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custom mo update

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dr. M.S. (Matthijs) Berends
2022-12-28 14:20:10 +01:00
parent fe09e9252b
commit ba3b237bdf
5 changed files with 66 additions and 52 deletions
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20
man/add_custom_microorganisms.Rd
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@ -10,7 +10,7 @@ add_custom_microorganisms(x)
clear_custom_microorganisms()
}
\arguments{
\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "mo", "genus" and "species"}
\item{x}{a \link{data.frame} resembling the \link{microorganisms} data set, at least containing columns "genus" and "species"}
}
\description{
With \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
@ -24,7 +24,7 @@ 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:
\enumerate{
\item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least columns "ab" and "name") 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 Create a data set in the structure of the \link{microorganisms} data set (containing at the very least columns "genus" and "species") 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:
\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
@ -42,8 +42,7 @@ Upon package load, this file will be loaded and run through the \code{\link[=add
\if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
library(AMR)
add_custom_microorganisms(
data.frame(mo = "ENT_ASB_CLO",
genus = "Enterobacter",
data.frame(genus = "Enterobacter",
species = "asburiae/cloacae")
)
}\if{html}{\out{</div>}}
@ -61,24 +60,23 @@ mo_name("Enterobacter asburiae/cloacae")
# now add a custom entry - it will be considered by as.mo() and
# all mo_*() functions
add_custom_microorganisms(
data.frame(mo = "ENT_ASB_CLO",
genus = "Enterobacter",
data.frame(genus = "Enterobacter",
species = "asburiae/cloacae"
)
)
# "ENT_ASB_CLO" is now a new microorganism:
# E. asburiae/cloacae is now a new microorganism:
mo_name("Enterobacter asburiae/cloacae")
as.mo("ent_asb_clo")
mo_name("ent_asb_clo")
# its code:
as.mo("Enterobacter asburiae/cloacae")
# all internal algorithms will work as well:
mo_name("Ent asburia cloacae")
# and even the taxonomy was added based on the genus!
mo_family("ent_asb_clo")
mo_family("E. asburiae/cloacae")
mo_gramstain("Enterobacter asburiae/cloacae")
mo_info("ent_asb_clo")
mo_info("Enterobacter asburiae/cloacae")
}
}
\seealso{