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add labels_rsi_count
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@ -1,6 +1,6 @@
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Package: AMR
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Package: AMR
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Version: 0.3.0.9007
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Version: 0.3.0.9008
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Date: 2018-09-08
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Date: 2018-09-16
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Title: Antimicrobial Resistance Analysis
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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Authors@R: c(
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person(
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person(
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@ -87,6 +87,7 @@ export(is.rsi.eligible)
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export(key_antibiotics)
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export(key_antibiotics)
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export(key_antibiotics_equal)
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export(key_antibiotics_equal)
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export(kurtosis)
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export(kurtosis)
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export(labels_rsi_count)
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export(left_join_microorganisms)
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export(left_join_microorganisms)
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export(like)
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export(like)
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export(mo_aerobic)
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export(mo_aerobic)
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2
NEWS.md
2
NEWS.md
@ -25,6 +25,7 @@
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* Column names inputs of `EUCAST_rules`, `first_isolate` and `key_antibiotics`
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* Column names inputs of `EUCAST_rules`, `first_isolate` and `key_antibiotics`
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* Column names of datasets `microorganisms` and `septic_patients`
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* Column names of datasets `microorganisms` and `septic_patients`
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* All old syntaxes will still work with this version, but will throw warnings
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* All old syntaxes will still work with this version, but will throw warnings
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* Function `labels_rsi_count` to print datalabels on a RSI `ggplot2` model
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* Functions `as.atc` and `is.atc` to transform/look up antibiotic ATC codes as defined by the WHO. The existing function `guess_atc` is now an alias of `as.atc`.
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* Functions `as.atc` and `is.atc` to transform/look up antibiotic ATC codes as defined by the WHO. The existing function `guess_atc` is now an alias of `as.atc`.
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* Aliases for existing function `mo_property`: `mo_family`, `mo_genus`, `mo_species`, `mo_subspecies`, `mo_fullname`, `mo_shortname`, `mo_aerobic`, `mo_type` and `mo_gramstain`. They also come with support for German, Dutch, French, Italian, Spanish and Portuguese, and it defaults to the systems locale:
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* Aliases for existing function `mo_property`: `mo_family`, `mo_genus`, `mo_species`, `mo_subspecies`, `mo_fullname`, `mo_shortname`, `mo_aerobic`, `mo_type` and `mo_gramstain`. They also come with support for German, Dutch, French, Italian, Spanish and Portuguese, and it defaults to the systems locale:
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```r
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```r
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@ -70,6 +71,7 @@
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```
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```
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* Edited `ggplot_rsi` and `geom_rsi` so they can cope with `count_df`. The new `fun` parameter has value `portion_df` at default, but can be set to `count_df`.
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* Edited `ggplot_rsi` and `geom_rsi` so they can cope with `count_df`. The new `fun` parameter has value `portion_df` at default, but can be set to `count_df`.
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* Fix for `ggplot_rsi` when the `ggplot2` package was not loaded
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* Fix for `ggplot_rsi` when the `ggplot2` package was not loaded
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* Added datalabels function `labels_rsi_count` to `ggplot_rsi`
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* Added possibility to set any parameter to `geom_rsi` (and `ggplot_rsi`) so you can set your own preferences
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* Added possibility to set any parameter to `geom_rsi` (and `ggplot_rsi`) so you can set your own preferences
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* Fix for joins, where predefined suffices would not be honoured
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* Fix for joins, where predefined suffices would not be honoured
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* Added parameter `quote` to the `freq` function
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* Added parameter `quote` to the `freq` function
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@ -36,7 +36,7 @@
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#' ab_umcg("amcl") # AMCL
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#' ab_umcg("amcl") # AMCL
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ab_property <- function(x, property = 'official') {
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ab_property <- function(x, property = 'official') {
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property <- property[1]
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property <- property[1]
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if (!property %in% colnames(antibiotics)) {
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if (!property %in% colnames(AMR::antibiotics)) {
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stop("invalid property: ", property, " - use a column name of the `antibiotics` data set")
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stop("invalid property: ", property, " - use a column name of the `antibiotics` data set")
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}
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}
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if (!is.atc(x)) {
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if (!is.atc(x)) {
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@ -146,6 +146,10 @@ count_S <- function(...) {
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count_df <- function(data,
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count_df <- function(data,
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translate_ab = getOption("get_antibiotic_names", "official")) {
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translate_ab = getOption("get_antibiotic_names", "official")) {
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if (!"data.frame" %in% class(data)) {
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stop("`count_df` must be called on a data.frame")
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}
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if (data %>% select_if(is.rsi) %>% ncol() == 0) {
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if (data %>% select_if(is.rsi) %>% ncol() == 0) {
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stop("No columns with class 'rsi' found. See ?as.rsi.")
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stop("No columns with class 'rsi' found. See ?as.rsi.")
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}
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}
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@ -177,7 +181,7 @@ count_df <- function(data,
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res <- bind_rows(resS, resI, resR) %>%
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res <- bind_rows(resS, resI, resR) %>%
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mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
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mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
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tidyr::gather(Antibiotic, Count, -Interpretation, -data.groups)
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tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)
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if (!translate_ab == FALSE) {
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if (!translate_ab == FALSE) {
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if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {
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if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {
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@ -20,13 +20,16 @@
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#'
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#'
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#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions.
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#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}} functions.
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#' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})
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#' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})
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#' @param position position adjustment of bars, either \code{"fill"}, \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})
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#' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}
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#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable
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#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
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#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable
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#' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.
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#' @param translate_ab a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.
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#' @param fun function to transform \code{data}, either \code{\link{portion_df}} (default) or \code{\link{count_df}}
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#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
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#' @param nrow (when using \code{facet}) number of rows
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#' @param nrow (when using \code{facet}) number of rows
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#' @param datalabels show datalabels using \code{labels_rsi_count}, will at default only be shown when \code{fun = count_df}
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#' @param datalabels.size size of the datalabels
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#' @param datalabels.colour colour of the datalabels
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#' @param ... other parameters passed on to \code{geom_rsi}
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#' @param ... other parameters passed on to \code{geom_rsi}
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#' @details At default, the names of antibiotics will be shown on the plots using \code{\link{abname}}. This can be set with the option \code{get_antibiotic_names} (a logical value), so change it e.g. to \code{FALSE} with \code{options(get_antibiotic_names = FALSE)}.
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#' @details At default, the names of antibiotics will be shown on the plots using \code{\link{abname}}. This can be set with the option \code{get_antibiotic_names} (a logical value), so change it e.g. to \code{FALSE} with \code{options(get_antibiotic_names = FALSE)}.
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#'
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#'
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@ -35,12 +38,14 @@
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#'
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#'
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#' \code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2]{facet_wrap}}.
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#' \code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2]{facet_wrap}}.
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#'
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#'
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#' \code{scale_y_percent} transforms the y axis to a 0 to 100\% range.
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#' \code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_y_continuous}}.
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#'
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#'
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#' \code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R.
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#' \code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R, using \code{\link[ggplot2]{scale_fill_brewer}}.
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#'
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#'
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#' \code{theme_rsi} is a \code{\link[ggplot2]{theme}} with minimal distraction.
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#' \code{theme_rsi} is a \code{\link[ggplot2]{theme}} with minimal distraction.
