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(v0.6.1.9050) support staged install

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dr. M.S. (Matthijs) Berends
2019-06-01 20:40:49 +02:00
parent a665612cb8
commit 2667fff8a7
69 changed files with 256 additions and 259 deletions
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10
man/eucast_rules.Rd
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@@ -2,7 +2,6 @@
% Please edit documentation in R/eucast_rules.R
\name{eucast_rules}
\alias{eucast_rules}
\alias{eucast_rules_file}
\title{EUCAST rules}
\source{
\itemize{
@@ -20,14 +19,10 @@
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
}
}
For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like AMC. They can be separated by comma: \code{"AMC, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).
}
\usage{
eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
"expert", "other", "all"), verbose = FALSE, ...)
eucast_rules_file()
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
@@ -52,10 +47,7 @@ Apply susceptibility rules as defined by the European Committee on Antimicrobial
\strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link{as.rsi}} for that. \cr
\strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by \code{eucast_rules()} can be found by running this command: \cr
\code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets).
In the source code the file containing all rules is located \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{here}.
The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
}
\section{Antibiotics}{