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mirror of https://github.com/msberends/AMR.git synced 2025-07-10 14:21:48 +02:00

(v2.1.1.9163) cleanup

This commit is contained in:
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions

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@ -52,7 +52,7 @@
#' @details At default, the names of antibiotics will be shown on the plots using [ab_name()]. This can be set with the `translate_ab` argument. See [count_df()].
#'
#' [geom_sir()] will take any variable from the data that has an [`sir`] class (created with [as.sir()]) using [sir_df()] and will plot bars with the percentage S, I, and R. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
#'
#'
#' Additional functions include:
#'
#' * [facet_sir()] creates 2d plots (at default based on S/I/R) using [ggplot2::facet_wrap()].
@ -121,8 +121,10 @@
#' ) %>%
#' ggplot() +
#' geom_col(aes(x = x, y = y, fill = z)) +
#' scale_sir_colours(aesthetics = "fill",
#' Value4 = "S", Value5 = "I", Value6 = "R")
#' scale_sir_colours(
#' aesthetics = "fill",
#' Value4 = "S", Value5 = "I", Value6 = "R"
#' )
#' }
#' if (require("ggplot2") && require("dplyr")) {
#' # resistance of ciprofloxacine per age group
@ -212,7 +214,7 @@ ggplot_sir <- function(data,
meet_criteria(caption, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(x.title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(y.title, allow_class = "character", has_length = 1, allow_NULL = TRUE)
x_deparse <- deparse(substitute(x))
if (x_deparse != "x") {
x <- x_deparse
@ -309,7 +311,7 @@ geom_sir <- function(position = NULL,
if (identical(position, "fill")) {
position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
}
x_deparse <- deparse(substitute(x))
if (x_deparse != "x") {
x <- x_deparse
@ -323,7 +325,7 @@ geom_sir <- function(position = NULL,
} else if (tolower(x) %in% tolower(c("SIR", "sir", "interpretations", "result"))) {
x <- "interpretation"
}
ggplot2::geom_col(
data = function(x) {
sir_df(