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age_groups fix

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dr. M.S. (Matthijs) Berends
2019-02-27 11:36:12 +01:00
parent 4ba2ff68e0
commit 54162522bd
41 changed files with 450 additions and 386 deletions
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6
man/mo_source.Rd
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@ -17,13 +17,13 @@ get_mo_source()
These functions can be used to predefine your own reference to be used in \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}.
}
\details{
The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
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{set_mo_source} will check the file for validity: it must be a \code{data.frame}, must have a column named \code{"mo"} which contains values from \code{microorganisms$mo} and must have a reference column with your own defined values. If all tests pass, \code{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}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
\code{get_mo_source} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link{readRDS}}. If the original file has changed (the file defined with \code{path}), it will call \code{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 will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
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{get_mo_source} in only a couple of microseconds (a millionth of a second).
}
\section{Read more on our website!}{
@ -42,7 +42,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
# 1. We save it as 'home/me/ourcodes.xlsx'
# 2. We use it for input:
set_mo_source("C:\\path\\ourcodes.xlsx")
set_mo_source("home/me/ourcodes.xlsx")
#> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
# 3. And use it in our functions: