Merge pull request #188 from PatrickRWright/v_1_0_0

v 1.0.0
SwissClinicalTrialOrganisation · Apr 3, 2020 · 1b4a628 · 1b4a628
2 parents 6f37d89 + cde86dd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,29 +1,25 @@
 Package: secuTrialR
 Type: Package
-Title: Handling of data from the clinical data management system secuTrial 
-Version: 0.9.1
-Author:
-    c(person(given = "Pascal",
-             family = "Benkert",
+Title: Handling of Data from the Clinical Data Management System secuTrial
+Version: 1.0.0
+Authors@R:
+    c(person(given = "Patrick R.",
+             family = "Wright",
              role = c("cre", "aut"),
-             email = "pascal.benkert@usb.ch"),
-      person(given = "Alan",
+             email = "patrick.wright@usb.ch"),
+      person(given = "Alan G.",
              family = "Haynes",
              role = c("aut"),
              email = "alan.haynes@ctu.unibe.ch"),
       person(given = "Milica",
              family = "Markovic",
              role = c("aut"),
              email = "milica.markovic@usb.ch"),
-      person(given = "Constantin",
-             family = "Sluka",
-             role = c("aut"),
-             email = "constantin.sluka@usb.ch"),
-      person(given = "Patrick R.",
-             family = "Wright",
+      person(given = "Pascal",
+             family = "Benkert",
              role = c("aut"),
-             email = "patrick.wright@usb.ch"))
-Maintainer: Patrick R. Wright <patrick.wright@usb.ch>, Alan Haynes <alan.haynes@ctu.unibe.ch>, Milica Markovic <milica.markovic@usb.ch>
+             email = "pascal.benkert@usb.ch"))
+Maintainer: Patrick R. Wright <patrick.wright@usb.ch>
 Description: This R package is intended to standardize and simplify working with data
     exported from the clinical data management system (CDMS) secuTrial. The primary
     data export the package works with is a standard non-rectangular export.
@@ -46,7 +42,7 @@ Imports:
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Suggests: 
     knitr,
     lintr,

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# secuTrialR 1.0.0
+* clarify correct options in `read_secuTrial()` failure message (#187)
+* check for `project_setup` in `visit_structure()` (#181)
+
 # secuTrialR 0.9.1
 * added "Form meta data: Structure" export option information to `export_options` (#182)
 * added error handling for missing structure data when running `annual_recruitment()` and `return_random_participants()` (#182)

diff --git a/R/read_export_options.R b/R/read_export_options.R
@@ -317,5 +317,4 @@ print.secuTrialoptions <- function(x, ...) {
                    exportname = unlist(x$meta_names),
                    available = unlist(x$meta_available))
   print(df, row.names = FALSE)
-
 }
diff --git a/R/read_secuTrial.R b/R/read_secuTrial.R
@@ -35,7 +35,7 @@ read_secuTrial <- function(data_dir,
       check_export_options(d)
     },
     error = function(e) {
-      message("Input to read_secuTrial() appears to be incompatible. Is it rectangular? Have you exported CSV format?")
+      message("Input to read_secuTrial() appears to be incompatible. It should be in CSV format and not be rectangular.")
     }
   )
   # label

diff --git a/R/return_hidden_items.R b/R/return_hidden_items.R
@@ -21,7 +21,7 @@
 return_hidden_items <- function(x) {
   if (class(x) == "secuTrialdata") {
 
-    if(! x$export_options$hidden_fields) {
+    if (! x$export_options$hidden_fields) {
       stop("Form data of hidden fields was not exported and will thus not be in this export.")
     }
 

diff --git a/R/visit_structure.R b/R/visit_structure.R
@@ -22,6 +22,7 @@
 #' plot(vs)
 visit_structure <- function(x, sorted = TRUE) {
   if (class(x)[1] != "secuTrialdata") stop("'secuTrialdata object required'")
+  if (! x$export_options$proj_setup) stop("Project setup data needs to be in the export but is not.")
   vp <- x[[x$export_options$meta_names$visitplan]]
   if (any(is.na(vp$mnpvisid))) stop(paste("Visits do not appear to be a part of this database or",
                                          "only flexible visits defined\nvisit_structure requires",

diff --git a/README.Rmd b/README.Rmd
@@ -2,13 +2,14 @@
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 
-# secuTrialR ![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master) [![codecov](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR/branch/master/graphs/badge.svg)](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR) `r badger::badge_custom("dev version", installed.packages()["secuTrialR", "Version"], "blue", "https://github.com/SwissClinicalTrialOrganisation/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)
-
+# secuTrialR `r badger::badge_custom("version", installed.packages()["secuTrialR", "Version"], "blue", "https://github.com/SwissClinicalTrialOrganisation/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) [![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master)](https://travis-ci.com/github/SwissClinicalTrialOrganisation/secuTrialR) [![codecov](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR/branch/master/graphs/badge.svg)](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR)
 
