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(v0.8.0.9036) complete documentation rewrite

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dr. M.S. (Matthijs) Berends
2019-11-28 22:32:17 +01:00
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man/mo_source.Rd
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@ -14,24 +14,21 @@ get_mo_source()
\item{path}{location of your reference file, see Details}
}
\description{
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}}.
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()}}.
This is \strong{the fastest way} to have your organisation (or analysis) specific codes picked up and translated by this package.
}
\details{
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$mo} and must have a reference column with your own defined values. If all tests pass, \code{set_mo_source} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \code{\link{data.frame}}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$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{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.
\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{get_mo_source} in only a couple of microseconds (a millionth of a second).
}
\section{How it works}{
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).
\subsection{How it works}{
Imagine this data on a sheet of an Excel file (mo codes were looked up in the `microorganisms` data set). The first column contains the organisation specific codes, the second column contains an MO code from this package:
\preformatted{
| A | B |
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 |
--|--------------------|-------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COL |
@ -39,56 +36,46 @@ Imagine this data on a sheet of an Excel file (mo codes were looked up in the `m
4 | | |
}
We save it as \code{'home/me/ourcodes.xlsx'}. Now we have to set it as a source:
\preformatted{
set_mo_source("home/me/ourcodes.xlsx")
We save it as \code{"home/me/ourcodes.xlsx"}. Now we have to set it as a source:\preformatted{set_mo_source("home/me/ourcodes.xlsx")
# Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
}
It has now created a file "~/.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.
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.
And now we can use it in our functions:
\preformatted{
as.mo("lab_mo_ecoli")
[1] B_ESCHR_COL
And now we can use it in our functions:\preformatted{as.mo("lab_mo_ecoli")
\[1\] B_ESCHR_COLI
mo_genus("lab_mo_kpneumoniae")
[1] "Klebsiella"
# other input values still work too
as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
[1] B_ESCHR_COL B_ESCHR_COL B_ESCHR_COL
[1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
}
If we edit the Excel file to, let's say, this:
\preformatted{
| A | B |
--|--------------------|-------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COL |
3 | lab_mo_kpneumoniae | B_KLBSL_PNE |
4 | lab_Staph_aureus | B_STPHY_AUR |
5 | | |
If we edit the Excel file to, let's say, this:\preformatted{ | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
3 | lab_mo_kpneumoniae | B_KLBSL_PNMN |
4 | lab_Staph_aureus | B_STPHY_AURS |
5 | | |
}
...any new usage of an MO function in this package will update your data:
\preformatted{
as.mo("lab_mo_ecoli")
...any new usage of an MO function in this package will update your data:\preformatted{as.mo("lab_mo_ecoli")
# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
[1] B_ESCHR_COL
[1] B_ESCHR_COLI
mo_genus("lab_Staph_aureus")
[1] "Staphylococcus"
}
To remove the reference completely, just use any of these:
\preformatted{
set_mo_source("")
To remove the reference completely, just use any of these:\preformatted{set_mo_source("")
set_mo_source(NULL)
# Removed mo_source file '~/.mo_source.rds'.
}
}
}
\section{Read more on our website!}{
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}.