P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 18:46:13 +01:00
Code Releases Activity

test syntax fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-11-01 20:50:10 +01:00
parent 5476fecc73
commit e601fd259a
6 changed files with 11 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
R/eucast.R
View File

@ -20,13 +20,13 @@
#' #'
#' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables. #' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl} #' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
#' @param col_mo column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}
#' @param info print progress #' @param info print progress
#' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")} #' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}
#' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected #' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected
#' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Details #' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Details
#' @param col_bactid Deprecated. Use \code{col_mo} instead. #' @param col_bactid deprecated, use \code{col_mo} instead.
#' @param ... parameters that are passed on to \code{EUCAST_rules} #' @param ... parameters that are passed on to \code{EUCAST_rules}
#' @inheritParams first_isolate
#' @details To define antibiotics column names, input a text or use \code{NA} to skip a column (e.g. \code{tica = NA}). Non-existing columns will anyway be skipped with a warning. See the Antibiotics section for an explanation of the abbreviations. #' @details To define antibiotics column names, input a text or use \code{NA} to skip a column (e.g. \code{tica = NA}). Non-existing columns will anyway be skipped with a warning. See the Antibiotics section for an explanation of the abbreviations.
#' @section Antibiotics: #' @section Antibiotics:
#' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code}) #' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
@ -140,7 +140,7 @@
#' # 4 Klebsiella pneumoniae - - - - - S S #' # 4 Klebsiella pneumoniae - - - - - S S
#' # 5 Pseudomonas aeruginosa - - - - - S S #' # 5 Pseudomonas aeruginosa - - - - - S S
#' #'
#' b <- EUCAST_rules(a) # 18 results are forced as R or S #' b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
#' #'
#' b #' b
#' # mo vanc amox coli cfta cfur peni cfox #' # mo vanc amox coli cfta cfur peni cfox

2
R/first_isolate.R
View File

@ -22,7 +22,7 @@
#' @param tbl a \code{data.frame} containing isolates. #' @param tbl a \code{data.frame} containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date} #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}
#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive) #' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive)
#' @param col_mo column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}. #' @param col_mo column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.
#' @param col_testcode column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation. #' @param col_testcode column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.
#' @param col_specimen column name of the specimen type or group #' @param col_specimen column name of the specimen type or group
#' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU) #' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)

6
man/EUCAST.Rd
View File

@ -46,7 +46,7 @@ interpretive_reading(...)
\arguments{ \arguments{
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}} \item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
\item{col_mo}{column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}} \item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{info}{print progress} \item{info}{print progress}
@ -56,7 +56,7 @@ interpretive_reading(...)
\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details} \item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details}
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.} \item{col_bactid}{deprecated, use \code{col_mo} instead.}
\item{...}{parameters that are passed on to \code{EUCAST_rules}} \item{...}{parameters that are passed on to \code{EUCAST_rules}}
} }
@ -162,7 +162,7 @@ a
# 4 Klebsiella pneumoniae - - - - - S S # 4 Klebsiella pneumoniae - - - - - S S
# 5 Pseudomonas aeruginosa - - - - - S S # 5 Pseudomonas aeruginosa - - - - - S S
b <- EUCAST_rules(a) # 18 results are forced as R or S b <- EUCAST_rules(a, "mo") # 18 results are forced as R or S
b b
# mo vanc amox coli cfta cfur peni cfox # mo vanc amox coli cfta cfur peni cfox

4
man/MDRO.Rd
View File

@ -36,7 +36,7 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).} \item{country}{country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the \href{https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements}{list of ISO 3166-1 alpha-2 country codes}. Case-insensitive. Currently supported are \code{de} (Germany) and \code{nl} (the Netherlands).}
\item{col_mo}{column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}} \item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{info}{print progress} \item{info}{print progress}
@ -160,7 +160,7 @@ EUCAST_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{vanc}{column name of an antibiotic, see Details} \item{vanc}{column name of an antibiotic, see Details}
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.} \item{col_bactid}{deprecated, use \code{col_mo} instead.}
\item{...}{parameters that are passed on to methods} \item{...}{parameters that are passed on to methods}
} }

2
man/first_isolate.Rd
View File

@ -23,7 +23,7 @@ first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive)} \item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive)}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.} \item{col_testcode}{column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.}

2
man/key_antibiotics.Rd
View File

@ -20,7 +20,7 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
\arguments{ \arguments{
\item{tbl}{table with antibiotics coloms, like \code{amox} and \code{amcl}.} \item{tbl}{table with antibiotics coloms, like \code{amox} and \code{amcl}.}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. If this column has another class than \code{"mo"}, values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive} \item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive}