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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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data-raw/gpt_training_text_v2.1.1.9112.txt → data-raw/gpt_training_text_v2.1.1.9116.txt
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@@ -1,5 +1,5 @@
This files contains all context you must know about the AMR package for R.
First and foremost, you are trained on version 2.1.1.9112. Remember this whenever someone asks which AMR package version you’re at.
First and foremost, you are trained on version 2.1.1.9116. Remember this whenever someone asks which AMR package version you’re at.
--------------------------------
THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'NAMESPACE':
@@ -811,29 +811,29 @@ 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]
}
}
@@ -2051,7 +2051,7 @@ 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.
@@ -2116,9 +2116,15 @@ 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)
@@ -2204,7 +2210,7 @@ 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)
@@ -5405,7 +5411,10 @@ 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")