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Replace RSI with SIR

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Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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186
R/plot.R
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@ -27,23 +27,23 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
#' Plotting for Classes `rsi`, `mic` and `disk`
#' Plotting for Classes `sir`, `mic` and `disk`
#'
#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
#' Functions to plot classes `sir`, `mic` and `disk`, with support for base \R and `ggplot2`.
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()] (or their `random_*` variants, such as [random_mic()])
#' @param x,object values created with [as.mic()], [as.disk()] or [as.sir()] (or their `random_*` variants, such as [random_mic()])
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]
#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
#' @param main,title title of the plot
#' @param xlab,ylab axis title
#' @param colours_RSI colours to use for filling in the bars, must be a vector of three values (in the order R, S and I). The default colours are colour-blind friendly.
#' @param colours_SIR colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.
#' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
#' @param expand a [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
#' @details
#' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
#'
#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` argument are: `r vector_and(AMR::rsi_translation$guideline, quotes = TRUE, reverse = TRUE)`.
#' For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the `guideline` argument are: `r vector_and(AMR::clinical_breakpoints$guideline, quotes = TRUE, reverse = TRUE)`.
#'
#' Simply using `"CLSI"` or `"EUCAST"` as input will automatically select the latest version of that guideline.
#' @name plot
@ -55,11 +55,11 @@
#' @examples
#' some_mic_values <- random_mic(size = 100)
#' some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
#' some_rsi_values <- random_rsi(50, prob_RSI = c(0.30, 0.55, 0.05))
#' some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))
#'
#' plot(some_mic_values)
#' plot(some_disk_values)
#' plot(some_rsi_values)
#' plot(some_sir_values)
#'
#' # when providing the microorganism and antibiotic, colours will show interpretations:
#' plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
@ -74,7 +74,7 @@
#' autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
#' }
#' if (require("ggplot2")) {
#' autoplot(some_rsi_values)
#' autoplot(some_sir_values)
#' }
#' }
NULL
@ -90,7 +90,7 @@ plot.mic <- function(x,
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...) {
@ -100,7 +100,7 @@ plot.mic <- function(x,
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -112,8 +112,8 @@ plot.mic <- function(x,
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3)
if (length(colours_SIR) == 1) {
colours_SIR <- rep(colours_SIR, 3)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
@ -124,7 +124,7 @@ plot.mic <- function(x,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
colours_SIR = colours_SIR,
fn = as.mic,
language = language,
...
@ -132,7 +132,7 @@ plot.mic <- function(x,
barplot(x,
col = cols_sub$cols,
main = main,
ylim = c(0, max(x) * ifelse(any(colours_RSI %in% cols_sub$cols), 1.1, 1)),
ylim = c(0, max(x) * ifelse(any(colours_SIR %in% cols_sub$cols), 1.1, 1)),
ylab = ylab,
xlab = xlab,
axes = FALSE
@ -142,20 +142,20 @@ plot.mic <- function(x,
mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
}
if (any(colours_RSI %in% cols_sub$cols)) {
if (any(colours_SIR %in% cols_sub$cols)) {
legend_txt <- character(0)
legend_col <- character(0)
if (any(cols_sub$cols == colours_RSI[2] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- "Susceptible"
legend_col <- colours_RSI[2]
legend_col <- colours_SIR[1]
}
if (any(cols_sub$cols == colours_RSI[3] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_col <- c(legend_col, colours_RSI[3])
legend_col <- c(legend_col, colours_SIR[2])
}
if (any(cols_sub$cols == colours_RSI[1] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Resistant")
legend_col <- c(legend_col, colours_RSI[1])
legend_col <- c(legend_col, colours_SIR[3])
}
legend("top",
@ -181,7 +181,7 @@ barplot.mic <- function(height,
main = deparse(substitute(height)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...) {
@ -191,7 +191,7 @@ barplot.mic <- function(height,
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -213,7 +213,7 @@ barplot.mic <- function(height,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
colours_SIR = colours_SIR,
...
)
}
@ -228,7 +228,7 @@ autoplot.mic <- function(object,
title = deparse(substitute(object)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...) {
@ -239,7 +239,7 @@ autoplot.mic <- function(object,
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -264,7 +264,7 @@ autoplot.mic <- function(object,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
colours_SIR = colours_SIR,
fn = as.mic,
language = language,
...
