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(v1.6.0.9048) ab selectors overhaul

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dr. M.S. (Matthijs) Berends
2021-05-19 22:55:42 +02:00
parent 6920c0be41
commit 2413efd5c1
32 changed files with 1182 additions and 939 deletions
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54
man/antibiotic_class_selectors.Rd
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@ -58,12 +58,14 @@ tetracyclines(only_rsi_columns = FALSE)
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
}
\description{
These functions help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
}
\details{
\strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
All columns will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.) in the \link{antibiotics} data set. This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
These functions can be used in data set calls for selecting columns and filtering rows, see \emph{Examples}. They support base R, but work more convenient in dplyr functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}.
All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) in the \link{antibiotics} data set. This means that a selector like e.g. \code{\link[=aminoglycosides]{aminoglycosides()}} will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
The group of betalactams consists of all carbapenems, cephalosporins and penicillins.
}
@ -89,11 +91,31 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
# `example_isolates` is a data set available in the AMR package.
# See ?example_isolates.
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
# Base R ------------------------------------------------------------------
# select columns 'IPM' (imipenem) and 'MEM' (meropenem)
example_isolates[, carbapenems()]
# this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
example_isolates[, c("mo", aminoglycosides())]
# filter using any() or all()
example_isolates[any(carbapenems() == "R"), ]
subset(example_isolates, any(carbapenems() == "R"))
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
example_isolates[any(carbapenems()), ]
example_isolates[all(carbapenems()), ]
# filter with multiple antibiotic selectors using c()
example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]
# filter + select in one go: get penicillins in carbapenems-resistant strains
example_isolates[any(carbapenems() == "R"), penicillins()]
# dplyr -------------------------------------------------------------------
if (require("dplyr")) {
# this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):
@ -104,6 +126,20 @@ if (require("dplyr")) {
example_isolates \%>\%
select(mo, aminoglycosides())
# any() and all() work in dplyr's filter() too:
example_isolates \%>\%
filter(any(aminoglycosides() == "R"),
all(cephalosporins_2nd() == "R"))
# also works with c():
example_isolates \%>\%
filter(any(c(carbapenems(), aminoglycosides()) == "R"))
# not setting any/all will automatically apply all():
example_isolates \%>\%
filter(aminoglycosides() == "R")
#> i Assuming a filter on all 4 aminoglycosides.
# this will select columns 'mo' and all antimycobacterial drugs ('RIF'):
example_isolates \%>\%
select(mo, ab_class("mycobact"))
@ -122,12 +158,10 @@ if (require("dplyr")) {
select(penicillins()) # only the 'J01CA01' column will be selected
# with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
# with dplyr 1.0.0 and higher (that adds 'across()'), this is all equal:
# (though the row names on the first are more correct)
example_isolates \%>\% filter_carbapenems("R", "all")
example_isolates \%>\% filter(across(carbapenems(), ~. == "R"))
example_isolates[carbapenems() == "R", ]
example_isolates \%>\% filter(carbapenems() == "R")
example_isolates \%>\% filter(across(carbapenems(), ~.x == "R"))
}
}
\seealso{
\code{\link[=filter_ab_class]{filter_ab_class()}} for the \code{filter()} equivalent.
}