NA), demographics_complete = c(2, 2, 2, 2, 2, 0),
height = c(7, 6, 180, 165, 193.04, NA), weight = c(1, 1,
80, 54, 104, NA), bmi = c(204.1, 277.8, 24.7, 19.8, 27.9,
NA), comments = c("Character in a book, with some guessing",
"A mouse character from a good book", "completely made up",
"This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail",
"Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache",
NA), mugshot = c("mugshot-1.jpg", "mugshot-2.jpg", "mugshot-3.jpg",
"mugshot-4.jpg", "mugshot-5.jpg", NA), health_complete = c(1,
0, 2, 2, 0, 0), race___1 = c(0, 0, 0, 0, 1, 0), race___2 = c(0,
0, 0, 1, 0, 0), race___3 = c(0, 1, 0, 0, 0, 0), race___4 = c(0,
0, 1, 0, 0, 0), race___5 = c(1, 1, 1, 1, 0, 0), race___6 = c(0,
0, 0, 0, 1, 0), ethnicity = c(1, 1, 0, 1, 2, NA), interpreter_needed = c(0,
0, 1, NA, 0, NA), race_and_ethnicity_complete = c(2, 0, 2,
2, 2, 0)), row.names = c(NA, -6L), class = "data.frame")
25 changes: 25 additions & 0 deletions inst/test-data/specific-redcapr/read-oneshot/blank-for-gray-true.R
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structure(list(record_id = c(1, 2, 3, 4, 5, 6), name_first = c("Nutmeg",
"Tumtum", "Marcus", "Trudy", "John Lee", "blank-for-gray"), name_last = c("Nutmouse",
"Nutmouse", "Wood", "DAG", "Walker", "blank-for-gray"), address = c("14 Rose Cottage St.\nKenning UK, 323232",
"14 Rose Cottage Blvd.\nKenning UK 34243", "243 Hill St.\nGuthrie OK 73402",
"342 Elm\nDuncanville TX, 75116", "Hotel Suite\nNew Orleans LA, 70115",
NA), telephone = c("(405) 321-1111", "(405) 321-2222", "(405) 321-3333",
"(405) 321-4444", "(405) 321-5555", NA), email = c("[email protected]",
"[email protected]", "[email protected]", "[email protected]", "[email protected]",
NA), dob = structure(c(12294, 12121, -13051, -6269, -5375, NA
), class = "Date"), age = c(11, 11, 80, 61, 59, NA), sex = c(0,
1, 1, 0, 1, NA), demographics_complete = c(2, 2, 2, 2, 2, 0),
height = c(7, 6, 180, 165, 193.04, NA), weight = c(1, 1,
80, 54, 104, NA), bmi = c(204.1, 277.8, 24.7, 19.8, 27.9,
NA), comments = c("Character in a book, with some guessing",
"A mouse character from a good book", "completely made up",
"This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail",
"Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache",
NA), mugshot = c("mugshot-1.jpg", "mugshot-2.jpg", "mugshot-3.jpg",
"mugshot-4.jpg", "mugshot-5.jpg", NA), health_complete = c(1,
0, 2, 2, 0, NA), race___1 = c(0, 0, 0, 0, 1, 0), race___2 = c(0,
0, 0, 1, 0, 0), race___3 = c(0, 1, 0, 0, 0, 0), race___4 = c(0,
0, 1, 0, 0, 0), race___5 = c(1, 1, 1, 1, 0, 0), race___6 = c(0,
0, 0, 0, 1, 0), ethnicity = c(1, 1, 0, 1, 2, NA), interpreter_needed = c(0,
0, 1, NA, 0, NA), race_and_ethnicity_complete = c(2, 0, 2,
2, 2, NA)), row.names = c(NA, -6L), class = "data.frame")
8 changes: 8 additions & 0 deletions man/redcap_read.Rd
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