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#'
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#'
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#' \code{labels_rsi_count} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2]{geom_text}}
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#'
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#' \code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
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#' \code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
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#' @rdname ggplot_rsi
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#' @rdname ggplot_rsi
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#' @export
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#' @export
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@ -58,6 +63,7 @@
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#' geom_rsi() +
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#' geom_rsi() +
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#' scale_y_percent() +
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#' scale_y_percent() +
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#' scale_rsi_colours() +
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#' scale_rsi_colours() +
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#' labels_rsi_count() +
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#' theme_rsi()
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#' theme_rsi()
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#'
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#'
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#' # or better yet, simplify this using the wrapper function - a single command:
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#' # or better yet, simplify this using the wrapper function - a single command:
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@ -131,8 +137,11 @@ ggplot_rsi <- function(data,
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# params = list(),
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# params = list(),
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facet = NULL,
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facet = NULL,
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translate_ab = "official",
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translate_ab = "official",
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fun = portion_df,
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fun = count_df,
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nrow = NULL,
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nrow = NULL,
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datalabels = TRUE,
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datalabels.size = 3,
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datalabels.colour = "grey15",
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...) {
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...) {
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if (!"ggplot2" %in% rownames(installed.packages())) {
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if (!"ggplot2" %in% rownames(installed.packages())) {
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@ -174,11 +183,22 @@ ggplot_rsi <- function(data,
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# set RSI colours
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# set RSI colours
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p <- p + scale_rsi_colours()
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p <- p + scale_rsi_colours()
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}
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}
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if (fun_name == "portion_df") {
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if (is.null(position)) {
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position <- "fill"
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}
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if (fun_name == "portion_df"
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# portions, so use y scale with percentage
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# portions, so use y scale with percentage
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p <- p + scale_y_percent()
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p <- p + scale_y_percent()
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}
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}
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if (fun_name == "count_df" & datalabels == TRUE) {
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p <- p + labels_rsi_count(position = position,
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x = x,
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datalabels.size = datalabels.size,
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datalabels.colour = datalabels.colour)
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}
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if (!is.null(facet)) {
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if (!is.null(facet)) {
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p <- p + facet_rsi(facet = facet, nrow = nrow)
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p <- p + facet_rsi(facet = facet, nrow = nrow)
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}
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}
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@ -192,20 +212,19 @@ geom_rsi <- function(position = NULL,
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x = c("Antibiotic", "Interpretation"),
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x = c("Antibiotic", "Interpretation"),
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fill = "Interpretation",
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fill = "Interpretation",
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translate_ab = "official",
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translate_ab = "official",
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fun = portion_df,
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fun = count_df,
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...) {
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...) {
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fun_name <- deparse(substitute(fun))
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fun_name <- deparse(substitute(fun))
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if (!fun_name %in% c("portion_df", "count_df", "fun")) {
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if (!fun_name %in% c("portion_df", "count_df", "fun")) {
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stop("`fun` must be portion_df or count_df")
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stop("`fun` must be portion_df or count_df")
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}
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}
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y <- "Value"
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if (identical(fun, count_df)) {
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if (identical(fun, count_df)) {
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y <- "Count"
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if (missing(position) | is.null(position)) {
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if (missing(position) | is.null(position)) {
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position <- "dodge"
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position <- "fill"
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}
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}
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} else {
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} else {
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y <- "Percentage"
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if (missing(position) | is.null(position)) {
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if (missing(position) | is.null(position)) {
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position <- "stack"
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position <- "stack"
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}
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}
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@ -264,7 +283,6 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
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#' @export
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#' @export
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scale_y_percent <- function() {
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scale_y_percent <- function() {
