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reftbl in plots, speedup for as.sir() and mo_validate

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dr. M.S. (Matthijs) Berends
2023-07-10 16:43:46 +02:00
parent 70c601ca11
commit a4e2e25e3f
14 changed files with 128 additions and 65 deletions
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12
man/plot.Rd
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@ -24,6 +24,8 @@
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...
)
@ -38,6 +40,8 @@
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...
)
@ -54,6 +58,8 @@
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...
)
@ -68,6 +74,8 @@
colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
language = get_AMR_locale(),
expand = TRUE,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"),
...
)
@ -113,6 +121,10 @@
\item{expand}{a \link{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.}
\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}
}
\value{