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more examples and better handling of different projects

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Andreas Gammelgaard Damsbo 2024-02-06 14:01:03 +01:00
parent edd5334df8
commit 289f57ab76
2 changed files with 84 additions and 25 deletions
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76
R/redcap_wider.R
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@ -5,40 +5,70 @@ utils::globalVariables(c("redcap_wider",
#' @title Redcap Wider
#' @description Converts a list of REDCap data frames from long to wide format.
#' Handles longitudinal projects, but not yet repeated instruments.
#' @param list A list of data frames.
#' @param data A list of data frames.
#' @param event.glue A dplyr::glue string for repeated events naming
#' @param inst.glue A dplyr::glue string for repeated instruments naming
#' @return The list of data frames in wide format.
#' @export
#' @importFrom tidyr pivot_wider
#' @importFrom tidyselect all_of
#' @importFrom purrr reduce
#'
#' @examples
#' list <- list(data.frame(record_id = c(1,2,1,2),
#' # Longitudinal
#' list1 <- list(data.frame(record_id = c(1,2,1,2),
#' redcap_event_name = c("baseline", "baseline", "followup", "followup"),
#' age = c(25,26,27,28)),
#' data.frame(record_id = c(1,2),
#' redcap_event_name = c("baseline", "baseline"),
#' gender = c("male", "female")))
#' redcap_wider(list)
#' redcap_wider(list1)
#' # Simpel with two instruments
#' list2 <- list(data.frame(record_id = c(1,2),
#' age = c(25,26)),
#' data.frame(record_id = c(1,2),
#' gender = c("male", "female")))
#' redcap_wider(list2)
#' # Simple with single instrument
#' list3 <- list(data.frame(record_id = c(1,2),
#' age = c(25,26)))
#' redcap_wider(list3)
#' # Longitudinal with repeatable instruments
#' list4 <- list(data.frame(record_id = c(1,2,1,2),
#' redcap_event_name = c("baseline", "baseline", "followup", "followup"),
#' age = c(25,26,27,28)),
#' data.frame(record_id = c(1,1,1,1,2,2,2,2),
#' redcap_event_name = c("baseline", "baseline", "followup", "followup",
#' "baseline", "baseline", "followup", "followup"),
#' redcap_repeat_instrument = "walk",
#' redcap_repeat_instance=c(1,2,1,2,1,2,1,2),
#' dist = c(40, 32, 25, 33, 28, 24, 23, 36)),
#' data.frame(record_id = c(1,2),
#' redcap_event_name = c("baseline", "baseline"),
#' gender = c("male", "female")))
#'redcap_wider(list4)
redcap_wider <-
function(list,
function(data,
event.glue = "{.value}_{redcap_event_name}",
inst.glue = "{.value}_{redcap_repeat_instance}") {
all_names <- unique(do.call(c, lapply(list, names)))
if (!any(c("redcap_event_name", "redcap_repeat_instrument") %in%
all_names)) {
stop(
"The dataset does not include a 'redcap_event_name' variable.
redcap_wider only handles projects with repeating instruments or
longitudinal projects"
)
}
if (!is.repeated_longitudinal(data)) {
if (is.list(data)) {
if (length(data) == 1) {
out <- data[[1]]
} else {
out <- data |> purrr::reduce(dplyr::left_join)
}
} else if (is.data.frame(data)){
out <- data
}
id.name <- all_names[1]
l <- lapply(list, function(i) {
} else {
id.name <- do.call(c, lapply(data, names))[[1]]
l <- lapply(data, function(i) {
rep_inst <- "redcap_repeat_instrument" %in% names(i)
if (rep_inst) {
@ -81,13 +111,17 @@ redcap_wider <-
names_glue = event.glue
)
s[colnames(s) != "redcap_event_name"]
} else
(i[colnames(i) != "redcap_event_name"])
} else
(i)
} else {
i[colnames(i) != "redcap_event_name"]
}
} else {
i
}
})
## Additional conditioning is needed to handle repeated instruments.
out <- data.frame(Reduce(f = dplyr::full_join, x = l))
}
data.frame(Reduce(f = dplyr::full_join, x = l))
out
}

33
man/redcap_wider.Rd
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@ -5,13 +5,13 @@
\title{Redcap Wider}
\usage{
redcap_wider(
list,
data,
event.glue = "{.value}_{redcap_event_name}",
inst.glue = "{.value}_{redcap_repeat_instance}"
)
}
\arguments{
\item{list}{A list of data frames.}
\item{data}{A list of data frames.}
\item{event.glue}{A dplyr::glue string for repeated events naming}
@ -25,11 +25,36 @@ Converts a list of REDCap data frames from long to wide format.
Handles longitudinal projects, but not yet repeated instruments.
}
\examples{
list <- list(data.frame(record_id = c(1,2,1,2),
# Longitudinal
list1 <- list(data.frame(record_id = c(1,2,1,2),
redcap_event_name = c("baseline", "baseline", "followup", "followup"),
age = c(25,26,27,28)),
data.frame(record_id = c(1,2),
redcap_event_name = c("baseline", "baseline"),
gender = c("male", "female")))
redcap_wider(list)
redcap_wider(list1)
# Simpel with two instruments
list2 <- list(data.frame(record_id = c(1,2),
age = c(25,26)),
data.frame(record_id = c(1,2),
gender = c("male", "female")))
redcap_wider(list2)
# Simple with single instrument
list3 <- list(data.frame(record_id = c(1,2),
age = c(25,26)))
redcap_wider(list3)
# Longitudinal with repeatable instruments
list4 <- list(data.frame(record_id = c(1,2,1,2),
redcap_event_name = c("baseline", "baseline", "followup", "followup"),
age = c(25,26,27,28)),
data.frame(record_id = c(1,1,1,1,2,2,2,2),
redcap_event_name = c("baseline", "baseline", "followup", "followup",
"baseline", "baseline", "followup", "followup"),
redcap_repeat_instrument = "walk",
redcap_repeat_instance=c(1,2,1,2,1,2,1,2),
dist = c(40, 32, 25, 33, 28, 24, 23, 36)),
data.frame(record_id = c(1,2),
redcap_event_name = c("baseline", "baseline"),
gender = c("male", "female")))
redcap_wider(list4)
}