mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 16:42:10 +02:00
Fix for antibiogram()
in R <=3.4
This commit is contained in:
@ -70,7 +70,7 @@ antibiogram(
|
||||
\item{as_kable}{a \link{logical} to indicate whether the printing should be done using \code{\link[knitr:kable]{knitr::kable()}} (which is the default in non-interactive sessions)}
|
||||
}
|
||||
\description{
|
||||
Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker \emph{et al.} (2021, \doi{10.1177/20499361211011373}) and Barbieri \emph{et al.} (2021, \doi{10.1186/s13756-021-00939-2}), and allow reporting in e.g. R Markdown and Quarto as well.
|
||||
Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker \emph{et al.} and Barbieri \emph{et al.} (see \emph{Source}), and allow reporting in e.g. R Markdown and Quarto as well.
|
||||
}
|
||||
\details{
|
||||
This function returns a table with values between 0 and 100 for \emph{susceptibility}, not resistance.
|
||||
@ -113,10 +113,14 @@ Case example: Susceptibility of \emph{Pseudomonas aeruginosa} to TZP among respi
|
||||
|
||||
Code example:
|
||||
|
||||
\if{html}{\out{<div class="sourceCode r">}}\preformatted{antibiogram(your_data,
|
||||
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
|
||||
syndromic_group = ifelse(your_data$age >= 65 & your_data$gender == "Male",
|
||||
"Group 1", "Group 2"))
|
||||
\if{html}{\out{<div class="sourceCode r">}}\preformatted{library(dplyr)
|
||||
your_data \%>\%
|
||||
filter(ward == "ICU" & specimen_type == "Respiratory") \%>\%
|
||||
antibiogram(antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
|
||||
syndromic_group = ifelse(.$age >= 65 &
|
||||
.$gender == "Male" &
|
||||
.$condition == "Heart Disease",
|
||||
"Study Group", "Control Group"))
|
||||
}\if{html}{\out{</div>}}
|
||||
}
|
||||
|
||||
@ -210,11 +214,11 @@ antibiogram(ex1,
|
||||
|
||||
# Weighted-incidence syndromic combination antibiogram (WISCA) ---------
|
||||
|
||||
# the data set could contain a filter for e.g. respiratory specimens
|
||||
# the data set could contain a filter for e.g. respiratory specimens/ICU
|
||||
antibiogram(example_isolates,
|
||||
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
|
||||
mo_transform = "gramstain",
|
||||
minimum = 10, # this should be >= 30, but now just as example
|
||||
minimum = 10, # this should be >=30, but now just as example
|
||||
syndromic_group = ifelse(example_isolates$age >= 65 &
|
||||
example_isolates$gender == "M",
|
||||
"WISCA Group 1", "WISCA Group 2"
|
||||
|
Reference in New Issue
Block a user