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guess_ab
This commit is contained in:
@@ -41,7 +41,8 @@ before_script:
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cache:
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key: "$CI_COMMIT_REF_SLUG"
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paths:
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- /usr/lib/R/library/
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- /usr/local/lib/R/
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- /usr/lib/R/
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R 3:
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stage: build
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@@ -76,6 +76,7 @@ export(g.test)
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export(geom_rsi)
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export(get_locale)
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export(ggplot_rsi)
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export(guess_ab)
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export(guess_atc)
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export(guess_mo)
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export(header)
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1
NEWS.md
1
NEWS.md
@@ -7,6 +7,7 @@
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* Contains the complete manual of this package and all of its functions with an explanation of their parameters
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* Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis
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* Support for [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
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* Function `guess_ab` to find an antibiotic column in a table
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* Function `mo_failures()` to review values that could not be coerced to a valid MO code, using `as.mo()`. This latter function will now only show a maximum of 25 uncoerced values.
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* Function `mo_renamed()` to get a list of all returned values from `as.mo()` that have had taxonomic renaming
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* Function `age()` to calculate the (patients) age in years
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344
R/eucast_rules.R
344
R/eucast_rules.R
@@ -30,7 +30,7 @@
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#' @param ... parameters that are passed on to \code{eucast_rules}
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#' @inheritParams first_isolate
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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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#'
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#' Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
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#'
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@@ -158,69 +158,69 @@ eucast_rules <- function(tbl,
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info = TRUE,
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rules = c("breakpoints", "expert", "other", "all"),
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verbose = FALSE,
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amcl = 'amcl',
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amik = 'amik',
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amox = 'amox',
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ampi = 'ampi',
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azit = 'azit',
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azlo = 'azlo',
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aztr = 'aztr',
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cefa = 'cefa',
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cfep = 'cfep',
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cfot = 'cfot',
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cfox = 'cfox',
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cfra = 'cfra',
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cfta = 'cfta',
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cftr = 'cftr',
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cfur = 'cfur',
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chlo = 'chlo',
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cipr = 'cipr',
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clar = 'clar',
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clin = 'clin',
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clox = 'clox',
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coli = 'coli',
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czol = 'czol',
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dapt = 'dapt',
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doxy = 'doxy',
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erta = 'erta',
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eryt = 'eryt',
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fosf = 'fosf',
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fusi = 'fusi',
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gent = 'gent',
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imip = 'imip',
