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guess_ab
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@ -25,22 +25,27 @@
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\usage{
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eucast_rules(tbl, col_mo = NULL, info = TRUE,
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rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
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amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
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azit = "azit", azlo = "azlo", aztr = "aztr", cefa = "cefa",
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cfep = "cfep", cfot = "cfot", cfox = "cfox", cfra = "cfra",
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cfta = "cfta", cftr = "cftr", cfur = "cfur", chlo = "chlo",
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cipr = "cipr", clar = "clar", clin = "clin", clox = "clox",
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coli = "coli", czol = "czol", dapt = "dapt", doxy = "doxy",
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erta = "erta", eryt = "eryt", fosf = "fosf", fusi = "fusi",
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gent = "gent", imip = "imip", kana = "kana", levo = "levo",
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linc = "linc", line = "line", mero = "mero", mezl = "mezl",
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mino = "mino", moxi = "moxi", nali = "nali", neom = "neom",
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neti = "neti", nitr = "nitr", norf = "norf", novo = "novo",
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oflo = "oflo", oxac = "oxac", peni = "peni", pipe = "pipe",
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pita = "pita", poly = "poly", pris = "pris", qida = "qida",
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rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
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tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
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trim = "trim", trsu = "trsu", vanc = "vanc")
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amcl = guess_ab(), amik = guess_ab(), amox = guess_ab(),
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ampi = guess_ab(), azit = guess_ab(), azlo = guess_ab(),
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aztr = guess_ab(), cefa = guess_ab(), cfep = guess_ab(),
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cfot = guess_ab(), cfox = guess_ab(), cfra = guess_ab(),
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cfta = guess_ab(), cftr = guess_ab(), cfur = guess_ab(),
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chlo = guess_ab(), cipr = guess_ab(), clar = guess_ab(),
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clin = guess_ab(), clox = guess_ab(), coli = guess_ab(),
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czol = guess_ab(), dapt = guess_ab(), doxy = guess_ab(),
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erta = guess_ab(), eryt = guess_ab(), fosf = guess_ab(),
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fusi = guess_ab(), gent = guess_ab(), imip = guess_ab(),
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kana = guess_ab(), levo = guess_ab(), linc = guess_ab(),
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line = guess_ab(), mero = guess_ab(), mezl = guess_ab(),
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mino = guess_ab(), moxi = guess_ab(), nali = guess_ab(),
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neom = guess_ab(), neti = guess_ab(), nitr = guess_ab(),
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norf = guess_ab(), novo = guess_ab(), oflo = guess_ab(),
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oxac = guess_ab(), peni = guess_ab(), pipe = guess_ab(),
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pita = guess_ab(), poly = guess_ab(), pris = guess_ab(),
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qida = guess_ab(), rifa = guess_ab(), roxi = guess_ab(),
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siso = guess_ab(), teic = guess_ab(), tetr = guess_ab(),
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tica = guess_ab(), tige = guess_ab(), tobr = guess_ab(),
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trim = guess_ab(), trsu = guess_ab(), vanc = guess_ab())
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EUCAST_rules(...)
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@ -69,7 +74,7 @@ Apply susceptibility rules as defined by the European Committee on Antimicrobial
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}
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\section{Antibiotics}{
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To define antibiotics column names, input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
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To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
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Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
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24
man/guess_ab.Rd
Normal file
24
man/guess_ab.Rd
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@ -0,0 +1,24 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/guess_ab.R
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\name{guess_ab}
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\alias{guess_ab}
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\title{Guess antibiotic column}
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\usage{
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guess_ab(tbl = NULL, col = NULL, verbose = FALSE)
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}
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\arguments{
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\item{tbl}{a \code{data.frame}}
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\item{col}{a character to look for}
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\item{verbose}{a logical to indicate whether additional info should be printed}
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}
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\description{
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This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set.
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}
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\section{Read more on our website!}{
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\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
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}
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@ -5,13 +5,17 @@
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\alias{key_antibiotics_equal}
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\title{Key antibiotics for first \emph{weighted} isolates}
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\usage{
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key_antibiotics(tbl, col_mo = NULL, universal_1 = "amox",
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universal_2 = "amcl", universal_3 = "cfur", universal_4 = "pita",
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universal_5 = "cipr", universal_6 = "trsu", GramPos_1 = "vanc",
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GramPos_2 = "teic", GramPos_3 = "tetr", GramPos_4 = "eryt",
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GramPos_5 = "oxac", GramPos_6 = "rifa", GramNeg_1 = "gent",
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GramNeg_2 = "tobr", GramNeg_3 = "coli", GramNeg_4 = "cfot",
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GramNeg_5 = "cfta", GramNeg_6 = "mero", warnings = TRUE, ...)
