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(v1.4.0.9041) updates based on review

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dr. M.S. (Matthijs) Berends
2020-12-17 16:22:25 +01:00
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commit 81af41da3a
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36
man/mo_source.Rd
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@ -6,12 +6,17 @@
\alias{get_mo_source}
\title{User-defined reference data set for microorganisms}
\usage{
set_mo_source(path)
set_mo_source(
path,
destination = getOption("AMR_mo_source", "~/mo_source.rds")
)
get_mo_source()
get_mo_source(destination = getOption("AMR_mo_source", "~/mo_source.rds"))
}
\arguments{
\item{path}{location of your reference file, see Details. Can be \code{""}, \code{NULL} or \code{FALSE} to delete the reference file.}
\item{destination}{destination of the compressed data file, default to the user's home directory.}
}
\description{
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()}}.
@ -21,11 +26,11 @@ 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$mo}} and must have a reference column with your own defined values. If all tests pass, \code{\link[=set_mo_source]{set_mo_source()}} will read the file into R and will ask to export it to \code{"~/.mo_source.rds"}. The CRAN policy disallows packages to write to the file system, although '\emph{exceptions may be allowed in interactive sessions if the package obtains confirmation from the user}'. For this reason, this function only works in interactive sessions so that the user can \strong{specifically confirm and allow} that this file will be created.
\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \link{data.frame}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$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 destination of this file can be set with the \code{destination} parameter and defaults to the user's home directory. It can also be set as an \R option, using \verb{options(AMR_mo_source = "my/location/file.rds)}.
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 = ...)}.
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 and timestamp of the original file will be saved as an attribute to the compressed data file.
The function \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 (by checking the aforementioned options \code{mo_source} and \code{mo_source_datetime}), it will call \code{\link[=set_mo_source]{set_mo_source()}} to update the data file automatically if used in an interactive session.
The function \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 (by checking the location and timestamp of the original file), it will call \code{\link[=set_mo_source]{set_mo_source()}} to update the data file automatically if used in an interactive session.
Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file created with \code{\link[=set_mo_source]{set_mo_source()}} will then 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 (millionths of a second).
}
@ -41,13 +46,15 @@ Imagine this data on a sheet of an Excel file (mo codes were looked up in the \l
}
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")
#> NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'
#> (columns "Organisation XYZ" and "mo")
#> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
#> "Organisation XYZ" and "mo"
}
It has now created a file \code{"~/.mo_source.rds"} with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.
It has now created a file \code{"~/mo_source.rds"} with the contents of our Excel file. Only the first column with foreign values and the 'mo' column will be kept when creating the RDS file.
And now we can use it in our functions:\preformatted{as.mo("lab_mo_ecoli")
#> Class <mo>
#> [1] B_ESCHR_COLI
mo_genus("lab_mo_kpneumoniae")
@ -55,6 +62,9 @@ mo_genus("lab_mo_kpneumoniae")
# other input values still work too
as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
#> NOTE: Translation to one microorganism was guessed with uncertainty.
#> Use mo_uncertainties() to review it.
#> Class <mo>
#> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
}
@ -68,8 +78,10 @@ If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{
}
...any new usage of an MO function in this package will update your data file:\preformatted{as.mo("lab_mo_ecoli")
#> NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'
#> (columns "Organisation XYZ" and "mo")
#> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
#> "Organisation XYZ" and "mo"
#> Class <mo>
#> [1] B_ESCHR_COLI
mo_genus("lab_Staph_aureus")
@ -77,10 +89,10 @@ mo_genus("lab_Staph_aureus")
}
To delete the reference data file, just use \code{""}, \code{NULL} or \code{FALSE} as input for \code{\link[=set_mo_source]{set_mo_source()}}:\preformatted{set_mo_source(NULL)
# Removed mo_source file '~/.mo_source.rds'.
#> Removed mo_source file '/Users/me/mo_source.rds'
}
If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}}. If the mo_source file is manually deleted (i.e. without using \code{\link[=set_mo_source]{set_mo_source()}}), the references to the mo_source file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}}.
If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}}.
}
\section{Stable lifecycle}{