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(v2.1.1.9116) selectors as separate functions

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dr. M.S. (Matthijs) Berends
2024-12-13 09:44:54 +01:00
parent e231352617
commit 175a6777f3
16 changed files with 113 additions and 67 deletions
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40
man/AMR.Rd
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@ -61,29 +61,29 @@ Authors:
Other contributors:
\itemize{
\item Casper J. Albers (\href{https://orcid.org/0000-0002-9213-6743}{ORCID}) [thesis advisor]
\item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
\item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
\item Judith M. Fonville [contributor]
\item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]
\item Corinna Glasner (\href{https://orcid.org/0000-0003-1241-1328}{ORCID}) [thesis advisor]
\item Andrew P. Norgan (\href{https://orcid.org/0000-0002-2955-2066}{ORCID}) [contributor]
\item Anita Williams (\href{https://orcid.org/0000-0002-5295-8451}{ORCID}) [contributor]
\item Annick Lenglet (\href{https://orcid.org/0000-0003-2013-8405}{ORCID}) [contributor]
\item Anthony Underwood (\href{https://orcid.org/0000-0002-8547-4277}{ORCID}) [contributor]
\item Anton Mymrikov [contributor]
\item Bart C. Meijer [contributor]
\item Christian F. Luz (\href{https://orcid.org/0000-0001-5809-5995}{ORCID}) [contributor]
\item Dmytro Mykhailenko [contributor]
\item Eric H. L. C. M. Hazenberg [contributor]
\item Gwen Knight (\href{https://orcid.org/0000-0002-7263-9896}{ORCID}) [contributor]
\item Annick Lenglet (\href{https://orcid.org/0000-0003-2013-8405}{ORCID}) [contributor]
\item Christian F. Luz (\href{https://orcid.org/0000-0001-5809-5995}{ORCID}) [contributor]
\item Bart C. Meijer [contributor]
\item Dmytro Mykhailenko [contributor]
\item Anton Mymrikov [contributor]
\item Andrew P. Norgan (\href{https://orcid.org/0000-0002-2955-2066}{ORCID}) [contributor]
\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
\item Matthew Saab [contributor]
\item Jonas Salm [contributor]
\item Javier Sanchez (\href{https://orcid.org/0000-0003-2605-8094}{ORCID}) [contributor]
\item Rogier P. Schade [contributor]
\item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
\item Jason Stull (\href{https://orcid.org/0000-0002-9028-8153}{ORCID}) [contributor]
\item Anthony Underwood (\href{https://orcid.org/0000-0002-8547-4277}{ORCID}) [contributor]
\item Anita Williams (\href{https://orcid.org/0000-0002-5295-8451}{ORCID}) [contributor]
\item Javier Sanchez (\href{https://orcid.org/0000-0003-2605-8094}{ORCID}) [contributor]
\item Jonas Salm [contributor]
\item Judith M. Fonville [contributor]
\item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
\item Matthew Saab [contributor]
\item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
\item Rogier P. Schade [contributor]
\item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
\item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]
\item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
\item Casper J. Albers (\href{https://orcid.org/0000-0002-9213-6743}{ORCID}) [thesis advisor]
\item Corinna Glasner (\href{https://orcid.org/0000-0003-1241-1328}{ORCID}) [thesis advisor]
}
}

10
man/antibiotic_class_selectors.Rd
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@ -124,7 +124,7 @@ not_intrinsic_resistant(
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".}
}
\value{
(internally) a \link{character} vector of column names, with additional class \code{"ab_selector"}
When used inside selecting or filtering, this returns a \link{character} vector of column names, with additional class \code{"ab_selector"}. When used individually, this returns an \link[=as.ab]{'ab' vector} with all possible antimicrobial that the function would be able to select or filter.
}
\description{
These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group (according to the \link{antibiotics} data set), without the need to define the columns or antibiotic abbreviations.
@ -189,9 +189,15 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR
example_isolates
# you can use the selectors separately to retrieve all possible antimicrobials:
carbapenems()
# Though they are primarily intended to use for selections and filters.
# Examples sections below are split into 'dplyr', 'base R', and 'data.table':
\donttest{
\dontrun{
# dplyr -------------------------------------------------------------------
library(dplyr, warn.conflicts = FALSE)
@ -277,7 +283,7 @@ y <- example_isolates \%>\% filter(carbapenems() == "R")
z <- example_isolates \%>\% filter(if_all(carbapenems(), ~ .x == "R"))
identical(x, y) && identical(y, z)
}
# base R ------------------------------------------------------------------
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)

5
man/ggplot_sir.Rd
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@ -49,7 +49,10 @@ geom_sir(
facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)
scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)
scale_y_percent(
breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
limits = NULL
)
scale_sir_colours(..., aesthetics = "fill")