 An R package to handle data from the clinical data management system (CDMS) [secuTrial](https://www.secutrial.com/en/).
 
 ## Installing from github with devtools
 
+Please note that `R versions >= 3.5` should be used to run `secuTrialR`.
+
 ```{r, eval = FALSE}
 devtools::install_github("SwissClinicalTrialOrganisation/secuTrialR")
 ```
@@ -31,6 +32,11 @@ Thus, we suggest to work with exports which:
 You can use the `check_export_options()` function on a secuTrialdata object to identify where your export may differ.
 
 ## Basic usage
+
+An extensive applied manual/vignette is available
+[here](vignettes/secuTrialR-package-vignette.pdf)
+and probably the best place to get started.
+
 Load the package
 ```{r, echo = TRUE, warning=FALSE, message=FALSE}
 library(secuTrialR)
@@ -329,6 +335,14 @@ R CMD build secuTrialR
 R CMD check secuTrialR_0.9.0.tar.gz
 ```
 
+### Versioning and releases
+The version number is made up of three digits. The first digit
+is reserved for major releases which may break backwards compatibility.
+The second and third digits are used for medium and minor changes respectively.
+Versions released on CRAN will be tagged and saved as releases on GitHub.
+The version released on CRAN is regarded as the stable version while
+the master branch on GitHub is regarded as the current development version.
+
 ### Guidelines for contributors
 
 Requests for new features and bug fixes should first be documented as an [Issue](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/issues) on GitHub.

diff --git a/README.md b/README.md
@@ -2,13 +2,14 @@
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 
-# secuTrialR ![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master) [![codecov](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR/branch/master/graphs/badge.svg)](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR) [![](https://img.shields.io/badge/dev%20version-0.9.1-blue.svg)](https://github.com/SwissClinicalTrialOrganisation/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)
-
+# secuTrialR [![](https://img.shields.io/badge/version-1.0.0-blue.svg)](https://github.com/SwissClinicalTrialOrganisation/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) [![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master)](https://travis-ci.com/github/SwissClinicalTrialOrganisation/secuTrialR) [![codecov](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR/branch/master/graphs/badge.svg)](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR)
 
 An R package to handle data from the clinical data management system (CDMS) [secuTrial](https://www.secutrial.com/en/).
 
 ## Installing from github with devtools
 
+Please note that `R versions >= 3.5` should be used to run `secuTrialR`.
+
 
 ```r
 devtools::install_github("SwissClinicalTrialOrganisation/secuTrialR")
@@ -32,6 +33,11 @@ Thus, we suggest to work with exports which:
 You can use the `check_export_options()` function on a secuTrialdata object to identify where your export may differ.
 
 ## Basic usage
+
+An extensive applied manual/vignette is available
+[here](vignettes/secuTrialR-package-vignette.pdf)
+and probably the best place to get started.
+
 Load the package
 
 ```r
@@ -573,6 +579,14 @@ R CMD build secuTrialR
 R CMD check secuTrialR_0.9.0.tar.gz
 ```
 
+### Versioning and releases
+The version number is made up of three digits. The first digit
+is reserved for major releases which may break backwards compatibility.
+The second and third digits are used for medium and minor changes respectively.
+Versions released on CRAN will be tagged and saved as releases on GitHub.
+The version released on CRAN is regarded as the stable version while
+the master branch on GitHub is regarded as the current development version.
+
 ### Guidelines for contributors
 
 Requests for new features and bug fixes should first be documented as an [Issue](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/issues) on GitHub.

diff --git a/appveyor.yml b/appveyor.yml
@@ -16,8 +16,6 @@ environment:
     MINICONDA: C:\Miniconda3-x64
     R_ARCH: x64    
   matrix:
-    - R_VERSION: devel
-
     - R_VERSION: release
 
     - R_VERSION: oldrel

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html