@ -272,9 +272,9 @@ autoplot.mic <- function(object,
df <- as.data.frame(x, stringsAsFactors = TRUE)
colnames(df) <- c("mic", "count")
df$cols <- cols_sub$cols
df$cols[df$cols == colours_RSI[1]] <- "Resistant"
df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
df$cols[df$cols == colours_SIR[1]] <- "Susceptible"
df$cols[df$cols == colours_SIR[2]] <- plot_name_of_I(cols_sub$guideline)
df$cols[df$cols == colours_SIR[3]] <- "Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language
@ -283,12 +283,12 @@ autoplot.mic <- function(object,
)
p <- ggplot2::ggplot(df)
if (any(colours_RSI %in% cols_sub$cols)) {
if (any(colours_SIR %in% cols_sub$cols)) {
vals <- c(
"Resistant" = colours_RSI[1],
"Susceptible" = colours_RSI[2],
"Susceptible, incr. exp." = colours_RSI[3],
"Intermediate" = colours_RSI[3]
"Susceptible" = colours_SIR[1],
"Susceptible, incr. exp." = colours_SIR[2],
"Intermediate" = colours_SIR[2],
"Resistant" = colours_SIR[3]
)
names(vals) <- translate_into_language(names(vals), language = language)
p <- p +
@ -329,7 +329,7 @@ plot.disk <- function(x,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...) {
@ -339,7 +339,7 @@ plot.disk <- function(x,
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -351,8 +351,8 @@ plot.disk <- function(x,
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3)
if (length(colours_SIR) == 1) {
colours_SIR <- rep(colours_SIR, 3)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
@ -363,7 +363,7 @@ plot.disk <- function(x,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
colours_SIR = colours_SIR,
fn = as.disk,
language = language,
...
@ -372,7 +372,7 @@ plot.disk <- function(x,
barplot(x,
col = cols_sub$cols,
main = main,
ylim = c(0, max(x) * ifelse(any(colours_RSI %in% cols_sub$cols), 1.1, 1)),
ylim = c(0, max(x) * ifelse(any(colours_SIR %in% cols_sub$cols), 1.1, 1)),
ylab = ylab,
xlab = xlab,
axes = FALSE
@ -382,20 +382,20 @@ plot.disk <- function(x,
mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
}
if (any(colours_RSI %in% cols_sub$cols)) {
if (any(colours_SIR %in% cols_sub$cols)) {
legend_txt <- character(0)
legend_col <- character(0)
if (any(cols_sub$cols == colours_RSI[1] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
legend_txt <- "Resistant"
legend_col <- colours_RSI[1]
legend_col <- colours_SIR[3]
}
if (any(cols_sub$cols == colours_RSI[3] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, plot_name_of_I(cols_sub$guideline))
legend_col <- c(legend_col, colours_RSI[3])
legend_col <- c(legend_col, colours_SIR[2])
}
if (any(cols_sub$cols == colours_RSI[2] & cols_sub$count > 0)) {
if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
legend_txt <- c(legend_txt, "Susceptible")
legend_col <- c(legend_col, colours_RSI[2])
legend_col <- c(legend_col, colours_SIR[1])
}
legend("top",
x.intersp = 0.5,
@ -420,7 +420,7 @@ barplot.disk <- function(height,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...) {
@ -430,7 +430,7 @@ barplot.disk <- function(height,
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -452,7 +452,7 @@ barplot.disk <- function(height,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
colours_SIR = colours_SIR,
...
)
}
@ -467,7 +467,7 @@ autoplot.disk <- function(object,
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
guideline = "EUCAST",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...) {
@ -478,7 +478,7 @@ autoplot.disk <- function(object,
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -503,7 +503,7 @@ autoplot.disk <- function(object,
mo = mo,
ab = ab,
guideline = guideline,
colours_RSI = colours_RSI,
colours_SIR = colours_SIR,
fn = as.disk,
language = language,
...