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kana = 'kana',
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levo = 'levo',
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linc = 'linc',
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line = 'line',
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mero = 'mero',
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mezl = 'mezl',
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mino = 'mino',
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moxi = 'moxi',
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nali = 'nali',
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neom = 'neom',
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neti = 'neti',
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nitr = 'nitr',
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norf = 'norf',
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novo = 'novo',
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oflo = 'oflo',
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oxac = 'oxac',
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peni = 'peni',
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pipe = 'pipe',
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pita = 'pita',
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poly = 'poly',
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pris = 'pris',
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qida = 'qida',
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rifa = 'rifa',
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roxi = 'roxi',
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siso = 'siso',
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teic = 'teic',
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tetr = 'tetr',
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tica = 'tica',
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tige = 'tige',
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tobr = 'tobr',
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trim = 'trim',
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trsu = 'trsu',
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vanc = 'vanc') {
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amcl = guess_ab(),
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amik = guess_ab(),
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amox = guess_ab(),
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ampi = guess_ab(),
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azit = guess_ab(),
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azlo = guess_ab(),
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aztr = guess_ab(),
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cefa = guess_ab(),
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cfep = guess_ab(),
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cfot = guess_ab(),
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cfox = guess_ab(),
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cfra = guess_ab(),
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cfta = guess_ab(),
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cftr = guess_ab(),
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cfur = guess_ab(),
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chlo = guess_ab(),
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cipr = guess_ab(),
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clar = guess_ab(),
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clin = guess_ab(),
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clox = guess_ab(),
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coli = guess_ab(),
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czol = guess_ab(),
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dapt = guess_ab(),
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doxy = guess_ab(),
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erta = guess_ab(),
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eryt = guess_ab(),
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fosf = guess_ab(),
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fusi = guess_ab(),
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gent = guess_ab(),
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imip = guess_ab(),
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kana = guess_ab(),
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levo = guess_ab(),
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linc = guess_ab(),
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line = guess_ab(),
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mero = guess_ab(),
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mezl = guess_ab(),
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mino = guess_ab(),
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moxi = guess_ab(),
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nali = guess_ab(),
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neom = guess_ab(),
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neti = guess_ab(),
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nitr = guess_ab(),
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norf = guess_ab(),
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novo = guess_ab(),