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ggplot2::scale_y_continuous(breaks = seq(0, 1, 0.1),
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ggplot2::scale_y_continuous(breaks = seq(0, 1, 0.1),
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limits = c(0, 1),
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labels = percent(seq(0, 1, 0.1)))
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labels = percent(seq(0, 1, 0.1)))
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}
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}
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@ -282,3 +300,35 @@ theme_rsi <- function() {
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panel.grid.minor = ggplot2::element_blank(),
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panel.grid.minor = ggplot2::element_blank(),
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panel.grid.major.y = ggplot2::element_line(colour = "grey75"))
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panel.grid.major.y = ggplot2::element_line(colour = "grey75"))
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}
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}
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#' @rdname ggplot_rsi
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#' @export
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labels_rsi_count <- function(position = NULL,
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x = "Antibiotic",
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datalabels.size = 3,
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datalabels.colour = "grey15") {
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if (is.null(position)) {
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position <- "fill"
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}
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if (position == "fill") {
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position <- ggplot2::position_fill(vjust = 0.5)
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}
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ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
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x = x,
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y = "Value"),
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position = position,
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data = getlbls,
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inherit.aes = FALSE,
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size = datalabels.size,
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colour = datalabels.colour)
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}
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#' @importFrom dplyr %>% group_by mutate
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getlbls <- function(data) {
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data %>%
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count_df() %>%
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group_by(Antibiotic) %>%
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mutate(lbl = paste0(percent(Value / sum(Value, na.rm = TRUE), force_zero = TRUE),
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" (n=", Value, ")")) %>%
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mutate(lbl = ifelse(lbl == "0.0% (n=0)", "", lbl))
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}
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@ -22,7 +22,6 @@ globalVariables(c(".",
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"antibiotics",
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"antibiotics",
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"cnt",
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"cnt",
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"count",
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"count",
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"Count",
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"cum_count",
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"cum_count",
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"cum_percent",
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"cum_percent",
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"date_lab",
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"date_lab",
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@ -37,6 +36,7 @@ globalVariables(c(".",
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"key_ab",
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"key_ab",
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"key_ab_lag",
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"key_ab_lag",
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"key_ab_other",
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"key_ab_other",
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"lbl",
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"median",
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"median",
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"mic",
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"mic",
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"microorganisms",
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"microorganisms",
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@ -46,7 +46,6 @@ globalVariables(c(".",
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"other_pat_or_mo",
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"other_pat_or_mo",
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"Pasted",
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"Pasted",
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"patient_id",
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"patient_id",
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"Percentage",
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"prevalence",
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"prevalence",
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"R",
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"R",
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"real_first_isolate",
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"real_first_isolate",
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@ -54,4 +53,5 @@ globalVariables(c(".",
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"septic_patients",
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"septic_patients",
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"species",
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"species",
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"value",
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"value",
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"Value",
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"y"))
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"y"))
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@ -187,7 +187,7 @@ mo_aerobic <- function(x) {
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#' @export
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#' @export
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mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE, language = NULL) {
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mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE, language = NULL) {
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property <- tolower(property[1])
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property <- tolower(property[1])
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if (!property %in% colnames(microorganisms)) {
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if (!property %in% colnames(AMR::microorganisms)) {
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stop("invalid property: ", property, " - use a column name of the `microorganisms` data set")
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stop("invalid property: ", property, " - use a column name of the `microorganisms` data set")
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}
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}
|
||||||
result1 <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced
|
result1 <- as.mo(x = x, Becker = Becker, Lancefield = Lancefield) # this will give a warning if x cannot be coerced
|
||||||
|
@ -203,6 +203,10 @@ portion_df <- function(data,
|
|||||||
minimum = 30,
|
minimum = 30,
|
||||||
as_percent = FALSE) {
|
as_percent = FALSE) {
|
||||||
|
|
||||||
|
if (!"data.frame" %in% class(data)) {
|
||||||
|
stop("`portion_df` must be called on a data.frame")
|
||||||
|
}
|
||||||
|
|
||||||
if (data %>% select_if(is.rsi) %>% ncol() == 0) {
|
if (data %>% select_if(is.rsi) %>% ncol() == 0) {
|
||||||
stop("No columns with class 'rsi' found. See ?as.rsi.")
|
stop("No columns with class 'rsi' found. See ?as.rsi.")