@ -512,9 +512,9 @@ autoplot.disk <- function(object,
colnames(df) <- c("disk", "count")
df$cols <- cols_sub$cols
df$cols[df$cols == colours_RSI[1]] <- "Resistant"
df$cols[df$cols == colours_RSI[2]] <- "Susceptible"
df$cols[df$cols == colours_RSI[3]] <- plot_name_of_I(cols_sub$guideline)
df$cols[df$cols == colours_SIR[1]] <- "Susceptible"
df$cols[df$cols == colours_SIR[2]] <- plot_name_of_I(cols_sub$guideline)
df$cols[df$cols == colours_SIR[3]] <- "Resistant"
df$cols <- factor(translate_into_language(df$cols, language = language),
levels = translate_into_language(c("Susceptible", plot_name_of_I(cols_sub$guideline), "Resistant"),
language = language
@ -523,12 +523,12 @@ autoplot.disk <- function(object,
)
p <- ggplot2::ggplot(df)
if (any(colours_RSI %in% cols_sub$cols)) {
if (any(colours_SIR %in% cols_sub$cols)) {
vals <- c(
"Resistant" = colours_RSI[1],
"Susceptible" = colours_RSI[2],
"Susceptible, incr. exp." = colours_RSI[3],
"Intermediate" = colours_RSI[3]
"Susceptible" = colours_SIR[1],
"Susceptible, incr. exp." = colours_SIR[2],
"Intermediate" = colours_SIR[2],
"Resistant" = colours_SIR[3]
)
names(vals) <- translate_into_language(names(vals), language = language)
p <- p +
@ -558,11 +558,11 @@ fortify.disk <- function(object, ...) {
)
}
#' @method plot rsi
#' @method plot sir
#' @export
#' @importFrom graphics plot text axis
#' @rdname plot
plot.rsi <- function(x,
plot.sir <- function(x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
main = deparse(substitute(x)),
@ -627,22 +627,22 @@ plot.rsi <- function(x,
}
#' @method barplot rsi
#' @method barplot sir
#' @importFrom graphics barplot axis
#' @export
#' @noRd
barplot.rsi <- function(height,
barplot.sir <- function(height,
main = deparse(substitute(height)),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
...) {
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
language <- validate_language(language)
meet_criteria(expand, allow_class = "logical", has_length = 1)
@ -654,17 +654,15 @@ barplot.rsi <- function(height,
xlab <- translate_into_language(xlab, language = language)
}
if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3)
} else {
colours_RSI <- c(colours_RSI[2], colours_RSI[3], colours_RSI[1])
if (length(colours_SIR) == 1) {
colours_SIR <- rep(colours_SIR, 3)
}
main <- gsub(" +", " ", paste0(main, collapse = " "))
x <- table(height)
x <- x[c(1, 2, 3)]
barplot(x,
col = colours_RSI,
col = colours_SIR,
xlab = xlab,
main = main,
ylab = ylab,
@ -673,21 +671,21 @@ barplot.rsi <- function(height,
axis(2, seq(0, max(x)))
}
#' @method autoplot rsi
#' @method autoplot sir
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
autoplot.rsi <- function(object,
autoplot.sir <- function(object,
title = deparse(substitute(object)),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
...) {
stop_ifnot_installed("ggplot2")
meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
meet_criteria(colours_RSI, allow_class = "character", has_length = c(1, 3))
meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
# translate if not specifically set
if (missing(ylab)) {
@ -704,20 +702,20 @@ autoplot.rsi <- function(object,
title <- gsub(" +", " ", paste0(title, collapse = " "))
}
if (length(colours_RSI) == 1) {
colours_RSI <- rep(colours_RSI, 3)
if (length(colours_SIR) == 1) {
colours_SIR <- rep(colours_SIR, 3)
}
df <- as.data.frame(table(object), stringsAsFactors = TRUE)
colnames(df) <- c("rsi", "count")
colnames(df) <- c("sir", "count")
ggplot2::ggplot(df) +
ggplot2::geom_col(ggplot2::aes(x = rsi, y = count, fill = rsi)) +
ggplot2::geom_col(ggplot2::aes(x = sir, y = count, fill = sir)) +
# limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
ggplot2::scale_fill_manual(
values = c(
"R" = colours_RSI[1],
"S" = colours_RSI[2],
"I" = colours_RSI[3]
"S" = colours_SIR[1],
"I" = colours_SIR[2],
"R" = colours_SIR[3]
),
limits = force
) +
@ -725,10 +723,10 @@ autoplot.rsi <- function(object,
ggplot2::theme(legend.position = "none")
}
#' @method fortify rsi
#' @method fortify sir
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
fortify.rsi <- function(object, ...) {
fortify.sir <- function(object, ...) {
stats::setNames(
as.data.frame(table(object)),
c("x", "y")
@ -782,18 +780,18 @@ plot_name_of_I <- function(guideline) {
}
}
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, fn, language, ...) {
guideline <- get_guideline(guideline, AMR::rsi_translation)
plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, fn, language, ...) {
guideline <- get_guideline(guideline, AMR::clinical_breakpoints)
if (!is.null(mo) && !is.null(ab)) {
# interpret and give colour based on MIC values
mo <- as.mo(mo)
ab <- as.ab(ab)
rsi <- suppressWarnings(suppressMessages(as.rsi(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...)))
cols <- character(length = length(rsi))
cols[is.na(rsi)] <- "#BEBEBE"
cols[rsi == "R"] <- colours_RSI[1]
cols[rsi == "S"] <- colours_RSI[2]
cols[rsi == "I"] <- colours_RSI[3]
sir <- suppressWarnings(suppressMessages(as.sir(fn(names(x)), mo = mo, ab = ab, guideline = guideline, ...)))
cols <- character(length = length(sir))
cols[is.na(sir)] <- "#BEBEBE"
cols[sir == "S"] <- colours_SIR[1]
cols[sir == "I"] <- colours_SIR[2]
cols[sir == "R"] <- colours_SIR[3]
moname <- mo_name(mo, language = language)
abname <- ab_name(ab, language = language)
if (all(cols == "#BEBEBE")) {