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oflo = guess_ab(),
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oxac = guess_ab(),
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peni = guess_ab(),
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pipe = guess_ab(),
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pita = guess_ab(),
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poly = guess_ab(),
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pris = guess_ab(),
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qida = guess_ab(),
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rifa = guess_ab(),
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roxi = guess_ab(),
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siso = guess_ab(),
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teic = guess_ab(),
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tetr = guess_ab(),
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tica = guess_ab(),
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tige = guess_ab(),
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tobr = guess_ab(),
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trim = guess_ab(),
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trsu = guess_ab(),
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vanc = guess_ab()) {
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EUCAST_VERSION_BREAKPOINTS <- "8.1, 2018"
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EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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@@ -268,12 +268,80 @@ eucast_rules <- function(tbl,
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}
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# check columns
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if (identical(amcl, as.name("guess_ab"))) { amcl <- guess_ab(tbl, "amcl", verbose = verbose) }
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if (identical(amik, as.name("guess_ab"))) { amik <- guess_ab(tbl, "amik", verbose = verbose) }
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if (identical(amox, as.name("guess_ab"))) { amox <- guess_ab(tbl, "amox", verbose = verbose) }
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if (identical(ampi, as.name("guess_ab"))) { ampi <- guess_ab(tbl, "ampi", verbose = verbose) }
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if (identical(azit, as.name("guess_ab"))) { azit <- guess_ab(tbl, "azit", verbose = verbose) }
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if (identical(azlo, as.name("guess_ab"))) { azlo <- guess_ab(tbl, "azlo", verbose = verbose) }
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if (identical(aztr, as.name("guess_ab"))) { aztr <- guess_ab(tbl, "aztr", verbose = verbose) }
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if (identical(cefa, as.name("guess_ab"))) { cefa <- guess_ab(tbl, "cefa", verbose = verbose) }
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if (identical(cfep, as.name("guess_ab"))) { cfep <- guess_ab(tbl, "cfep", verbose = verbose) }
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if (identical(cfot, as.name("guess_ab"))) { cfot <- guess_ab(tbl, "cfot", verbose = verbose) }
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if (identical(cfox, as.name("guess_ab"))) { cfox <- guess_ab(tbl, "cfox", verbose = verbose) }
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if (identical(cfra, as.name("guess_ab"))) { cfra <- guess_ab(tbl, "cfra", verbose = verbose) }
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if (identical(cfta, as.name("guess_ab"))) { cfta <- guess_ab(tbl, "cfta", verbose = verbose) }
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if (identical(cftr, as.name("guess_ab"))) { cftr <- guess_ab(tbl, "cftr", verbose = verbose) }
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if (identical(cfur, as.name("guess_ab"))) { cfur <- guess_ab(tbl, "cfur", verbose = verbose) }
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if (identical(chlo, as.name("guess_ab"))) { chlo <- guess_ab(tbl, "chlo", verbose = verbose) }
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if (identical(cipr, as.name("guess_ab"))) { cipr <- guess_ab(tbl, "cipr", verbose = verbose) }
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if (identical(clar, as.name("guess_ab"))) { clar <- guess_ab(tbl, "clar", verbose = verbose) }
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if (identical(clin, as.name("guess_ab"))) { clin <- guess_ab(tbl, "clin", verbose = verbose) }
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if (identical(clox, as.name("guess_ab"))) { clox <- guess_ab(tbl, "clox", verbose = verbose) }
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if (identical(coli, as.name("guess_ab"))) { coli <- guess_ab(tbl, "coli", verbose = verbose) }
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if (identical(czol, as.name("guess_ab"))) { czol <- guess_ab(tbl, "czol", verbose = verbose) }
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if (identical(dapt, as.name("guess_ab"))) { dapt <- guess_ab(tbl, "dapt", verbose = verbose) }
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if (identical(doxy, as.name("guess_ab"))) { doxy <- guess_ab(tbl, "doxy", verbose = verbose) }