|
||||||
}
|
}
|
||||||
@ -240,7 +244,7 @@ portion_df <- function(data,
|
|||||||
|
|
||||||
res <- bind_rows(resS, resI, resR) %>%
|
res <- bind_rows(resS, resI, resR) %>%
|
||||||
mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
|
mutate(Interpretation = factor(Interpretation, levels = c("R", "I", "S"), ordered = TRUE)) %>%
|
||||||
tidyr::gather(Antibiotic, Percentage, -Interpretation, -data.groups)
|
tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups)
|
||||||
|
|
||||||
if (!translate_ab == FALSE) {
|
if (!translate_ab == FALSE) {
|
||||||
if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {
|
if (!tolower(translate_ab) %in% tolower(colnames(AMR::antibiotics))) {
|
||||||
|
@ -161,7 +161,8 @@ Adjust it with any parameter you know from the `ggplot2` package:
|
|||||||
```r
|
```r
|
||||||
septic_patients %>%
|
septic_patients %>%
|
||||||
select(amox, nitr, fosf, trim, cipr) %>%
|
select(amox, nitr, fosf, trim, cipr) %>%
|
||||||
ggplot_rsi(width = 0.5, colour = "black", size = 1, linetype = 2, alpha = 0.25)
|
ggplot_rsi(datalabels = FALSE,
|
||||||
|
width = 0.5, colour = "black", size = 1, linetype = 2, alpha = 0.25)
|
||||||
```
|
```
|
||||||
|
|
||||||
![example_3_rsi](man/figures/rsi_example3.png)
|
![example_3_rsi](man/figures/rsi_example3.png)
|
||||||
@ -174,7 +175,8 @@ septic_patients %>%
|
|||||||
group_by(hospital_id) %>%
|
group_by(hospital_id) %>%
|
||||||
ggplot_rsi(x = "hospital_id",
|
ggplot_rsi(x = "hospital_id",
|
||||||
facet = "Antibiotic",
|
facet = "Antibiotic",
|
||||||
nrow = 1) +
|
nrow = 1,
|
||||||
|
datalabels = FALSE) +
|
||||||
labs(title = "AMR of Anti-UTI Drugs Per Hospital",
|
labs(title = "AMR of Anti-UTI Drugs Per Hospital",
|
||||||
x = "Hospital")
|
x = "Hospital")
|
||||||
```
|
```
|
||||||
|
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@ -7,15 +7,17 @@
|
|||||||
\alias{scale_y_percent}
|
\alias{scale_y_percent}
|
||||||
\alias{scale_rsi_colours}
|
\alias{scale_rsi_colours}
|
||||||
\alias{theme_rsi}
|
\alias{theme_rsi}
|
||||||
|
\alias{labels_rsi_count}
|
||||||
\title{AMR bar plots with \code{ggplot}}
|
\title{AMR bar plots with \code{ggplot}}
|
||||||
\usage{
|
\usage{
|
||||||
ggplot_rsi(data, position = NULL, x = "Antibiotic",
|
ggplot_rsi(data, position = NULL, x = "Antibiotic",
|
||||||
fill = "Interpretation", facet = NULL, translate_ab = "official",
|
fill = "Interpretation", facet = NULL, translate_ab = "official",
|
||||||
fun = portion_df, nrow = NULL, ...)
|
fun = count_df, nrow = NULL, datalabels = TRUE,
|
||||||
|
datalabels.size = 3, datalabels.colour = "grey15", ...)
|
||||||
|
|
||||||
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
|
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"),
|
||||||
fill = "Interpretation", translate_ab = "official",
|
fill = "Interpretation", translate_ab = "official", fun = count_df,
|
||||||
fun = portion_df, ...)
|
...)
|
||||||
|
|
||||||
facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL)
|
facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL)
|
||||||
|
|
||||||
@ -24,11 +26,14 @@ scale_y_percent()
|
|||||||
scale_rsi_colours()
|
scale_rsi_colours()
|
||||||
|
|
||||||
theme_rsi()
|
theme_rsi()
|
||||||
|
|
||||||
|
labels_rsi_count(position = NULL, x = "Antibiotic",
|
||||||
|
datalabels.size = 3, datalabels.colour = "grey15")
|
||||||
}
|
}
|
||||||
\arguments{
|
\arguments{
|
||||||
\item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}
|
\item{data}{a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})}
|
||||||
|
|
||||||
\item{position}{position adjustment of bars, either \code{"fill"}, \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} (default when \code{fun} is \code{\link{count_df}})}
|
\item{position}{position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}}
|
||||||
|
|
||||||
\item{x}{variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable}
|
\item{x}{variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable}
|
||||||
|
|
||||||
@ -38,10 +43,16 @@ theme_rsi()
|
|||||||
|
|
||||||
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.}
|
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations into, using \code{\link{abname}}. Default behaviour is to translate to official names according to the WHO. Use \code{translate_ab = FALSE} to disable translation.}
|
||||||
|
|
||||||
\item{fun}{function to transform \code{data}, either \code{\link{portion_df}} (default) or \code{\link{count_df}}}
|
\item{fun}{function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}}
|
||||||
|
|
||||||
\item{nrow}{(when using \code{facet}) number of rows}
|
\item{nrow}{(when using \code{facet}) number of rows}
|
||||||
|
|
||||||
|
\item{datalabels}{show datalabels using \code{labels_rsi_count}, will at default only be shown when \code{fun = count_df}}
|
||||||
|
|
||||||
|
\item{datalabels.size}{size of the datalabels}
|
||||||
|
|
||||||
|
\item{datalabels.colour}{colour of the datalabels}
|
||||||
|
|
||||||
\item{...}{other parameters passed on to \code{geom_rsi}}
|
\item{...}{other parameters passed on to \code{geom_rsi}}
|
||||||
}
|
}
|
||||||
\description{
|
\description{
|
||||||
@ -55,12 +66,14 @@ At default, the names of antibiotics will be shown on the plots using \code{\lin
|
|||||||
|
|
||||||
\code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2]{facet_wrap}}.
