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(v1.5.0.9026) vignette update, support for GISA

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dr. M.S. (Matthijs) Berends
2021-02-25 12:31:12 +01:00
parent a673407904
commit 1737d56ae4
36 changed files with 604 additions and 480 deletions
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11
man/ggplot_rsi.Rd
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@ -24,8 +24,8 @@ ggplot_rsi(
minimum = 30,
language = get_locale(),
nrow = NULL,
colours = c(S = "#61a8ff", SI = "#61a8ff", I = "#61f7ff", IR = "#ff6961", R =
"#ff6961"),
colours = c(S = "#3CAEA3", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B", R =
"#ED553B"),
datalabels = TRUE,
datalabels.size = 2.5,
datalabels.colour = "grey15",
@ -100,7 +100,7 @@ labels_rsi_count(
\item{nrow}{(when using \code{facet}) number of rows}
\item{colours}{a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} for standard \link[ggplot2:ggplot]{ggplot2} colours. The default colours are colour-blind friendly.}
\item{colours}{a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} for standard \link[ggplot2:ggplot]{ggplot2} colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.}
\item{datalabels}{show datalabels using \code{\link[=labels_rsi_count]{labels_rsi_count()}}}
@ -208,11 +208,6 @@ example_isolates \%>\%
CIP) \%>\%
ggplot_rsi(x = "age_group")
# for colourblind mode, use divergent colours from the viridis package:
example_isolates \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\%
ggplot_rsi() +
scale_fill_viridis_d()
# a shorter version which also adjusts data label colours:
example_isolates \%>\%
select(AMX, NIT, FOS, TMP, CIP) \%>\%

4
man/plot.Rd
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@ -72,7 +72,7 @@
)
}
\arguments{
\item{x}{MIC values created with \code{\link[=as.mic]{as.mic()}} or disk diffusion values created with \code{\link[=as.disk]{as.disk()}}}
\item{x, data}{MIC values created with \code{\link[=as.mic]{as.mic()}} or disk diffusion values created with \code{\link[=as.disk]{as.disk()}}}
\item{main, title}{title of the plot}
@ -99,6 +99,8 @@ The \code{ggplot} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model
Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support for base R and \code{ggplot2}.
}
\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 \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".
Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.