diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 3a0c14de..e4d9c3b7 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -123,7 +123,7 @@ jobs:
run: |
brew install mariadb-connector-c
- - name: Install dependencies
+ - name: Install package dependencies
if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
run: |
remotes::install_deps(dependencies = TRUE)
@@ -137,22 +137,22 @@ jobs:
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
- # - name: Run R CMD check
- # if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
- # env:
- # _R_CHECK_CRAN_INCOMING_: false
- # run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
- # shell: Rscript {0}
+ - name: Run R CMD check
+ if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
+ env:
+ _R_CHECK_CRAN_INCOMING_: false
+ run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+ shell: Rscript {0}
- name: Run R CMD check on older R versions
- # if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
+ if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
run: |
- R CMD check data-raw/AMR_*.tar.gz --no-manual --as-cran
+ R CMD check data-raw/AMR_*.tar.gz --no-manual --no-build-vignettes
- name: Show testthat output
if: always()
diff --git a/DESCRIPTION b/DESCRIPTION
index fc8083e2..85885258 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.4.0.9058
+Version: 1.4.0.9059
Date: 2021-01-04
Title: Antimicrobial Resistance Analysis
Authors@R: c(
diff --git a/NEWS.md b/NEWS.md
index 40a68ab8..83df7775 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.4.0.9058
+# AMR 1.4.0.9059
## Last updated: 4 January 2021
### New
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index f0d84d02..0276b60c 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -458,7 +458,7 @@ meet_criteria <- function(object,
stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth)
return(invisible())
}
- if (is.null(dim(object)) && length(object) == 1 && is.na(object)) {
+ if (is.null(dim(object)) && length(object) == 1 && suppressWarnings(is.na(object))) { # suppressWarnings for functions
stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
return(invisible())
}
@@ -527,23 +527,36 @@ meet_criteria <- function(object,
}
get_current_data <- function(arg_name, call) {
+ if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) {
+ if (is.na(arg_name)) {
+ warning_("this function can only be used in R >= 3.2", call = call)
+ return(data.frame())
+ } else {
+ stop_("argument `", arg_name, "` is missing with no default", call = call)
+ }
+ }
+
# try a (base R) method, by going over the complete system call stack with sys.frames()
not_set <- TRUE
frms <- lapply(sys.frames(), function(el) {
- if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
- # dplyr? - an element `.data` will be in the system call stack
- not_set <<- FALSE
- el$`.data`
- } else if (tryCatch(not_set == TRUE && any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
- # otherwise try base R:
- # an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
- # an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
- if (is.data.frame(el$xx)) {
+ if (".Generic" %in% names(el)) {
+ if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
+ # dplyr? - an element `.data` will be in the system call stack
not_set <<- FALSE
- el$xx
- } else if (is.data.frame(el$x)) {
- not_set <<- FALSE
- el$x
+ el$`.data`
+ } else if (tryCatch(not_set == TRUE && any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
+ # otherwise try base R:
+ # an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
+ # an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
+ if (tryCatch(is.data.frame(el$xx), error = function(e) FALSE)) {
+ not_set <<- FALSE
+ el$xx
+ } else if (tryCatch(is.data.frame(el$x))) {
+ not_set <<- FALSE
+ el$x
+ } else {
+ NULL
+ }
} else {
NULL
}
diff --git a/R/ab_class_selectors.R b/R/ab_class_selectors.R
index 673447ea..f3211490 100644
--- a/R/ab_class_selectors.R
+++ b/R/ab_class_selectors.R
@@ -27,7 +27,9 @@
#'
#' These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
#' @inheritParams filter_ab_class
-#' @details All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
+#' @details These functions only work in R 3.2 (2015) and later.
+#'
+#' All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the [antibiotics] data set. This means that a selector like e.g. [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
#' @rdname antibiotic_class_selectors
#' @seealso [filter_ab_class()] for the `filter()` equivalent.
#' @name antibiotic_class_selectors
@@ -161,7 +163,12 @@ tetracyclines <- function() {
ab_selector <- function(ab_class, function_name) {
meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
-
+
+ if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) {
+ warning_(function_name, "() can only be used in R >= 3.2", call = FALSE)
+ return(NULL)
+ }
+
vars_df <- get_current_data(arg_name = NA, call = -3)
ab_in_data <- get_column_abx(vars_df, info = FALSE)
diff --git a/data-raw/AMR_1.4.0.9058.tar.gz b/data-raw/AMR_1.4.0.9059.tar.gz
similarity index 79%
rename from data-raw/AMR_1.4.0.9058.tar.gz
rename to data-raw/AMR_1.4.0.9059.tar.gz
index 4bdc18cc..5ea064c4 100644
Binary files a/data-raw/AMR_1.4.0.9058.tar.gz and b/data-raw/AMR_1.4.0.9059.tar.gz differ
diff --git a/docs/404.html b/docs/404.html
index dc184c34..576efc7e 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9058
+ 1.4.0.9059
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index f8426757..e6a80ec3 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9058
+ 1.4.0.9059
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 4116a500..99b0cafa 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9058
+ 1.4.0.9059
diff --git a/docs/authors.html b/docs/authors.html
index cb175c91..85a4a984 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9058
+ 1.4.0.9059
diff --git a/docs/index.html b/docs/index.html
index 8f977006..b9642e1d 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -43,7 +43,7 @@
AMR (for R)
- 1.4.0.9058
+ 1.4.0.9059
diff --git a/docs/news/index.html b/docs/news/index.html
index 52d71f3a..efaee483 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9058
+ 1.4.0.9059
@@ -236,9 +236,9 @@
Source: NEWS.md
-
-
diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd
index f87f9146..23b2b354 100644
--- a/man/antibiotic_class_selectors.Rd
+++ b/man/antibiotic_class_selectors.Rd
@@ -53,6 +53,8 @@ tetracyclines()
These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.
}
\details{
+These functions only work in R 3.2 (2015) and later.
+
All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the \link{antibiotics} data set. This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
}
\section{Reference data publicly available}{