Increment to v 0.2.0 and closes #10

Form timestamp fields also captured now.

R/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapRITS
 Title: REDCap Repeating Instrument Table Splitter
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
     person("Paul", "Egeler", email = "paul.egeler@spectrumhealth.org", role = c("aut", "cre")),
     person("Spectrum Health, Grand Rapids, MI", role = "cph"))

R/NEWS.md

@@ -1,3 +1,8 @@
+# REDCapRITS 0.2.0 (Release date: 2019-??-??)
+
+  * [feature] User can now separate each form into its own data.frame, regardless if it is a repeating instrument or not. (#10)
+  * [bug] Handles auto-generated form timestamp fields.
+
 # REDCapRITS 0.1.0 (Release date: 2019-07-01)
 
   * [feature] User can now specify the name of the 'primary' table, which previously was left blank. (#9)

R/R/REDCap_split.r

@@ -134,12 +134,13 @@ REDCap_split <- function(records,
 
     # Split the table based on instrument
     out <- split.data.frame(records, records$redcap_repeat_instrument)
+    primary_table_index <- which(names(out) == "")
 
     if (forms == "repeating" && primary_table_name %in% subtables) {
       warning("The label given to the primary table is already used by a repeating instrument. The primary table label will be left blank.")
       primary_table_name <- ""
     } else if (primary_table_name > "") {
-      names(out)[[which(names(out) == "")]] <- primary_table_name
+      names(out)[[primary_table_index]] <- primary_table_name
     }
 
     # Delete the variables that are not relevant
@@ -153,7 +154,7 @@ REDCap_split <- function(records,
             fields[!fields[,2] %in% subtables, 1]
           )
         )
-        out[[which(names(out) == primary_table_name)]] <- out[[which(names(out) == primary_table_name)]][out_fields]
+        out[[primary_table_index]] <- out[[primary_table_index]][out_fields]
 
       } else {
 
@@ -169,6 +170,24 @@ REDCap_split <- function(records,
       }
 
     }
+
+    if (forms == "all") {
+
+      out <- c(
+        split_non_repeating_forms(
+          out[[primary_table_index]],
+          universal_fields,
+          fields[!fields[,2] %in% subtables,]
+        ),
+        out[-primary_table_index]
+      )
+
+    }
+
+  } else {
+
+    out <- split_non_repeating_forms(records, universal_fields, fields)
+
   }
 
   out

R/R/utils.r

@@ -15,6 +15,20 @@ match_fields_to_form <- function(metadata, vars_in_data) {
 
   fields <- rbind(fields, form_complete_fields)
 
+  # Process survey timestamps
+  timestamps <- intersect(vars_in_data, paste0(form_names, "_timestamp"))
+  if (length(timestamps)) {
+
+    timestamp_fields <- data.frame(
+      field_name = timestamps,
+      form_name = sub("_timestamp$", "", timestamps),
+      stringsAsFactors = FALSE
+    )
+
+    fields <- rbind(fields, timestamp_fields)
+
+  }
+
   # Process checkbox fields
   if (any(metadata$field_type == "checkbox")) {
 
@@ -74,3 +88,19 @@ match_fields_to_form <- function(metadata, vars_in_data) {
   fields
 
   }
+
+
+split_non_repeating_forms <- function(table, universal_fields, fields) {
+
+  forms <- unique(fields[[2]])
+
+  x <- lapply(
+    forms,
+    function (x) {
+      table[names(table) %in% union(universal_fields, fields[fields[,2] == x,1])]
+  })
+
+  structure(x, names = forms)
+
+}
+

R/tests/testthat/test-forms-arg.R

@@ -0,0 +1,63 @@
+context("Using the `forms = 'all'` argument")
+
+# Global variables --------------------------------------------------------
+
+# Cars
+metadata <- jsonlite::fromJSON(
+  get_data_location(
+    "ExampleProject_metadata.json"
+  )
+)
+
+records <- jsonlite::fromJSON(
+  get_data_location(
+    "ExampleProject_records.json"
+  )
+)
+
+redcap_output_json <- REDCap_split(records, metadata, forms = "all")
+
+# Longitudinal
+file_paths <- sapply(
+  c(
+    records = "WARRIORtestForSoftwa_DATA_2018-06-21_1431.csv",
+    metadata = "WARRIORtestForSoftwareUpgrades_DataDictionary_2018-06-21.csv"
+  ), get_data_location
+)
+
+redcap <- lapply(file_paths, read.csv, stringsAsFactors = FALSE)
+redcap[["metadata"]] <- with(redcap, metadata[metadata[,1] > "",])
+redcap_output_long <- with(redcap, REDCap_split(records, metadata, forms = "all"))
+redcap_long_names <- names(redcap[[1]])
+
+# Tests -------------------------------------------------------------------
+
+test_that("Each form is an element in the list", {
+
+  expect_length(redcap_output_json, 3L)
+  expect_identical(names(redcap_output_json), c("motor_trend_cars", "grouping", "sale"))
+
+})
+
+test_that("All variables land somewhere", {
+
+  expect_true(setequal(names(records), Reduce("union", sapply(redcap_output_json, names))))
+
+})
+
+
+test_that("Primary table name is ignored", {
+  expect_identical(
+    REDCap_split(records, metadata, "HELLO", "all"),
+    redcap_output_json
+  )
+})
+
+test_that("Supports longitudinal data", {
+
+  # setdiff(redcap_long_names, Reduce("union", sapply(redcap_output_long, names)))
+  ##  [1] "informed_consent_and_addendum_timestamp"
+
+  expect_true(setequal(redcap_long_names, Reduce("union", sapply(redcap_output_long, names))))
+
+})

R/tests/testthat/test-longitudinal.R

@@ -13,5 +13,5 @@ test_that("CSV export matches reference", {
   redcap_output <- with(redcap, REDCap_split(records, metadata))
 
 
-  expect_known_hash(redcap_output, "dff3a52955")
+  expect_known_hash(redcap_output, "0934bcb292")
 })