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if (identical(erta, as.name("guess_ab"))) { erta <- guess_ab(tbl, "erta", verbose = verbose) }
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if (identical(eryt, as.name("guess_ab"))) { eryt <- guess_ab(tbl, "eryt", verbose = verbose) }
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if (identical(fosf, as.name("guess_ab"))) { fosf <- guess_ab(tbl, "fosf", verbose = verbose) }
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if (identical(fusi, as.name("guess_ab"))) { fusi <- guess_ab(tbl, "fusi", verbose = verbose) }
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if (identical(gent, as.name("guess_ab"))) { gent <- guess_ab(tbl, "gent", verbose = verbose) }
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if (identical(imip, as.name("guess_ab"))) { imip <- guess_ab(tbl, "imip", verbose = verbose) }
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if (identical(kana, as.name("guess_ab"))) { kana <- guess_ab(tbl, "kana", verbose = verbose) }
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if (identical(levo, as.name("guess_ab"))) { levo <- guess_ab(tbl, "levo", verbose = verbose) }
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if (identical(linc, as.name("guess_ab"))) { linc <- guess_ab(tbl, "linc", verbose = verbose) }
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if (identical(line, as.name("guess_ab"))) { line <- guess_ab(tbl, "line", verbose = verbose) }
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if (identical(mero, as.name("guess_ab"))) { mero <- guess_ab(tbl, "mero", verbose = verbose) }
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if (identical(mezl, as.name("guess_ab"))) { mezl <- guess_ab(tbl, "mezl", verbose = verbose) }
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if (identical(mino, as.name("guess_ab"))) { mino <- guess_ab(tbl, "mino", verbose = verbose) }
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if (identical(moxi, as.name("guess_ab"))) { moxi <- guess_ab(tbl, "moxi", verbose = verbose) }
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if (identical(nali, as.name("guess_ab"))) { nali <- guess_ab(tbl, "nali", verbose = verbose) }
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if (identical(neom, as.name("guess_ab"))) { neom <- guess_ab(tbl, "neom", verbose = verbose) }
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if (identical(neti, as.name("guess_ab"))) { neti <- guess_ab(tbl, "neti", verbose = verbose) }
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if (identical(nitr, as.name("guess_ab"))) { nitr <- guess_ab(tbl, "nitr", verbose = verbose) }
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if (identical(norf, as.name("guess_ab"))) { norf <- guess_ab(tbl, "norf", verbose = verbose) }
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if (identical(novo, as.name("guess_ab"))) { novo <- guess_ab(tbl, "novo", verbose = verbose) }
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if (identical(oflo, as.name("guess_ab"))) { oflo <- guess_ab(tbl, "oflo", verbose = verbose) }
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if (identical(oxac, as.name("guess_ab"))) { oxac <- guess_ab(tbl, "oxac", verbose = verbose) }
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if (identical(peni, as.name("guess_ab"))) { peni <- guess_ab(tbl, "peni", verbose = verbose) }
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if (identical(pipe, as.name("guess_ab"))) { pipe <- guess_ab(tbl, "pipe", verbose = verbose) }
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if (identical(pita, as.name("guess_ab"))) { pita <- guess_ab(tbl, "pita", verbose = verbose) }
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if (identical(poly, as.name("guess_ab"))) { poly <- guess_ab(tbl, "poly", verbose = verbose) }
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if (identical(pris, as.name("guess_ab"))) { pris <- guess_ab(tbl, "pris", verbose = verbose) }
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if (identical(qida, as.name("guess_ab"))) { qida <- guess_ab(tbl, "qida", verbose = verbose) }
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if (identical(rifa, as.name("guess_ab"))) { rifa <- guess_ab(tbl, "rifa", verbose = verbose) }
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if (identical(roxi, as.name("guess_ab"))) { roxi <- guess_ab(tbl, "roxi", verbose = verbose) }
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if (identical(siso, as.name("guess_ab"))) { siso <- guess_ab(tbl, "siso", verbose = verbose) }
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if (identical(teic, as.name("guess_ab"))) { teic <- guess_ab(tbl, "teic", verbose = verbose) }
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if (identical(tetr, as.name("guess_ab"))) { tetr <- guess_ab(tbl, "tetr", verbose = verbose) }
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if (identical(tica, as.name("guess_ab"))) { tica <- guess_ab(tbl, "tica", verbose = verbose) }
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if (identical(tige, as.name("guess_ab"))) { tige <- guess_ab(tbl, "tige", verbose = verbose) }
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if (identical(tobr, as.name("guess_ab"))) { tobr <- guess_ab(tbl, "tobr", verbose = verbose) }
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if (identical(trim, as.name("guess_ab"))) { trim <- guess_ab(tbl, "trim", verbose = verbose) }
