Merge pull request #14 from SpectrumHealthResearch/issue12

REDCap_split() now compatible with tibbles

R/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapRITS
 Title: REDCap Repeating Instrument Table Splitter
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: c(
     person("Paul", "Egeler", email = "paul.egeler@spectrumhealth.org", role = c("aut", "cre")),
     person("Spectrum Health, Grand Rapids, MI", role = "cph"))
@@ -14,7 +14,8 @@ Suggests:
     httr,
     jsonlite,
     testthat,
-    Hmisc
+    Hmisc,
+    readr
 License: GPL-3
 Encoding: UTF-8
 LazyData: true

R/NEWS.md

@@ -1,4 +1,8 @@
-# REDCapRITS 0.2.0 (Release date: 2019-??-??)
+# REDCapRITS 0.2.1 (Release date: 2019-07-26)
+
+  * [bug] Can now accept `"tbl_df"` objects and `NA`s in the `redcap_repeat_instrument` field. (#12)
+
+# REDCapRITS 0.2.0 (Release date: 2019-07-08)
 
   * [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.

R/R/REDCap_split.r

@@ -87,7 +87,7 @@ REDCap_split <- function(records,
 
   # Process user input
   records  <- process_user_input(records)
-  metadata <- process_user_input(metadata)
+  metadata <- as.data.frame(process_user_input(metadata)) # See issue #12
 
   # Get the variable names in the dataset
   vars_in_data <- names(records)
@@ -100,6 +100,15 @@ REDCap_split <- function(records,
     stop("There are no repeating instruments in this dataset.")
   }
 
+  # Remove NAs from `redcap_repeat_instrument` (see issue #12)
+  if(any(is.na(records$redcap_repeat_instrument))) {
+    records$redcap_repeat_instrument <- ifelse(
+      is.na(records$redcap_repeat_instrument),
+      "",
+      as.character(records$redcap_repeat_instrument)
+    )
+  }
+
   # Standardize variable names for metadata
   names(metadata) <- metadata_names
 

R/tests/testthat/test-csv-exports.R

@@ -13,10 +13,10 @@ records <- read.csv(
   )
 )
 
+redcap_output_csv1 <- REDCap_split(records, metadata)
+
 # Test that basic CSV export matches reference ------------------------------
 test_that("CSV export matches reference", {
-  redcap_output_csv1 <- REDCap_split(records, metadata)
-
   expect_known_hash(redcap_output_csv1, "f74558d1939c17d9ff0e08a19b956e26")
 })
 
@@ -29,3 +29,42 @@ if (requireNamespace("Hmisc", quietly = TRUE)) {
   })
 }
 
+
+if (requireNamespace("readr", quietly = TRUE)) {
+
+  context("Compatibility with readr")
+
+  metadata <- readr::read_csv(
+    get_data_location(
+      "ExampleProject_DataDictionary_2018-06-07.csv"
+    )
+  )
+
+  records <- readr::read_csv(
+    get_data_location(
+      "ExampleProject_DATA_2018-06-07_1129.csv"
+    )
+  )
+
+  redcap_output_readr <- REDCap_split(records, metadata)
+
+  expect_matching_elements <- function(FUN) {
+    FUN <- match.fun(FUN)
+    expect_identical(
+      lapply(redcap_output_readr, FUN),
+      lapply(redcap_output_csv1, FUN)
+    )
+  }
+
+  test_that("Result of data read in with `readr` will match result with `read.csv`", {
+
+    # The list itself
+    expect_identical(length(redcap_output_readr), length(redcap_output_csv1))
+    expect_identical(names(redcap_output_readr), names(redcap_output_csv1))
+
+    # Each element of the list
+    expect_matching_elements(names)
+    expect_matching_elements(dim)
+  })
+
+}