These functions can be used to predefine your own reference to be used in \code{\link[=as.mo]{as.mo()}} and consequently all \verb{mo_*} functions like \code{\link[=mo_genus]{mo_genus()}} and \code{\link[=mo_gramstain]{mo_gramstain()}}.
The reference file can be a text file seperated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \code{\link{data.frame}}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$mo}} and must have a reference column with your own defined values. If all tests pass, \code{\link[=set_mo_source]{set_mo_source()}} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link[=as.mo]{as.mo()}} and consequently all \verb{mo_*} functions like \code{\link[=mo_genus]{mo_genus()}} and \code{\link[=mo_gramstain]{mo_gramstain()}}). The location of the original file will be saved as option with \code{options(mo_source = path)}. Its timestamp will be saved with \code{options(mo_source_datetime = ...)}.
\code{\link[=get_mo_source]{get_mo_source()}} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link[=readRDS]{readRDS()}}. If the original file has changed (the file defined with \code{path}), it will call \code{\link[=set_mo_source]{set_mo_source()}} to update the data file automatically.
Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file used by this package will have a size of 0.1 kB and can be read by \code{\link[=get_mo_source]{get_mo_source()}} in only a couple of microseconds (a millionth of a second).
Imagine this data on a sheet of an Excel file (mo codes were looked up in the \code{microorganisms} data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:\preformatted{ | A | B |
It has now created a file \code{"~/.mo_source.rds"} with the contents of our Excel file, but only the first column with foreign values and the 'mo' column will be kept.
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.