|
\code{facet_rsi} creates 2d plots (at default based on S/I/R) using \code{\link[ggplot2]{facet_wrap}}.
|
||||||
|
|
||||||
\code{scale_y_percent} transforms the y axis to a 0 to 100\% range.
|
\code{scale_y_percent} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2]{scale_y_continuous}}.
|
||||||
|
|
||||||
\code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R.
|
\code{scale_rsi_colours} sets colours to the bars: green for S, yellow for I and red for R, using \code{\link[ggplot2]{scale_fill_brewer}}.
|
||||||
|
|
||||||
\code{theme_rsi} is a \code{\link[ggplot2]{theme}} with minimal distraction.
|
\code{theme_rsi} is a \code{\link[ggplot2]{theme}} with minimal distraction.
|
||||||
|
|
||||||
|
\code{labels_rsi_count} print datalabels on the bars with percentage and amount of isolates using \code{\link[ggplot2]{geom_text}}
|
||||||
|
|
||||||
\code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
|
\code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
|
||||||
}
|
}
|
||||||
\examples{
|
\examples{
|
||||||
@ -77,6 +90,7 @@ ggplot(df) +
|
|||||||
geom_rsi() +
|
geom_rsi() +
|
||||||
scale_y_percent() +
|
scale_y_percent() +
|
||||||
scale_rsi_colours() +
|
scale_rsi_colours() +
|
||||||
|
labels_rsi_count() +
|
||||||
theme_rsi()
|
theme_rsi()
|
||||||
|
|
||||||
# or better yet, simplify this using the wrapper function - a single command:
|
# or better yet, simplify this using the wrapper function - a single command:
|
||||||
|
@ -41,4 +41,6 @@ test_that("counts work", {
|
|||||||
expect_error(count_S("test", minimum = "test"))
|
expect_error(count_S("test", minimum = "test"))
|
||||||
expect_error(count_S("test", as_percent = "test"))
|
expect_error(count_S("test", as_percent = "test"))
|
||||||
|
|
||||||
|
expect_error(count_df(c("A", "B", "C")))
|
||||||
|
|
||||||
})
|
})
|
||||||
|
@ -112,7 +112,7 @@ test_that("old rsi works", {
|
|||||||
|
|
||||||
# portion_df
|
# portion_df
|
||||||
expect_equal(
|
expect_equal(
|
||||||
septic_patients %>% select(amox) %>% portion_df() %>% pull(Percentage),
|
septic_patients %>% select(amox) %>% portion_df() %>% pull(Value),
|
||||||
c(septic_patients$amox %>% portion_S(),
|
c(septic_patients$amox %>% portion_S(),
|
||||||
septic_patients$amox %>% portion_I(),
|
septic_patients$amox %>% portion_I(),
|
||||||
septic_patients$amox %>% portion_R())
|
septic_patients$amox %>% portion_R())
|
||||||
@ -165,4 +165,6 @@ test_that("prediction of rsi works", {
|
|||||||
col_ab = "mero",
|
col_ab = "mero",
|
||||||
col_date = "date",
|
col_date = "date",
|
||||||
info = TRUE))
|
info = TRUE))
|
||||||
|
|
||||||
|
expect_error(portion_df(c("A", "B", "C")))
|
||||||
})
|
})
|
||||||
|
Loading…
Reference in New Issue
Block a user