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if (identical(trsu, as.name("guess_ab"))) { trsu <- guess_ab(tbl, "trsu", verbose = verbose) }
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if (identical(vanc, as.name("guess_ab"))) { vanc <- guess_ab(tbl, "vanc", verbose = verbose) }
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col.list <- c(amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot,
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cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
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czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
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levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr,
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novo, norf, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa,
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roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
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if (length(col.list) < 63) {
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warning('Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.',
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immediate. = TRUE,
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call. = FALSE)
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}
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col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
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amcl <- col.list[amcl]
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amik <- col.list[amik]
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@@ -339,8 +407,8 @@ eucast_rules <- function(tbl,
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trsu <- col.list[trsu]
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vanc <- col.list[vanc]
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amount_changed <- 0
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amount_affected_rows <- integer(0)
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number_changed <- 0
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number_affected_rows <- integer(0)
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verbose_info <- data.frame(rule_type = character(0),
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rule_set = character(0),
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force_to = character(0),
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@@ -352,7 +420,7 @@ eucast_rules <- function(tbl,
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# helper function for editing the table
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edit_rsi <- function(to, rule, rows, cols) {
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cols <- unique(cols[!is.na(cols)])
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cols <- unique(cols[!is.na(cols) & !is.null(cols)])
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if (length(rows) > 0 & length(cols) > 0) {
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before <- as.character(unlist(as.list(tbl_original[rows, cols])))
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tryCatch(
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@@ -376,8 +444,8 @@ eucast_rules <- function(tbl,
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tbl[rows, cols] <<- to
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))
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after <- as.character(unlist(as.list(tbl_original[rows, cols])))
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amount_changed <<- amount_changed + sum(before != after, na.rm = TRUE)
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amount_affected_rows <<- unique(c(amount_affected_rows, rows))
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number_changed <<- number_changed + sum(before != after, na.rm = TRUE)
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number_affected_rows <<- unique(c(number_affected_rows, rows))
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changed_results <<- changed_results + sum(before != after, na.rm = TRUE) # will be reset at start of every rule
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if (verbose == TRUE) {
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@@ -399,7 +467,7 @@ eucast_rules <- function(tbl,
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}
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}
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na.rm <- function(col) {
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if (is.na(col)) {
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if (is.null(col)) {
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""
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} else {
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col
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@@ -420,7 +488,7 @@ eucast_rules <- function(tbl,
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}
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# since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table)
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if (!is.na(ampi) & !is.na(amox)) {
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if (!is.null(ampi) & !is.null(amox)) {
