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Remove RSI from package, add extra MIC scale functions

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dr. M.S. (Matthijs) Berends
2023-12-03 11:34:48 +01:00
parent 6f417d0ef2
commit c7461766ce
21 changed files with 260 additions and 580 deletions
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60
man/plot.Rd
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@ -2,10 +2,13 @@
% Please edit documentation in R/plot.R
\name{plot}
\alias{plot}
\alias{scale_x_mic}
\alias{scale_y_mic}
\alias{scale_colour_mic}
\alias{scale_fill_mic}
\alias{plot.mic}
\alias{autoplot.mic}
\alias{fortify.mic}
\alias{scale_x_mic}
\alias{plot.disk}
\alias{autoplot.disk}
\alias{fortify.disk}
@ -14,6 +17,14 @@
\alias{fortify.sir}
\title{Plotting for Classes \code{sir}, \code{mic} and \code{disk}}
\usage{
scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_y_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
\method{plot}{mic}(
x,
mo = NULL,
@ -48,16 +59,6 @@
\method{fortify}{mic}(object, ...)
scale_x_mic(
keep_operators = "edges",
mic_range = NULL,
...,
drop = FALSE,
guide = waiver(),
position = "bottom",
na.translate = TRUE
)
\method{plot}{disk}(
x,
main = deparse(substitute(x)),
@ -114,6 +115,12 @@ scale_x_mic(
\method{fortify}{sir}(object, ...)
}
\arguments{
\item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
\item{mic_range}{a manual range to plot the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{...}{arguments passed on to methods}
\item{x, object}{values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.sir]{as.sir()}} (or their \verb{random_*} variants, such as \code{\link[=random_mic]{random_mic()}})}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
@ -135,14 +142,6 @@ scale_x_mic(
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}.}
\item{...}{arguments passed on to methods}
\item{keep_operators}{a \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
\item{mic_range}{a manual range to plot the MIC values, e.g., \code{mic_range = c(0.001, 32)}. Use \code{NA} to set no limit on one side, e.g., \code{mic_range = c(NA, 32)}.}
\item{drop, guide, position, na.translate}{arguments passed on to \code{\link[ggplot2:scale_discrete]{ggplot2::scale_x_discrete()}}}
}
\value{
The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
@ -152,7 +151,7 @@ The \code{fortify()} functions return a \link{data.frame} as an extension for us
\description{
Functions to plot classes \code{sir}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.
Especially \code{\link[=scale_x_mic]{scale_x_mic()}} is a relevant wrapper to plot MIC values for \code{ggplot2}. It allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
Especially the \code{\link[=scale_*_mic]{scale_*_mic()}} functions are relevant wrappers to plot MIC values for \code{ggplot2}. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
}
\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.
@ -175,17 +174,6 @@ plot(some_mic_values, mo = "S. aureus", ab = "ampicillin")
plot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
\donttest{
if (require("ggplot2")) {
autoplot(some_mic_values)
}
if (require("ggplot2")) {
autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
}
if (require("ggplot2")) {
autoplot(some_sir_values)
}
}
# Plotting using scale_x_mic()
\donttest{
@ -212,5 +200,15 @@ if (require("ggplot2")) {
scale_x_mic(mic_range = c(1, 128)) +
labs(title = "with scale_x_mic() using a manual range")
}
if (require("ggplot2")) {
autoplot(some_mic_values)
}
if (require("ggplot2")) {
autoplot(some_disk_values, mo = "Escherichia coli", ab = "cipro")
}
if (require("ggplot2")) {
autoplot(some_sir_values)
}
}
}