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mirror of https://github.com/msberends/AMR.git synced 2025-07-08 08:32:04 +02:00

(v1.1.0.9013) lose dependencies

This commit is contained in:
2020-05-19 13:18:01 +02:00
parent 19703eb5d3
commit cb1814f5ff
16 changed files with 24 additions and 135 deletions

View File

@ -429,8 +429,8 @@ percentage <- function(x, digits = NULL, ...) {
# prevent dependency on package 'backports'
# these functions were not available in previous versions of R (last checked: R 4.0.0)
# see here for the full list: https://github.com/r-lib/backports
strrep = function(x, times) {
x = as.character(x)
strrep <- function(x, times) {
x <- as.character(x)
if (length(x) == 0L)
return(x)
unlist(.mapply(function(x, times) {
@ -441,18 +441,18 @@ strrep = function(x, times) {
paste0(replicate(times, x), collapse = "")
}, list(x = x, times = times), MoreArgs = list()), use.names = FALSE)
}
trimws <- function (x, which = c("both", "left", "right")) {
which = match.arg(which)
mysub = function(re, x) sub(re, "", x, perl = TRUE)
trimws <- function(x, which = c("both", "left", "right")) {
which <- match.arg(which)
mysub <- function(re, x) sub(re, "", x, perl = TRUE)
if (which == "left")
return(mysub("^[ \t\r\n]+", x))
if (which == "right")
return(mysub("[ \t\r\n]+$", x))
mysub("[ \t\r\n]+$", mysub("^[ \t\r\n]+", x))
}
isFALSE <- function (x) {
isFALSE <- function(x) {
is.logical(x) && length(x) == 1L && !is.na(x) && !x
}
deparse1 = function (expr, collapse = " ", width.cutoff = 500L, ...) {
deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
paste(deparse(expr, width.cutoff, ...), collapse = collapse)
}

2
R/ab.R
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@ -352,7 +352,7 @@ print.ab <- function(x, ...) {
#' @exportMethod as.data.frame.ab
#' @export
#' @noRd
as.data.frame.ab <- function (x, ...) {
as.data.frame.ab <- function(x, ...) {
nm <- deparse1(substitute(x))
if (!"nm" %in% names(list(...))) {
as.data.frame.vector(as.ab(x), ..., nm = nm)

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@ -1,72 +0,0 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
if ("cleaner" %in% rownames(utils::installed.packages())) {
freq <- get("freq", envir = asNamespace("cleaner"))
freq.default <- get("freq.default", envir = asNamespace("cleaner"))
} else {
freq <- ""
freq.default <- ""
}
#' @method freq mo
#' @export
#' @noRd
freq.mo <- function(x, ...) {
x_noNA <- as.mo(x[!is.na(x)]) # as.mo() to get the newest mo codes
grams <- mo_gramstain(x_noNA, language = NULL)
digits <- list(...)$digits
if (is.null(digits)) {
digits <- 2
}
freq.default(x = x, ...,
.add_header = list(`Gram-negative` = paste0(format(sum(grams == "Gram-negative", na.rm = TRUE),
big.mark = ",",
decimal.mark = "."),
" (", percentage(sum(grams == "Gram-negative", na.rm = TRUE) / length(grams), digits = digits),
")"),
`Gram-positive` = paste0(format(sum(grams == "Gram-positive", na.rm = TRUE),
big.mark = ",",
decimal.mark = "."),
" (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), digits = digits),
")"),
`No of genera` = n_distinct(mo_genus(x_noNA, language = NULL)),
`No of species` = n_distinct(paste(mo_genus(x_noNA, language = NULL),
mo_species(x_noNA, language = NULL)))))
}
#' @method freq rsi
#' @export
#' @noRd
freq.rsi <- function(x, ...) {
x_name <- deparse(substitute(x))
x_name <- gsub(".*[$]", "", x_name)
ab <- suppressMessages(suppressWarnings(as.ab(x_name)))
if (!is.na(ab)) {
freq.default(x = x, ...,
.add_header = list(Drug = paste0(ab_name(ab), " (", ab, ", ", ab_atc(ab), ")"),
group = ab_group(ab),
`%SI` = susceptibility(x, minimum = 0, as_percent = TRUE)))
} else {
freq.default(x = x, ...,
.add_header = list(`%SI` = susceptibility(x, minimum = 0, as_percent = TRUE)))
}
}

2
R/mo.R
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@ -1578,7 +1578,7 @@ summary.mo <- function(object, ...) {
#' @exportMethod as.data.frame.mo
#' @export
#' @noRd
as.data.frame.mo <- function (x, ...) {
as.data.frame.mo <- function(x, ...) {
nm <- deparse1(substitute(x))
if (!"nm" %in% names(list(...))) {
as.data.frame.vector(as.mo(x), ..., nm = nm)