Merge pull request #254 from aghaynes/master

Fix CRAN notes
SwissClinicalTrialOrganisation · Mar 2, 2023 · f0034ed · f0034ed
2 parents ec2c390 + 7082668
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Showing 14 changed files with 17 additions and 15 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: 1.1.0
+Version: 1.1.1
 Authors@R:
     c(person(given = "Alan G.",
              family = "Haynes",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# secuTrialR 1.1.1
+* fix CRAN notes - remove codecov badge, check class via inherits
+
 # secuTrialR 1.1.0
 * warning regarding overwritten `pat_id` variable 
 

diff --git a/R/annual_recruitment.R b/R/annual_recruitment.R
@@ -29,7 +29,7 @@
 #' annual_recruitment(sT_export, rm_regex = "\\(.*\\)$")
 #'
 annual_recruitment <- function(x, rm_regex = "") {
-  if (class(x) == "secuTrialdata") {
+  if (inherits(x, "secuTrialdata")) {
     # wrap plot_recruitment to retrieve data
     recruitment_data <- plot_recruitment(x, return_data = TRUE)
     # construct header

diff --git a/R/check_export_options.R b/R/check_export_options.R
@@ -28,7 +28,7 @@
 #'
 #' secuTrialR:::check_export_options(sT_export)
 check_export_options <- function(dat) {
-  if (class(dat) != "secuTrialdata") {
+  if (!inherits(dat, "secuTrialdata")) {
     stop("check_export_options requires objects of the class 'secuTrialdata' as input.")
   }
   eo <- dat$export_options

diff --git a/R/diff_secuTrial.R b/R/diff_secuTrial.R
@@ -31,7 +31,7 @@
 #' diff_secuTrial(ctu06_v1, ctu06_v2)
 #'
 diff_secuTrial <- function(x, y) {
-  if (class(x) == "secuTrialdata" & class(y) == "secuTrialdata") {
+  if (inherits(x, "secuTrialdata") & inherits(y, "secuTrialdata")) {
 
     # comparisons are only possible if the project setup was exported
     if (! x$export_options$proj_setup & y$export_options$proj_setup) {

diff --git a/R/get.R b/R/get.R
@@ -20,7 +20,7 @@
 #' participants <- get_participants(sT_export)
 #'
 get_participants <- function(dat) {
-  if (class(dat) != "secuTrialdata") {
+  if (!inherits(dat, "secuTrialdata")) {
     stop("get_participants requires objects of the class 'secuTrialdata' as input.")
   }
 

diff --git a/R/links_secuTrial.R b/R/links_secuTrial.R
@@ -38,7 +38,7 @@
 #' links_secuTrial(sT_export, forms = "^ctu05")
 #' }
 links_secuTrial <- function(object, forms = NULL, formcol = "#d8b365", varcol = "#e5f5f9", plot = TRUE) {
-  if (!class(object) == "secuTrialdata") stop("object of class secuTrialdata expected")
+  if (!inherits(object, "secuTrialdata")) stop("object of class secuTrialdata expected")
   obj <- object[2:length(object)]
 
 

diff --git a/R/plot_recruitment.R b/R/plot_recruitment.R
@@ -31,7 +31,7 @@
 #' plot_recruitment(sT_export, rm_regex = "\\(.*\\)$")
 #'
 plot_recruitment <- function(x, return_data = FALSE, show_centres = TRUE, cex = 1, rm_regex = "") {
-  if (class(x) == "secuTrialdata") {
+  if (inherits(x, "secuTrialdata")) {
 
     # check for meta data Structure available
     if (! x$export_options$structure) {

diff --git a/R/return_hidden_items.R b/R/return_hidden_items.R
@@ -19,7 +19,7 @@
 #' return_hidden_items(sT_export)
 #'
 return_hidden_items <- function(x) {
-  if (class(x) == "secuTrialdata") {
+  if (inherits(x, "secuTrialdata")) {
 
     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/return_random_participants.R b/R/return_random_participants.R
@@ -32,7 +32,7 @@
 #'                            centres = c("Inselspital Bern (RPACK)", "Charité Berlin (RPACK)"))
 #'
 return_random_participants <- function(x, centres = "all", percent = 0.1, date = "1900-01-01", seed = 1) {
-  if (class(x) == "secuTrialdata") {
+  if (inherits(x, "secuTrialdata")) {
 
      # check for meta data Structure available
      if (! x$export_options$structure) {

diff --git a/R/return_scores.R b/R/return_scores.R
@@ -19,7 +19,7 @@
 #' return_scores(sT_export)
 #'
 return_scores <- function(x) {
-  if (class(x) == "secuTrialdata") {
+  if (inherits(x, "secuTrialdata")) {
     curr_items <- x[[x$export_options$meta_names$items]]
     scores <- curr_items[grep("calculated|berechnet", curr_items$itemtype), ]
     scores_relevant_col <- scores[, c("ffcolname", "itemtype", "fflabel")]

diff --git a/R/subset.R b/R/subset.R
@@ -47,7 +47,7 @@
 #' get_participants(sT_subset5)
 #'
 subset_secuTrial <- function(dat, participant = NULL, centre = NULL, exclude = FALSE) {
-  if (class(dat) != "secuTrialdata") {
+  if (!inherits(dat, "secuTrialdata")) {
     stop("subset_secuTrial() requires objects of the class 'secuTrialdata' as input parameter 'dat'.")
   }
   if (!is.null(participant) & !dat$export_options$add_id) {
@@ -88,7 +88,7 @@ subset_secuTrial <- function(dat, participant = NULL, centre = NULL, exclude = F
   participant_sel <- new_dat[[meta["casenodes"]]][["mnppid"]]
 
   for (tab in names(new_dat)) {
-    if (class(new_dat[[tab]]) != "data.frame") {
+    if (!inherits(new_dat[[tab]], "data.frame")) {
       next
     }
     if ("mnppid" %in% names(new_dat[[tab]])) {

diff --git a/README.Rmd b/README.Rmd
@@ -12,7 +12,7 @@ output:
 
 # secuTrialR
 
-`r badger::badge_custom("dev version", as.character(packageVersion("secuTrialR")), "blue", "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) [![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master)](https://travis-ci.com/github/SwissClinicalTrialOrganisation/secuTrialR) [![Actions Status](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/workflows/R-CMD-check/badge.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/actions) [![codecov](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR/branch/master/graphs/badge.svg)](https://codecov.io/github/SwissClinicalTrialOrganisation/secuTrialR)
+`r badger::badge_custom("dev version", as.character(packageVersion("secuTrialR")), "blue", "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) [![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master)](https://travis-ci.com/github/SwissClinicalTrialOrganisation/secuTrialR) [![Actions Status](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/workflows/R-CMD-check/badge.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/actions) 
 
 An R package to handle data from the clinical data management system (CDMS) [secuTrial](https://www.secutrial.com/en/).
 

diff --git a/README.md b/README.md
@@ -2,14 +2,13 @@
 
 # secuTrialR
 
-[![](https://img.shields.io/badge/dev%20version-1.1.0-blue.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR)
+[![](https://img.shields.io/badge/dev%20version-1.1.1-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)
 [![travis](https://api.travis-ci.com/SwissClinicalTrialOrganisation/secuTrialR.svg?branch=master)](https://travis-ci.com/github/SwissClinicalTrialOrganisation/secuTrialR)
 [![Actions
 Status](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/workflows/R-CMD-check/badge.svg)](https://github.com/SwissClinicalTrialOrganisation/secuTrialR/actions)
-[![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/).