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(v1.1.0.9019) mo_source fix

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dr. M.S. (Matthijs) Berends
2020-05-25 01:01:14 +02:00
parent f5ff2e6634
commit ae1969b941
73 changed files with 619 additions and 571 deletions
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10
man/ab_property.Rd
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@ -74,12 +74,14 @@ Use these functions to return a specific property of an antibiotic from the \lin
\details{
All output will be \link{translate}d where possible.
The function \code{\link[=ab_url]{ab_url()}} will return the direct URL to the official WHO website. A warning will be returned if the reauired ATC code is not available.
The function \code{\link[=ab_url]{ab_url()}} will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.
}
\section{Maturing lifecycle}{
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_maturing.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{maturing}. The unlying code of a maturing function has been roughed out, but finer details might still change. This function needs wider usage and more extensive testing in order to optimise the unlying code.
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{Source}{

8
man/mo_property.Rd
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@ -111,6 +111,14 @@ All output will be \link{translate}d where possible.
The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
}
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}
The \link[AMR:lifecycle]{lifecycle} of this function is \strong{stable}. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.
If the unlying code needs breaking changes, they will occur gradually. For example, a parameter will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.
}
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}

38
man/mo_source.Rd
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@ -4,14 +4,14 @@
\alias{mo_source}
\alias{set_mo_source}
\alias{get_mo_source}
\title{Use predefined reference data set}
\title{User-defined reference data set for microorganisms}
\usage{
set_mo_source(path)
get_mo_source()
}
\arguments{
\item{path}{location of your reference file, see Details}
\item{path}{location of your reference file, see Details. Can be \code{""}, \code{NULL} or \code{FALSE} to delete the reference file.}
}
\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()}}.
@ -25,10 +25,12 @@ The reference file can be a text file seperated with commas (CSV) or tabs or pip
\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).
\subsection{How it works}{
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).
}
\section{How to setup}{
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 |
Imagine this data on a sheet of an Excel file (mo codes were looked up in the \link{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_COLI |
@ -37,23 +39,24 @@ Imagine this data on a sheet of an Excel file (mo codes were looked up in the \c
}
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'.
#> NOTE: Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'
#> (columns "Organisation XYZ" and "mo")
}
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.
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")
[1] B_ESCHR_COLI
#> [1] B_ESCHR_COLI
mo_genus("lab_mo_kpneumoniae")
[1] "Klebsiella"
#> [1] "Klebsiella"
# other input values still work too
as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli"))
[1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
#> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI
}
If we edit the Excel file to, let's say, by adding row 4 like this:\preformatted{ | A | B |
If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{ | A | B |
--|--------------------|--------------|
1 | Organisation XYZ | mo |
2 | lab_mo_ecoli | B_ESCHR_COLI |
@ -63,18 +66,21 @@ If we edit the Excel file to, let's say, by 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")
# Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
[1] B_ESCHR_COLI
#> NOTE: Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'
#> (columns "Organisation XYZ" and "mo")
#> [1] B_ESCHR_COLI
mo_genus("lab_Staph_aureus")
[1] "Staphylococcus"
#> [1] "Staphylococcus"
}
To remove the reference data file completely, just use \code{""} or \code{NULL} as input for \verb{[set_mo_source()]}:\preformatted{set_mo_source(NULL)
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'.
}
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()}}.
}
}
\section{Stable lifecycle}{
\if{html}{\figure{lifecycle_stable.svg}{options: style=margin-bottom:5px} \cr}