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dr. M.S. (Matthijs) Berends
2023-01-19 12:54:53 +01:00
parent b94bc6c67b
commit 593d740b84
78 changed files with 85 additions and 25 deletions
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man/add_custom_microorganisms.Rd Normal file → Executable file
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@ -22,10 +22,10 @@ This function will fill in missing taxonomy for you, if specific taxonomic colum
There are two ways to automate this process:
\strong{Method 1:} Save the microorganisms to a local or remote file (can even be the internet). To use this method:
\strong{Method 1:} Using the , which is the preferred method. To use this method:
\enumerate{
\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least column "genus") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
\item Set the file location to the \code{AMR_custom_mo} \R option: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
\item Set the file location to the \code{AMR_custom_mo} \R option: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
options(AMR_custom_mo = "~/my_custom_mo.rds")
@ -34,14 +34,13 @@ options(AMR_custom_mo = "~/my_custom_mo.rds")
Upon package load, this file will be loaded and run through the \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} function.
}
\strong{Method 2:} Save the microorganism directly to your \code{.Rprofile} file. An important downside is that this requires to load the \code{AMR} package at every start-up. To use this method:
\strong{Method 2:} Loading the microorganism directly from your \code{.Rprofile} file. An important downside is that this requires the \code{AMR} package to be installed or else this method will fail. To use this method:
\enumerate{
\item Edit the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}.
\item Add a text like below and save the file:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
library(AMR)
add_custom_microorganisms(
AMR::add_custom_microorganisms(
data.frame(genus = "Enterobacter",
species = "asburiae/cloacae")
)
@ -52,7 +51,6 @@ Use \code{\link[=clear_custom_microorganisms]{clear_custom_microorganisms()}} to
}
\examples{
\donttest{
# a combination of species is not formal taxonomy, so
# this will result in only "Enterobacter asburiae":
mo_name("Enterobacter asburiae/cloacae")
@ -83,13 +81,15 @@ mo_info("Enterobacter asburiae/cloacae")
# the function tries to be forgiving:
add_custom_microorganisms(
data.frame(GENUS = "ESCHERICHIA / KLEBSIELLA SLASHLINE",
data.frame(GENUS = "BACTEROIDES / PARABACTEROIDES SLASHLINE",
SPECIES = "SPECIES")
)
mo_name("ESCHERICHIA / KLEBSIELLA")
mo_rank("ESCHERICHIA / KLEBSIELLA")
mo_name("BACTEROIDES / PARABACTEROIDES")
mo_rank("BACTEROIDES / PARABACTEROIDES")
# taxonomy still works, although a slashline genus was given as input:
mo_family("Escherichia/Klebsiella")
mo_family("Bacteroides/Parabacteroides")
# for groups and complexes, set them as species or subspecies:
add_custom_microorganisms(