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https://github.com/msberends/AMR.git
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(v1.4.0.9059) ab class selector fix
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parent
82cfa24ea4
commit
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18
.github/workflows/check.yaml
vendored
18
.github/workflows/check.yaml
vendored
@ -123,7 +123,7 @@ jobs:
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run: |
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brew install mariadb-connector-c
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- name: Install dependencies
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- name: Install package dependencies
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if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
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run: |
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remotes::install_deps(dependencies = TRUE)
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@ -137,22 +137,22 @@ jobs:
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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# - name: Run R CMD check
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# if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
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# env:
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# _R_CHECK_CRAN_INCOMING_: false
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# run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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# shell: Rscript {0}
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- name: Run R CMD check
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if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
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env:
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_R_CHECK_CRAN_INCOMING_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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- name: Run R CMD check on older R versions
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# if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
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if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
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env:
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_FORCE_SUGGESTS_: false
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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run: |
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R CMD check data-raw/AMR_*.tar.gz --no-manual --as-cran
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R CMD check data-raw/AMR_*.tar.gz --no-manual --no-build-vignettes
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- name: Show testthat output
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if: always()
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.4.0.9058
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Version: 1.4.0.9059
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Date: 2021-01-04
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.4.0.9058
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# AMR 1.4.0.9059
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## <small>Last updated: 4 January 2021</small>
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### New
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* 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()`):
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@ -458,7 +458,7 @@ meet_criteria <- function(object,
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stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth)
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return(invisible())
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}
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if (is.null(dim(object)) && length(object) == 1 && is.na(object)) {
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if (is.null(dim(object)) && length(object) == 1 && suppressWarnings(is.na(object))) { # suppressWarnings for functions
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stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
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return(invisible())
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}
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@ -527,23 +527,36 @@ meet_criteria <- function(object,
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}
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get_current_data <- function(arg_name, call) {
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if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) {
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if (is.na(arg_name)) {
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warning_("this function can only be used in R >= 3.2", call = call)
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return(data.frame())
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} else {
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stop_("argument `", arg_name, "` is missing with no default", call = call)
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}
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}
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# try a (base R) method, by going over the complete system call stack with sys.frames()
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not_set <- TRUE
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frms <- lapply(sys.frames(), function(el) {
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if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
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# dplyr? - an element `.data` will be in the system call stack
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not_set <<- FALSE
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el$`.data`
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} else if (tryCatch(not_set == TRUE && any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
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# otherwise try base R:
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# an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
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# an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
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if (is.data.frame(el$xx)) {
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if (".Generic" %in% names(el)) {
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if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
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# dplyr? - an element `.data` will be in the system call stack
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not_set <<- FALSE
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el$xx
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} else if (is.data.frame(el$x)) {
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not_set <<- FALSE
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el$x
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el$`.data`
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} else if (tryCatch(not_set == TRUE && any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
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# otherwise try base R:
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# an element `x` will be in this environment for only cols, e.g. `example_isolates[, carbapenems()]`
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# an element `xx` will be in this environment for rows + cols, e.g. `example_isolates[c(1:3), carbapenems()]`
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if (tryCatch(is.data.frame(el$xx), error = function(e) FALSE)) {
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not_set <<- FALSE
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el$xx
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} else if (tryCatch(is.data.frame(el$x))) {
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not_set <<- FALSE
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el$x
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} else {
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NULL
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}
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} else {
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NULL
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}
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@ -27,7 +27,9 @@
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#'
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#' 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.
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#' @inheritParams filter_ab_class
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#' @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.
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#' @details These functions only work in R 3.2 (2015) and later.
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#'
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#' 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.
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#' @rdname antibiotic_class_selectors
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#' @seealso [filter_ab_class()] for the `filter()` equivalent.
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#' @name antibiotic_class_selectors
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@ -162,6 +164,11 @@ ab_selector <- function(ab_class, function_name) {
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meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
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meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
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if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) {
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warning_(function_name, "() can only be used in R >= 3.2", call = FALSE)
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return(NULL)
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}
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vars_df <- get_current_data(arg_name = NA, call = -3)
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ab_in_data <- get_column_abx(vars_df, info = FALSE)
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Binary file not shown.
@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1409058" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9058">
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<a href="#amr-1409058" class="anchor"></a>AMR 1.4.0.9058<small> Unreleased </small>
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<div id="amr-1409059" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9059">
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<a href="#amr-1409059" class="anchor"></a>AMR 1.4.0.9059<small> Unreleased </small>
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</h1>
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<div id="last-updated-4-january-2021" class="section level2">
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<h2 class="hasAnchor">
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-01-04T10:27Z
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last_built: 2021-01-04T11:28Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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@ -82,7 +82,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -281,7 +281,8 @@
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
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<p>These functions only work in R 3.2 (2015) and later.</p>
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<p>All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the <a href='antibiotics.html'>antibiotics</a> data set. This means that a selector like e.g. <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
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<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
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</span>
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</div>
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@ -53,6 +53,8 @@ tetracyclines()
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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.
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}
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\details{
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These functions only work in R 3.2 (2015) and later.
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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.
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}
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\section{Reference data publicly available}{
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