Merge pull request #253 from aghaynes/master

warning regarding overwritten variable, increment version to 1.1.0
SwissClinicalTrialOrganisation · Mar 1, 2023 · ec2c390 · ec2c390
2 parents 8acfb6a + a3ee024
commit ec2c390
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Showing 4 changed files with 10 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: secuTrialR
 Type: Package
 Title: Handling of Data from the Clinical Data Management System 'secuTrial'
-Version: 1.0.12
+Version: 1.1.0
 Authors@R:
     c(person(given = "Alan G.",
              family = "Haynes",
@@ -57,7 +57,7 @@ Imports:
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.2
 Suggests: 
     knitr,
     lintr,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# secuTrialR 1.1.0
+* warning regarding overwritten `pat_id` variable 
+
 # secuTrialR 1.0.12
 * adapt `as.data.frame.secuTrialData()` to allow named character vectors as option `data.frames` to specify custom names for data.frames (#250) 
 

diff --git a/R/read_export_table.R b/R/read_export_table.R
@@ -118,6 +118,9 @@ read_export_table <- function(data_dir, file_name, export_options,
   # adding pat_id (only possible if Add-ID was exported in ExportSearchTool)
   if (add_pat_id & ("mnppid" %in% names(loaded_table))) {
     if (export_options$add_id) {
+      if("pat_id" %in% names(loaded_table)){
+        warning("variable 'pat_id' replaced with the additional id")
+      }
       loaded_table <- add_pat_id_col(table = loaded_table,
                                      id = "pat_id",
                                      casenodes_table = casenodes_table)

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 # secuTrialR
 
-[![](https://img.shields.io/badge/dev%20version-1.0.12-blue.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR)
+[![](https://img.shields.io/badge/dev%20version-1.1.0-blue.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR)
 [![](https://www.r-pkg.org/badges/version/secuTrialR?color=green)](https://cran.r-project.org/package=secuTrialR)
 [![AppVeyor Build
 Status](https://ci.appveyor.com/api/projects/status/github/SwissClinicalTrialOrganisation/secuTrialR?branch=master&svg=true)](https://ci.appveyor.com/project/SwissClinicalTrialOrganisation/secuTrialR)
@@ -136,8 +136,7 @@ bmd_export
 ```
 
     ## secuTrial data imported from:
-    ## /Users/runner/work/_temp/Library/secuTrialR/extdata/sT_exports/BMD/s_export_CSV-
-    ## xls_BMD_short_en_utf8.zip 
+    ## /Users/runner/work/_temp/Library/secuTrialR/extdata/sT_exports/BMD/s_export_CSV-xls_BMD_short_en_utf8.zip 
     ##  table nrow ncol  meta original_name
     ##     vp    1   10  TRUE        vp.xls
     ##   vpfs    1    2  TRUE      vpfs.xls