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if (verbose == TRUE) {
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cat(bgGreen("\n VERBOSE: transforming",
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length(which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R"))),
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@@ -435,7 +503,7 @@ eucast_rules <- function(tbl,
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tbl[which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "S"
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tbl[which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "I"
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tbl[which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "R"
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} else if (is.na(ampi) & !is.na(amox)) {
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} else if (is.null(ampi) & !is.null(amox)) {
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# ampicillin column is missing, but amoxicillin is available
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message(blue(paste0("NOTE: Using column `", bold(amox), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
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ampi <- amox
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@@ -471,21 +539,21 @@ eucast_rules <- function(tbl,
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cat(rule)
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}
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if (!is.na(ampi)) {
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if (!is.null(ampi)) {
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edit_rsi(to = 'S',
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rule = c(rule_group, rule),
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rows = which(tbl$order == 'Enterobacteriales'
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& tbl[, ampi] == 'S'),
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cols = amox)
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}
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if (!is.na(ampi)) {
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if (!is.null(ampi)) {
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edit_rsi(to = 'I',
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rule = c(rule_group, rule),
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||||
rows = which(tbl$order == 'Enterobacteriales'
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& tbl[, ampi] == 'I'),
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cols = amox)
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}
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if (!is.na(ampi)) {
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||||
if (!is.null(ampi)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$order == 'Enterobacteriales'
|
||||
@@ -502,7 +570,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(peni) & !is.na(cfox)) {
|
||||
if (!is.null(peni) & !is.null(cfox)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Staphylococcus"
|
||||
@@ -516,21 +584,21 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, cfox] == 'S'),
|
||||
cols = c(oxac, clox))
|
||||
}
|
||||
if (!is.na(cfox)) {
|
||||
if (!is.null(cfox)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Staphylococcus"
|
||||
& tbl[, cfox] == 'R'),
|
||||
cols = all_betalactam)
|
||||
}
|
||||
if (!is.na(ampi)) {
|
||||
if (!is.null(ampi)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Staphylococcus saprophyticus"
|
||||
& tbl[, ampi] == 'S'),
|
||||
cols = c(amox, amcl, pipe, pita))
|
||||
}
|
||||
if (!is.na(cfox)) {
|
||||
if (!is.null(cfox)) {
|
||||
# inferred from cefoxitin
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
@@ -548,14 +616,14 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, cfox] == 'R'),
|
||||
cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)]))
|
||||
}
|
||||
if (!is.na(norf)) {
|
||||
if (!is.null(norf)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Staphylococcus"
|
||||
& tbl[, norf] == 'S'),
|
||||
cols = c(cipr, levo, moxi, oflo))
|
||||
}
|
||||
if (!is.na(eryt)) {
|
||||
if (!is.null(eryt)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Staphylococcus"
|
||||
@@ -572,7 +640,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, eryt] == 'R'),
|
||||
cols = c(azit, clar, roxi))
|
||||
}
|
||||
if (!is.na(tetr)) {
|
||||
if (!is.null(tetr)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Staphylococcus"
|
||||
@@ -589,14 +657,14 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(ampi)) { # penicillin group
|
||||
if (!is.null(ampi)) { # penicillin group
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Enterococcus faecium"
|
||||
& tbl[, ampi] == 'R'),
|
||||
cols = all_betalactam)
|
||||
}
|
||||
if (!is.na(ampi)) {
|
||||
if (!is.null(ampi)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Enterococcus"
|
||||
@@ -613,7 +681,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, ampi] == 'R'),
|
||||
cols = c(amox, amcl, pipe, pita))
|
||||
}
|
||||
if (!is.na(norf)) {
|
||||
if (!is.null(norf)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Enterococcus"
|
||||
@@ -640,7 +708,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
|
||||
