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(v1.4.0.9059) ab class selector fix

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dr. M.S. (Matthijs) Berends 2021-01-04 12:29:25 +01:00
parent 82cfa24ea4
commit c9de74c81a
17 changed files with 64 additions and 41 deletions
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18
.github/workflows/check.yaml vendored
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@ -123,7 +123,7 @@ jobs:
run: | run: |
brew install mariadb-connector-c 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' if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
run: | run: |
remotes::install_deps(dependencies = TRUE) remotes::install_deps(dependencies = TRUE)
@ -137,22 +137,22 @@ jobs:
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0} shell: Rscript {0}
# - name: Run R CMD check - name: Run R CMD check
# 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: env:
# _R_CHECK_CRAN_INCOMING_: false _R_CHECK_CRAN_INCOMING_: false
# run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
# shell: Rscript {0} shell: Rscript {0}
- name: Run R CMD check on older R versions - 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: env:
_R_CHECK_CRAN_INCOMING_: false _R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false _R_CHECK_FORCE_SUGGESTS_: false
_R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose
run: | 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 - name: Show testthat output
if: always() if: always()

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.4.0.9058 Version: 1.4.0.9059
Date: 2021-01-04 Date: 2021-01-04
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9058 # AMR 1.4.0.9059
## <small>Last updated: 4 January 2021</small> ## <small>Last updated: 4 January 2021</small>
### New ### 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()`): * 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()`):

41
R/aa_helper_functions.R
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@ -458,7 +458,7 @@ meet_criteria <- function(object,
stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth) stop_if(allow_NULL == FALSE, "argument `", obj_name, "` must not be NULL", call = call_depth)
return(invisible()) 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) stop_if(allow_NA == FALSE, "argument `", obj_name, "` must not be NA", call = call_depth)
return(invisible()) return(invisible())
} }
@ -527,23 +527,36 @@ meet_criteria <- function(object,
} }
get_current_data <- function(arg_name, call) { 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() # try a (base R) method, by going over the complete system call stack with sys.frames()
not_set <- TRUE not_set <- TRUE
frms <- lapply(sys.frames(), function(el) { frms <- lapply(sys.frames(), function(el) {
if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) { if (".Generic" %in% names(el)) {
# dplyr? - an element `.data` will be in the system call stack if (tryCatch(not_set == TRUE && ".data" %in% names(el) && is.data.frame(el$`.data`), error = function(e) FALSE)) {
not_set <<- FALSE # dplyr? - an element `.data` will be in the system call stack
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)) {
not_set <<- FALSE not_set <<- FALSE
el$xx el$`.data`
} else if (is.data.frame(el$x)) { } else if (tryCatch(not_set == TRUE && any(c("x", "xx") %in% names(el)), error = function(e) FALSE)) {
not_set <<- FALSE # otherwise try base R:
el$x # 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 { } else {
NULL NULL
} }

11
R/ab_class_selectors.R
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@ -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. #' 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 #' @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 #' @rdname antibiotic_class_selectors
#' @seealso [filter_ab_class()] for the `filter()` equivalent. #' @seealso [filter_ab_class()] for the `filter()` equivalent.
#' @name antibiotic_class_selectors #' @name antibiotic_class_selectors
@ -161,7 +163,12 @@ tetracyclines <- function() {
ab_selector <- function(ab_class, function_name) { ab_selector <- function(ab_class, function_name) {
meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1) 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) 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) vars_df <- get_current_data(arg_name = NA, call = -3)
ab_in_data <- get_column_abx(vars_df, info = FALSE) ab_in_data <- get_column_abx(vars_df, info = FALSE)

BIN
data-raw/AMR_1.4.0.9058.tar.gz → data-raw/AMR_1.4.0.9059.tar.gz
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Binary file not shown.

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1409058" class="section level1"> <div id="amr-1409059" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9058"> <h1 class="page-header" data-toc-text="1.4.0.9059">
<a href="#amr-1409058" class="anchor"></a>AMR 1.4.0.9058<small> Unreleased </small> <a href="#amr-1409059" class="anchor"></a>AMR 1.4.0.9059<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-4-january-2021" class="section level2"> <div id="last-updated-4-january-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-01-04T10:27Z last_built: 2021-01-04T11:28Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

5
docs/reference/antibiotic_class_selectors.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>
@ -281,7 +281,8 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<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> <p>These functions only work in R 3.2 (2015) and later.</p>
<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>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2> <h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference data publicly available</h2>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9058</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9059</span>
</span> </span>
</div> </div>

2
man/antibiotic_class_selectors.Rd
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@ -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. 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{ \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. 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}{ \section{Reference data publicly available}{