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(v1.3.0.9038) prefinal 1.4.0

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dr. M.S. (Matthijs) Berends
2020-10-04 19:26:43 +02:00
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man/mo_source.Rd
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@ -21,7 +21,7 @@ This is \strong{the fastest way} to have your organisation (or analysis) specifi
\details{
The reference file can be a text file separated 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 will 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 \link{data.frame}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$mo}} and must have a reference column with your own defined values. If all tests pass, \code{\link[=set_mo_source]{set_mo_source()}} will read the file into R and export it to \code{"~/.mo_source.rds"} after the user \strong{specifically confirms and allows} that this file will be created. For this reason, this function only works in interactive sessions.
\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \link{data.frame}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$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 will ask to export it to \code{"~/.mo_source.rds"}. The CRAN policy disallows packages to write to the file system, although '\emph{exceptions may be allowed in interactive sessions if the package obtains confirmation from the user}'. For this reason, this function only works in interactive sessions so that the user can \strong{specifically confirm and allow} that this file will be created.
The created compressed data file \code{"~/.mo_source.rds"} will 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 an R option with \code{options(mo_source = path)}. Its timestamp will be saved with \code{options(mo_source_datetime = ...)}.