@@ -657,14 +725,14 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, peni] == 'R'),
|
||||
cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl))
|
||||
}
|
||||
if (!is.na(norf)) {
|
||||
if (!is.null(norf)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
|
||||
& tbl[, norf] == 'S'),
|
||||
cols = c(levo, moxi))
|
||||
}
|
||||
if (!is.na(eryt)) {
|
||||
if (!is.null(eryt)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
|
||||
@@ -681,7 +749,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, eryt] == 'R'),
|
||||
cols = c(azit, clar, roxi))
|
||||
}
|
||||
if (!is.na(tetr)) {
|
||||
if (!is.null(tetr)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)"
|
||||
@@ -698,14 +766,14 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
|
||||
& tbl[, peni] == 'S'),
|
||||
cols = c(ampi, amox, amcl, pipe, pita))
|
||||
}
|
||||
if (!is.na(ampi)) {
|
||||
if (!is.null(ampi)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
|
||||
@@ -722,14 +790,14 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, ampi] == 'R'),
|
||||
cols = c(amox, amcl, pipe, pita))
|
||||
}
|
||||
if (!is.na(norf)) {
|
||||
if (!is.null(norf)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
|
||||
& tbl[, norf] == 'S'),
|
||||
cols = c(levo, moxi))
|
||||
}
|
||||
if (!is.na(eryt)) {
|
||||
if (!is.null(eryt)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
|
||||
@@ -746,7 +814,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, eryt] == 'R'),
|
||||
cols = c(azit, clar, roxi))
|
||||
}
|
||||
if (!is.na(tetr)) {
|
||||
if (!is.null(tetr)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
|
||||
@@ -768,14 +836,14 @@ eucast_rules <- function(tbl,
|
||||
"intermedius", "mitis", "mutans", "oligofermentans", "oralis",
|
||||
"parasanguinis", "peroris", "pseudopneumoniae", "salivarius",
|
||||
"sanguinis", "sinensis", "sobrinus", "thermophilus", "vestibularis")
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
|
||||
& tbl[, peni] == 'S'),
|
||||
cols = c(ampi, amox, amcl, pipe, pita))
|
||||
}
|
||||
if (!is.na(ampi)) {
|
||||
if (!is.null(ampi)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
|
||||
@@ -802,7 +870,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(ampi)) {
|
||||
if (!is.null(ampi)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
|
||||
@@ -819,14 +887,14 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, ampi] == 'R'),
|
||||
cols = c(amox, pipe))
|
||||
}
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
|
||||
& tbl[, peni] == 'S'),
|
||||
cols = c(ampi, amox, amcl, pipe, pita))
|
||||
}
|
||||
if (!is.na(amcl)) {
|
||||
if (!is.null(amcl)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
|
||||
@@ -843,14 +911,14 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, amcl] == 'R'),
|
||||
cols = pita)
|
||||
}
|
||||
if (!is.na(nali)) {
|
||||
if (!is.null(nali)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
|
||||
& tbl[, nali] == 'S'),
|
||||
cols = c(cipr, levo, moxi, oflo))
|
||||
}
|
||||
if (!is.na(tetr)) {
|
||||
if (!is.null(tetr)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
|
||||
@@ -867,7 +935,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(amcl)) {
|
||||
if (!is.null(amcl)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
|
||||
@@ -884,14 +952,14 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, amcl] == 'R'),
|
||||
cols = pita)
|
||||
}
|
||||
if (!is.na(nali)) {
|
||||
if (!is.null(nali)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
|
||||
& tbl[, nali] == 'S'),
|
||||
cols = c(cipr, levo, moxi, oflo))
|
||||
}
|
||||
if (!is.na(eryt)) {
|
||||
if (!is.null(eryt)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
|
||||
@@ -908,7 +976,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, eryt] == 'R'),
|
||||
cols = c(azit, clar, roxi))
|
||||
}
|
||||
if (!is.na(tetr)) {
|
||||
if (!is.null(tetr)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Moraxella catarrhalis"
|
||||
@@ -925,7 +993,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
|
||||
@@ -961,7 +1029,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
|
||||
@@ -991,7 +1059,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Pasteurella multocida"
|
||||
@@ -1018,7 +1086,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(eryt)) {
|
||||
if (!is.null(eryt)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
|
||||
@@ -1035,7 +1103,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, eryt] == 'R'),
|
||||
cols = c(azit, clar))
|
||||
}
|
||||
if (!is.na(tetr)) {
|
||||
if (!is.null(tetr)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
|
||||
@@ -1062,7 +1130,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(norf)) {
|
||||
if (!is.null(norf)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
|
||||
@@ -1079,7 +1147,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, norf] == 'R'),
|
||||
cols = fluoroquinolones)
|
||||
}
|
||||
if (!is.na(cipr)) {
|
||||
if (!is.null(cipr)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
|
||||
@@ -1106,7 +1174,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Kingella kingae"
|
||||
@@ -1123,7 +1191,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, peni] == 'R'),
|
||||
cols = c(ampi, amox))
|
||||
}
|
||||
if (!is.na(eryt)) {
|
||||
if (!is.null(eryt)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Kingella kingae"
|
||||
@@ -1140,7 +1208,7 @@ eucast_rules <- function(tbl,
