From 0ce516c297ed7ecb89455431c7ce22b4fc46e4e5 Mon Sep 17 00:00:00 2001
From: Andreas Gammelgaard Damsbo <andreas@gdamsbo.dk>
Date: Tue, 6 Feb 2024 08:43:24 +0100
Subject: [PATCH] generics field has been removed and is now handled with
 simpel internal helper function is.repeated_longitudinal()

---
 R/read_redcap_tables.R | 66 ++++++++++++++++--------------------------
 R/utils.r              | 27 +++++++++++++++++
 2 files changed, 52 insertions(+), 41 deletions(-)

diff --git a/R/read_redcap_tables.R b/R/read_redcap_tables.R
index 6bcc92a..b28909a 100644
--- a/R/read_redcap_tables.R
+++ b/R/read_redcap_tables.R
@@ -31,47 +31,40 @@ read_redcap_tables <- function(uri,
                                events = NULL,
                                forms = NULL,
                                raw_or_label = "label",
-                               split_forms = "all",
-                               generics = c(
-                                 "redcap_event_name",
-                                 "redcap_repeat_instrument",
-                                 "redcap_repeat_instance"
-                               )) {
-
-
+                               split_forms = "all") {
   # Getting metadata
   m <-
-    REDCapR::redcap_metadata_read (redcap_uri = uri, token = token)[["data"]]
-
-  if (!is.null(fields)){
+    REDCapR::redcap_metadata_read(redcap_uri = uri, token = token)[["data"]]
 
+  if (!is.null(fields)) {
     fields_test <- fields %in% unique(m$field_name)
 
-    if (any(!fields_test)){
-      print(paste0("The following field names are invalid: ", paste(fields[!fields_test],collapse=", "),"."))
+    if (any(!fields_test)) {
+      print(paste0("The following field names are invalid: ", paste(fields[!fields_test], collapse = ", "), "."))
       stop("Not all supplied field names are valid")
     }
   }
 
 
-  if (!is.null(forms)){
-
+  if (!is.null(forms)) {
     forms_test <- forms %in% unique(m$form_name)
 
-    if (any(!forms_test)){
-      print(paste0("The following form names are invalid: ", paste(forms[!forms_test],collapse=", "),"."))
+    if (any(!forms_test)) {
+      print(paste0("The following form names are invalid: ", paste(forms[!forms_test], collapse = ", "), "."))
       stop("Not all supplied form names are valid")
     }
   }
 
-  if (!is.null(events)){
-    arm_event_inst <- REDCapR::redcap_event_instruments(redcap_uri = uri,
-                                                        token = token)
+  if (!is.null(events)) {
+    arm_event_inst <- REDCapR::redcap_event_instruments(
+      redcap_uri = uri,
+      token = token
+    )
 
     event_test <- events %in% unique(arm_event_inst$data$unique_event_name)
 
-    if (any(!event_test)){
-      print(paste0("The following event names are invalid: ", paste(events[!event_test],collapse=", "),"."))
+    if (any(!event_test)) {
+      print(paste0("The following event names are invalid: ", paste(events[!event_test], collapse = ", "), "."))
       stop("Not all supplied event names are valid")
     }
   }
@@ -95,28 +88,19 @@ read_redcap_tables <- function(uri,
   }
 
   # Processing metadata to reflect focused dataset
-  if (!is.null(c(fields,forms,events))){
-    m <- focused_metadata(m,names(d))
-  }
+  m <- focused_metadata(m, names(d))
 
 
+    # Splitting
+    l <- REDCap_split(d,
+      m,
+      forms = split_forms,
+      primary_table_name = ""
+    )
 
-  if (any(generics %in% names(d))){
-  # Splitting
-  l <- REDCap_split(d,
-                    m,
-                    forms = split_forms,
-                    primary_table_name = "")
-
-  # Sanitizing split list by removing completely empty rows apart from colnames
-  # in "generics"
-  sanitize_split(l,c(names(d)[1],generics))
-  } else {
-    # If none of generics are present, the data base is not longitudinal,
-    # and does not have repeatable events, and therefore splitting does not
-    # make sense. But now we handle that as well.
-    d
-  }
+    # Sanitizing split list by removing completely empty rows apart from colnames
+    # in "generics"
+    sanitize_split(l, c(names(d)[1], generics))
 
 }
 
diff --git a/R/utils.r b/R/utils.r
index 86e4e02..6ed91e4 100644
--- a/R/utils.r
+++ b/R/utils.r
@@ -416,3 +416,30 @@ d2w <- function(x, lang = "en", neutrum=FALSE, everything=FALSE) {
 
   out
 }
+
+#' Test if repeatable or longitudinal
+#'
+#' @param data data set
+#' @param generics default is "redcap_event_name", "redcap_repeat_instrument"
+#' and "redcap_repeat_instance"
+#'
+#' @return logical
+#' @examples
+#' is.repeated_longitudinal(c("record_id", "age", "record_id", "gender"))
+#'
+is.repeated_longitudinal <- function(data, generics = c(
+  "redcap_event_name",
+  "redcap_repeat_instrument",
+  "redcap_repeat_instance"
+)) {
+  if (is.list(data)) {
+    names <- data |>
+      lapply(names) |>
+      purrr::list_c()
+  } else if (is.data.frame(data)) {
+    names <- names(data)
+  } else if (is.vector(data)) {
+    names <- data
+  }
+  any(generics %in% names)
+}