fix for check

Author: DanChaltiel

R/data.R

@@ -20,7 +20,8 @@ edc_example = function(N=50, seed=42, outdated=FALSE){
   x2 = .example_mixed(N, seed)
   x3 = .example_ae(N, seed)
   rtn = c(x1, x2, x3) %>% 
-    map(~{
+    imap(~{
+      if(.y=="long_pure") return(.x)
       .x %>% 
         mutate(
           crfstat=sample(c("Complete","No Data","Incomplete"), 

R/patient_gridplot.R

@@ -36,7 +36,7 @@
 edc_patient_gridplot = function(sort_rows=TRUE, sort_cols=TRUE, gradient=FALSE,
                                 axes_flip=FALSE, show_grid=TRUE, preprocess=NULL,
                                 palette=c("Yes"="#00468BFF", "No"="#ED0000FF"),
-                                datasets=get_datasets(), lookup=get_lookup()){
+                                datasets=get_datasets(), lookup=edc_lookup()){
   subjid_cols = get_subjid_cols(lookup=lookup)
   if(is.null(preprocess)) preprocess=identity
   if(is_formula(preprocess)) preprocess=as_function(preprocess)

R/split_mixed.R

@@ -85,7 +85,8 @@ table_format = function(df, id=get_subjid_cols(), ...,
 #' @examples
 #' #db = read_trialmaster("filename.zip", pw="xx")
 #' db = edc_example() %>% 
-#'   edc_split_mixed(c(ae, starts_with("long")))
+#'   edc_split_mixed(c(ae, starts_with("long")), 
+#'                   ignore_cols="crfstat")
 #'   
 #' names(db)
 #' edc_lookup()
@@ -101,10 +102,11 @@ edc_split_mixed = function(database, datasets=everything(),
   check_dots_empty()
   .lookup = database$.lookup
   patient_id = get_subjid_cols(lookup=.lookup)
- 
-  if(is.null(ignore_cols)){
-    ignore_cols = c(get_crfname_cols(lookup=.lookup), 
-                    get_meta_cols(lookup=.lookup, min_pct=0.95))
+  
+  ignore_cols_default = c(get_crfname_cols(lookup=.lookup), 
+                          get_meta_cols(lookup=.lookup, min_pct=0.95))
+  if(!is.null(ignore_cols)){
+    ignore_cols = c(ignore_cols_default, ignore_cols)
   }
 
   db_mixed = database %>% 

man/EDCimport-package.Rd

@@ -7,21 +7,22 @@ test_that("Split mixed", {
   db = edc_example(N=100) 
 
   #all datasets
-  mixed_data_all = edc_split_mixed(db, verbose=FALSE)
+  mixed_data_all = edc_split_mixed(db, verbose=FALSE, ignore_cols="crfstat")
   expect_equal(edc_lookup(dataset)$dataset,
                c("ae", "ae_long", "ae_short", "data1", "data2", "data3", "enrol", "long_mixed",
                  "long_mixed_long", "long_mixed_short", "long_pure", "short"))
 
   #tidyselection
-  mixed_data = edc_split_mixed(db, c(short, "enrol", starts_with("long")), verbose=FALSE)
+  mixed_data = edc_split_mixed(db, datasets=c(short, "enrol", starts_with("long")), 
+                               ignore_cols="crfstat", verbose=FALSE)
 
   expect_equal(edc_lookup(dataset)$dataset,
                c("ae", "data1", "data2", "data3", "enrol", "long_mixed", "long_mixed_long", 
                  "long_mixed_short", "long_pure", "short"))
   expect_equal(nrow(mixed_data$long_mixed_short), 100)
   expect_equal(nrow(mixed_data$long_mixed_long), 200)
   expect_equal(ncol(mixed_data$long_mixed_short), 3)
-  expect_equal(ncol(mixed_data$long_mixed_long), 3)
+  expect_equal(ncol(mixed_data$long_mixed_long), 4)
 
   #content
   expect_true(all(c("long_mixed_short", "long_mixed_long") %in% names(mixed_data)))
@@ -30,6 +31,6 @@ test_that("Split mixed", {
   expect_equal(nrow(mixed_data$long_mixed_short), 100)
   expect_equal(nrow(mixed_data$long_mixed_long), 200)
   expect_equal(ncol(mixed_data$long_mixed_short), 3)
-  expect_equal(ncol(mixed_data$long_mixed_long), 3)
+  expect_equal(ncol(mixed_data$long_mixed_long), 4)
 
 })