includes read_redcap_table

DESCRIPTION

@@ -1,11 +1,10 @@
 Package: REDCapRITS
 Title: REDCap Repeating Instrument Table Splitter Fork
-Version: 0.2.2.1
+Version: 0.2.3
 Authors@R: c(
     person("Paul", "Egeler", email = "paul.egeler@spectrumhealth.org", role = c("aut")),
      person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", role = c("cre", "ctb","cph"),
            comment = c(ORCID = "0000-0002-7559-1154")))
-Copyright: Spectrum Health, Grand Rapids, MI
 Description: This is a fork of REDCapRITS by Paul Egeler and Spectrum Health. See
     [https://github.com/SpectrumHealthResearch/REDCapRITS](https://github.com/SpectrumHealthResearch/REDCapRITS).
     Split REDCap repeating instruments output into multiple tables. 
@@ -32,7 +31,10 @@ LazyData: true
 RoxygenNote: 7.2.3
 URL: https://github.com/agdamsbo/REDCapRITS
 BugReports: https://github.com/agdamsbo/REDCapRITS/issues
+Imports: 
+    REDCapR
 Collate: 
     'utils.r'
     'process_user_input.r'
     'REDCap_split.r'
+    'read_redcap_tables.R'

NAMESPACE

@@ -1,3 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
 export(REDCap_split)
+export(read_redcap_tables)
+importFrom(REDCapR,redcap_metadata_read)
+importFrom(REDCapR,redcap_read)

R/read_redcap_tables.R

@@ -0,0 +1,71 @@
+#' Download REDCap data
+#'
+#' Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split
+#' including some clean-up. Works with longitudinal projects with repeating
+#' instruments.
+#' @param uri REDCap database uri
+#' @param token API token
+#' @param records records to download
+#' @param fields fields to download
+#' @param events events to download
+#' @param forms forms to download
+#' @param raw_or_label raw or label tags
+#' @param generics vector of auto-generated generic variable names to
+#' ignore when discarding empty rows
+#' @param ... ekstra parameters for REDCapR::redcap_read_oneshot
+#'
+#' @return list of instruments
+#' @importFrom REDCapR redcap_metadata_read redcap_read
+#' @export
+#'
+#' @examples
+#' # Examples will be provided later
+read_redcap_tables <- function(uri,
+                               token,
+                               records = NULL,
+                               fields = NULL,
+                               events = NULL,
+                               forms = NULL,
+                               raw_or_label = "label",
+                               generics = c(
+                                 "record_id",
+                                 "redcap_event_name",
+                                 "redcap_repeat_instrument",
+                                 "redcap_repeat_instance"
+                               ),
+                               ...) {
+  # Notes to self: Based on the metadata, this functionality could be
+  # introduced without using the REDCapRITS package.. To be tried..
+  #
+  # This does not handle repeated instruments!! This should be implemented.
+
+  d <- REDCapR::redcap_read_oneshot(
+    redcap_uri = uri,
+    token = token,
+    fields = fields,
+    events = events,
+    forms = forms,
+    records = records,
+    raw_or_label = raw_or_label,
+    ...
+  )
+
+  m <-
+    REDCapR::redcap_metadata_read (redcap_uri = uri, token = token)
+
+  l <- REDCap_split(d$data,
+                    m$data[m$data$field_name %in% names(d$data), ],
+                    forms = "all")
+
+  lapply(l, function(i) {
+    if (ncol(i) > 2) {
+      s <- data.frame(i[, !colnames(i) %in% generics])
+      i[!apply(is.na(s), MARGIN = 1, FUN = all), ]
+    } else {
+      i
+    }
+  })
+
+}
+
+

man/read_redcap_tables.Rd

@@ -0,0 +1,50 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/read_redcap_tables.R
+\name{read_redcap_tables}
+\alias{read_redcap_tables}
+\title{Download REDCap data}
+\usage{
+read_redcap_tables(
+  uri,
+  token,
+  records = NULL,
+  fields = NULL,
+  events = NULL,
+  forms = NULL,
+  raw_or_label = "label",
+  generics = c("record_id", "redcap_event_name", "redcap_repeat_instrument",
+    "redcap_repeat_instance"),
+  ...
+)
+}
+\arguments{
+\item{uri}{REDCap database uri}
+
+\item{token}{API token}
+
+\item{records}{records to download}
+
+\item{fields}{fields to download}
+
+\item{events}{events to download}
+
+\item{forms}{forms to download}
+
+\item{raw_or_label}{raw or label tags}
+
+\item{generics}{vector of auto-generated generic variable names to
+ignore when discarding empty rows}
+
+\item{...}{ekstra parameters for REDCapR::redcap_read_oneshot}
+}
+\value{
+list of instruments
+}
+\description{
+Wrapper function for using REDCapR::redcap_read and REDCapRITS::REDCap_split
+including some clean-up. Works with longitudinal projects with repeating
+instruments.
+}
+\examples{
+# Examples will be provided later
+}

tests/testthat/test-read_redcap_tables.R

@@ -0,0 +1,7 @@
+# Unit Test
+
+# Test that the function throws an error when uri and token are not provided
+test_that("read_redcap_tables throws error when uri and token are not provided",
+          {
+            testthat::expect_error(read_redcap_tables(uri, token))
+          })