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key_antibiotics(tbl, col_mo = NULL, universal_1 = guess_ab(tbl,
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"amox"), universal_2 = guess_ab(tbl, "amcl"),
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universal_3 = guess_ab(tbl, "cfur"), universal_4 = guess_ab(tbl,
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"pita"), universal_5 = guess_ab(tbl, "cipr"),
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universal_6 = guess_ab(tbl, "trsu"), GramPos_1 = guess_ab(tbl,
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"vanc"), GramPos_2 = guess_ab(tbl, "teic"), GramPos_3 = guess_ab(tbl,
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"tetr"), GramPos_4 = guess_ab(tbl, "eryt"), GramPos_5 = guess_ab(tbl,
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"oxac"), GramPos_6 = guess_ab(tbl, "rifa"), GramNeg_1 = guess_ab(tbl,
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"gent"), GramNeg_2 = guess_ab(tbl, "tobr"), GramNeg_3 = guess_ab(tbl,
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"coli"), GramNeg_4 = guess_ab(tbl, "cfot"), GramNeg_5 = guess_ab(tbl,
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"cfta"), GramNeg_6 = guess_ab(tbl, "mero"), warnings = TRUE, ...)
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key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
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ignore_I = TRUE, points_threshold = 2, info = FALSE)
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37
man/mdro.Rd
37
man/mdro.Rd
@ -8,21 +8,26 @@
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\title{Determine multidrug-resistant organisms (MDRO)}
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\usage{
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mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
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amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
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azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
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cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
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cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
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clar = "clar", clin = "clin", clox = "clox", coli = "coli",
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czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
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eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
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imip = "imip", kana = "kana", levo = "levo", linc = "linc",
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line = "line", mero = "mero", metr = "metr", mino = "mino",
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moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
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nitr = "nitr", novo = "novo", norf = "norf", oflo = "oflo",
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peni = "peni", pipe = "pipe", pita = "pita", poly = "poly",
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qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso",
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teic = "teic", tetr = "tetr", tica = "tica", tige = "tige",
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tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc")
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amcl = guess_ab(), amik = guess_ab(), amox = guess_ab(),
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ampi = guess_ab(), azit = guess_ab(), aztr = guess_ab(),
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cefa = guess_ab(), cfra = guess_ab(), cfep = guess_ab(),
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cfot = guess_ab(), cfox = guess_ab(), cfta = guess_ab(),
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cftr = guess_ab(), cfur = guess_ab(), chlo = guess_ab(),
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cipr = guess_ab(), clar = guess_ab(), clin = guess_ab(),
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clox = guess_ab(), coli = guess_ab(), czol = guess_ab(),
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dapt = guess_ab(), doxy = guess_ab(), erta = guess_ab(),
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eryt = guess_ab(), fosf = guess_ab(), fusi = guess_ab(),
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gent = guess_ab(), imip = guess_ab(), kana = guess_ab(),
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levo = guess_ab(), linc = guess_ab(), line = guess_ab(),
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mero = guess_ab(), metr = guess_ab(), mino = guess_ab(),
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moxi = guess_ab(), nali = guess_ab(), neom = guess_ab(),
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neti = guess_ab(), nitr = guess_ab(), novo = guess_ab(),
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norf = guess_ab(), oflo = guess_ab(), peni = guess_ab(),
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pipe = guess_ab(), pita = guess_ab(), poly = guess_ab(),
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qida = guess_ab(), rifa = guess_ab(), roxi = guess_ab(),
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siso = guess_ab(), teic = guess_ab(), tetr = guess_ab(),
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tica = guess_ab(), tige = guess_ab(), tobr = guess_ab(),
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trim = guess_ab(), trsu = guess_ab(), vanc = guess_ab())
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brmo(..., country = "nl")
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@ -172,7 +177,7 @@ When \code{country} will be left blank, guidelines will be taken from EUCAST Exp
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}
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\section{Antibiotics}{
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To define antibiotics column names, input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
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To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.
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Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
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