Remove RSI from package, add extra MIC scale functions

man/AMR-deprecated.Rd

@@ -1,59 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/zz_deprecated.R
-\docType{data}
-\name{AMR-deprecated}
-\alias{AMR-deprecated}
-\alias{NA_rsi_}
-\alias{as.rsi}
-\alias{facet_rsi}
-\alias{geom_rsi}
-\alias{ggplot_rsi}
-\alias{ggplot_rsi_predict}
-\alias{is.rsi}
-\alias{is.rsi.eligible}
-\alias{labels_rsi_count}
-\alias{n_rsi}
-\alias{random_rsi}
-\alias{rsi_df}
-\alias{rsi_predict}
-\alias{scale_rsi_colours}
-\alias{theme_rsi}
-\title{Deprecated Functions}
-\format{
-An object of class \code{rsi} (inherits from \code{ordered}, \code{factor}) of length 1.
-}
-\usage{
-NA_rsi_
-
-as.rsi(x, ...)
-
-facet_rsi(...)
-
-geom_rsi(...)
-
-ggplot_rsi(...)
-
-ggplot_rsi_predict(...)
-
-is.rsi(...)
-
-is.rsi.eligible(...)
-
-labels_rsi_count(...)
-
-n_rsi(...)
-
-random_rsi(...)
-
-rsi_df(...)
-
-rsi_predict(...)
-
-scale_rsi_colours(...)
-
-theme_rsi(...)
-}
-\description{
-These functions are so-called '\link{Deprecated}'. \strong{They will be removed in a future release.} Using the functions will give a warning with the name of the function it has been replaced by (if there is one).
-}
-\keyword{internal}

man/as.mic.Rd

@@ -4,16 +4,19 @@
 \name{as.mic}
 \alias{as.mic}
 \alias{mic}
-\alias{NA_mic_}
 \alias{is.mic}
+\alias{NA_mic_}
+\alias{rescale_mic}
 \alias{droplevels.mic}
 \title{Transform Input to Minimum Inhibitory Concentrations (MIC)}
 \usage{
 as.mic(x, na.rm = FALSE, keep_operators = "all")
 
+is.mic(x)
+
 NA_mic_
 
-is.mic(x)
+rescale_mic(x, mic_range, keep_operators = "edges", as.mic = TRUE)
 
 \method{droplevels}{mic}(x, as.mic = FALSE, ...)
 }
@@ -24,6 +27,8 @@ is.mic(x)
 
 \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{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept - the default is \code{FALSE}}
 
 \item{...}{arguments passed on to methods}
@@ -77,6 +82,8 @@ Using \code{\link[=as.double]{as.double()}} or \code{\link[=as.numeric]{as.numer
 
 Use \code{\link[=droplevels]{droplevels()}} to drop unused levels. At default, it will return a plain factor. Use \code{droplevels(..., as.mic = TRUE)} to maintain the \code{mic} class.
 
+With \code{\link[=rescale_mic]{rescale_mic()}}, existing MIC ranges can be rescaled to a defined range of MIC values. This can be useful to better compare MIC distributions.
+
 \code{NA_mic_} is a missing value of the new \code{mic} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
 }
 \examples{
@@ -92,6 +99,9 @@ fivenum(mic_data)
 quantile(mic_data)
 all(mic_data < 512)
 
+# rescale MICs using rescale_mic()
+rescale_mic(mic_data, mic_range = c(4, 16))
+
 # interpret MIC values
 as.sir(
   x = as.mic(2),

man/ggplot_pca.Rd

@@ -130,16 +130,18 @@ if (require("dplyr")) {
   summary(pca_result)
 
   # old base R plotting method:
-  biplot(pca_result)
+  biplot(pca_result, main = "Base R biplot")
 
   # new ggplot2 plotting method using this package:
   if (require("ggplot2")) {
-    ggplot_pca(pca_result)
-
+    ggplot_pca(pca_result) +
+      labs(title = "ggplot2 biplot")
+  }
+  if (require("ggplot2")) {
     # still extendible with any ggplot2 function
     ggplot_pca(pca_result) +
       scale_colour_viridis_d() +
-      labs(title = "Title here")
+      labs(title = "ggplot2 biplot")
   }
 }
 }

man/plot.Rd

@@ -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)
+}
 }
 }