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fixes
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Package: AMR
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Package: AMR
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Version: 1.8.2.9106
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Version: 1.8.2.9107
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Date: 2023-02-06
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Date: 2023-02-06
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9106
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# AMR 1.8.2.9107
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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@ -94,7 +94,9 @@ TAXONOMY_VERSION <- list(
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)
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)
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globalVariables(c(
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globalVariables(c(
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".mo",
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".rowid",
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".rowid",
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".syndromic_group",
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"ab",
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"ab",
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"ab_txt",
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"ab_txt",
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"affect_ab_name",
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"affect_ab_name",
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@ -105,8 +107,9 @@ globalVariables(c(
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"atc_group1",
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"atc_group1",
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"atc_group2",
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"atc_group2",
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"base_ab",
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"base_ab",
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"ci_min",
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"ci_max",
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"ci_max",
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"ci_min",
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"clinical_breakpoints",
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"code",
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"code",
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"cols",
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"cols",
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"count",
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"count",
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@ -130,14 +133,15 @@ globalVariables(c(
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"language",
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"language",
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"lookup",
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"lookup",
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"method",
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"method",
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"mic",
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"mic ",
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"mic ",
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"mic",
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"microorganism",
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"microorganism",
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"microorganisms",
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"microorganisms",
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"microorganisms.codes",
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"microorganisms.codes",
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"mo",
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"mo",
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"name",
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"name",
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"new",
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"new",
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"numerator",
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"observations",
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"observations",
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"old",
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"old",
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"old_name",
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"old_name",
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@ -149,13 +153,15 @@ globalVariables(c(
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"reference.rule_group",
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"reference.rule_group",
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"reference.version",
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"reference.version",
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"rowid",
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"rowid",
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"sir",
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"clinical_breakpoints",
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"rule_group",
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"rule_group",
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"rule_name",
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"rule_name",
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"S",
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"se_max",
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"se_max",
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"se_min",
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"se_min",
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"SI",
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"sir",
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"species",
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"species",
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"syndromic_group",
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"total",
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"total",
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"txt",
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"txt",
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"type",
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"type",
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@ -363,7 +363,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
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if (is.data.frame(data)) {
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if (is.data.frame(data)) {
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if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
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if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
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out <- tryCatch(suppressWarnings(c(...)), error = function(e) NULL)
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out <- tryCatch(suppressWarnings(unlist(list(...))), error = function(e) NULL)
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if (!is.null(out)) {
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if (!is.null(out)) {
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df <- data[, out, drop = FALSE]
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df <- data[, out, drop = FALSE]
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} else {
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} else {
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@ -43,6 +43,8 @@
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#' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see *Source*.
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#' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see *Source*.
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#' @param combine_SI a [logical] to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (defaults to `TRUE`)
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#' @param combine_SI a [logical] to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (defaults to `TRUE`)
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#' @param sep a separating character for antibiotic columns in combination antibiograms
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#' @param sep a separating character for antibiotic columns in combination antibiograms
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#' @param object an [antibiogram()] object
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#' @param ... method extensions
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#' @details This function returns a table with values between 0 and 100 for *susceptibility*, not resistance.
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#' @details This function returns a table with values between 0 and 100 for *susceptibility*, not resistance.
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#'
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#'
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#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms.
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#' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms.
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@ -314,7 +316,7 @@ antibiogram <- function(x,
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if (identical(select, import_fn("select", "dplyr", error_on_fail = FALSE))) {
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if (identical(select, import_fn("select", "dplyr", error_on_fail = FALSE))) {
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antibiotics <- suppressWarnings(x %>% select({{ antibiotics }}) %>% colnames())
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antibiotics <- suppressWarnings(x %>% select({{ antibiotics }}) %>% colnames())
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} else {
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} else {
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antibiotics <- x %>% select(antibiotics) %>% colnames()
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antibiotics <- colnames(x[, antibiotics, drop = FALSE])
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}
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}
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}
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}
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@ -447,9 +449,9 @@ plot.antibiogram <- function(x, ...) {
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df <- df[order(df$mo), , drop = FALSE]
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df <- df[order(df$mo), , drop = FALSE]
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}
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}
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mo_levels = unique(df$mo)
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mo_levels = unique(df$mo)
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mfrow_old <- par()$mfrow
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mfrow_old <- graphics::par()$mfrow
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sqrt_levels <- sqrt(length(mo_levels))
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sqrt_levels <- sqrt(length(mo_levels))
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par(mfrow = c(ceiling(sqrt_levels), floor(sqrt_levels)))
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graphics::par(mfrow = c(ceiling(sqrt_levels), floor(sqrt_levels)))
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for (i in seq_along(mo_levels)) {
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for (i in seq_along(mo_levels)) {
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mo <- mo_levels[i]
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mo <- mo_levels[i]
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df_sub <- df[df$mo == mo, , drop = FALSE]
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df_sub <- df[df$mo == mo, , drop = FALSE]
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@ -463,12 +465,14 @@ plot.antibiogram <- function(x, ...) {
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main = mo,
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main = mo,
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legend = NULL)
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legend = NULL)
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}
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}
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par(mfrow = mfrow_old)
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graphics::par(mfrow = mfrow_old)
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}
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}
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#' @export
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#' @export
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#' @noRd
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#' @noRd
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barplot.antibiogram <- plot.antibiogram
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barplot.antibiogram <- function(height, ...) {
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plot(height, ...)
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}
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#' @method autoplot antibiogram
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#' @method autoplot antibiogram
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#' @rdname antibiogram
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#' @rdname antibiogram
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@ -63,6 +63,10 @@ antibiogram(
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\item{sep}{a separating character for antibiotic columns in combination antibiograms}
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\item{sep}{a separating character for antibiotic columns in combination antibiograms}
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\item{...}{method extensions}
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\item{object}{an \code{\link[=antibiogram]{antibiogram()}} object}
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\item{as_kable}{a \link{logical} to indicate whether the printing should be done using \code{\link[knitr:kable]{knitr::kable()}} (which is the default in non-interactive sessions)}
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\item{as_kable}{a \link{logical} to indicate whether the printing should be done using \code{\link[knitr:kable]{knitr::kable()}} (which is the default in non-interactive sessions)}
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}
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}
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\description{
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\description{
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