|
||||
& tbl[, eryt] == 'R'),
|
||||
cols = c(azit, clar))
|
||||
}
|
||||
if (!is.na(tetr)) {
|
||||
if (!is.null(tetr)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% "^Kingella kingae"
|
||||
@@ -1442,7 +1510,7 @@ eucast_rules <- function(tbl,
|
||||
cat(rule)
|
||||
}
|
||||
# rule 8.3
|
||||
if (!is.na(peni)) {
|
||||
if (!is.null(peni)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)'
|
||||
@@ -1450,14 +1518,14 @@ eucast_rules <- function(tbl,
|
||||
cols = c(aminopenicillins, cephalosporins, carbapenems))
|
||||
}
|
||||
# rule 8.6
|
||||
if (!is.na(ampi)) {
|
||||
if (!is.null(ampi)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == 'Enterococcus'
|
||||
& tbl[, ampi] == 'R'),
|
||||
cols = c(ureidopenicillins, carbapenems))
|
||||
}
|
||||
if (!is.na(amox)) {
|
||||
if (!is.null(amox)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == 'Enterococcus'
|
||||
@@ -1476,7 +1544,7 @@ eucast_rules <- function(tbl,
|
||||
cat(rule)
|
||||
}
|
||||
# rule 9.3
|
||||
if (!is.na(tica) & !is.na(pipe)) {
|
||||
if (!is.null(tica) & !is.null(pipe)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$family == 'Enterobacteriaceae'
|
||||
@@ -1496,7 +1564,7 @@ eucast_rules <- function(tbl,
|
||||
cat(rule)
|
||||
}
|
||||
# rule 10.2
|
||||
# if (!is.na(ampi)) {
|
||||
# if (!is.null(ampi)) {
|
||||
# you should know first if the are B-lactamase positive, so do not run for now
|
||||
# edit_rsi(to = 'R',
|
||||
# rule = c(rule_group, rule),
|
||||
@@ -1516,7 +1584,7 @@ eucast_rules <- function(tbl,
|
||||
cat(rule)
|
||||
}
|
||||
# rule 11.1
|
||||
if (!is.na(eryt)) {
|
||||
if (!is.null(eryt)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl[, eryt] == 'S'),
|
||||
@@ -1542,7 +1610,7 @@ eucast_rules <- function(tbl,
|
||||
cat(rule)
|
||||
}
|
||||
# rule 12.2
|
||||
if (!is.na(tobr)) {
|
||||
if (!is.null(tobr)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == 'Staphylococcus'
|
||||
@@ -1550,7 +1618,7 @@ eucast_rules <- function(tbl,
|
||||
cols = c(kana, amik))
|
||||
}
|
||||
# rule 12.3
|
||||
if (!is.na(gent)) {
|
||||
if (!is.null(gent)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == 'Staphylococcus'
|
||||
@@ -1558,7 +1626,7 @@ eucast_rules <- function(tbl,
|
||||
cols = aminoglycosides)
|
||||
}
|
||||
# rule 12.8
|
||||
if (!is.na(gent) & !is.na(tobr)) {
|
||||
if (!is.null(gent) & !is.null(tobr)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$family == 'Enterobacteriaceae'
|
||||
@@ -1567,7 +1635,7 @@ eucast_rules <- function(tbl,
|
||||
cols = gent)
|
||||
}
|
||||
# rule 12.9
|
||||
if (!is.na(gent) & !is.na(tobr)) {
|
||||
if (!is.null(gent) & !is.null(tobr)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$family == 'Enterobacteriaceae'
|
||||
@@ -1588,7 +1656,7 @@ eucast_rules <- function(tbl,
|
||||
cat(rule)
|
||||
}
|
||||
# rule 13.2
|
||||
if (!is.na(moxi)) {
|
||||
if (!is.null(moxi)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$genus == 'Staphylococcus'
|
||||
@@ -1596,7 +1664,7 @@ eucast_rules <- function(tbl,
|
||||
cols = fluoroquinolones)
|
||||
}
|
||||
# rule 13.4
|
||||
if (!is.na(moxi)) {
|
||||
if (!is.null(moxi)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% '^Streptococcus pneumoniae'
|
||||
@@ -1604,7 +1672,7 @@ eucast_rules <- function(tbl,
|
||||
cols = fluoroquinolones)
|
||||
}
|
||||
# rule 13.5
|
||||
if (!is.na(cipr)) {
|
||||
if (!is.null(cipr)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$family == 'Enterobacteriaceae'
|
||||
@@ -1612,7 +1680,7 @@ eucast_rules <- function(tbl,
|
||||
cols = fluoroquinolones)
|
||||
}
|
||||
# rule 13.8
|
||||
if (!is.na(cipr)) {
|
||||
if (!is.null(cipr)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl$fullname %like% '^Neisseria gonorrhoeae'
|
||||
@@ -1639,7 +1707,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(amcl)) {
|
||||
if (!is.null(amcl)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl[, amcl] == 'R'),
|
||||
@@ -1654,7 +1722,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(pita)) {
|
||||
if (!is.null(pita)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl[, pita] == 'R'),
|
||||
@@ -1669,7 +1737,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(trsu)) {
|
||||
if (!is.null(trsu)) {
|
||||
edit_rsi(to = 'R',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl[, trsu] == 'R'),
|
||||
@@ -1684,7 +1752,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(ampi)) {
|
||||
if (!is.null(ampi)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl[, ampi] == 'S'),
|
||||
@@ -1699,7 +1767,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(pipe)) {
|
||||
if (!is.null(pipe)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl[, pipe] == 'S'),
|
||||
@@ -1714,7 +1782,7 @@ eucast_rules <- function(tbl,
|
||||
changed_results <- 0
|
||||
cat(rule)
|
||||
}
|
||||
if (!is.na(trim)) {
|
||||
if (!is.null(trim)) {
|
||||
edit_rsi(to = 'S',
|
||||
rule = c(rule_group, rule),
|
||||
rows = which(tbl[, trim] == 'S'),
|
||||
@@ -1737,7 +1805,7 @@ eucast_rules <- function(tbl,
|
||||
} else {
|
||||
wouldve <- ""
|
||||
}
|
||||
if (amount_changed == 0) {
|
||||
if (number_changed == 0) {
|
||||
colour <- green
|
||||
} else {
|
||||
colour <- blue
|
||||
@@ -1745,11 +1813,11 @@ eucast_rules <- function(tbl,
|
||||
decimal.mark <- getOption("OutDec")
|
||||
big.mark <- ifelse(decimal.mark != ",", ",", ".")
|
||||
cat(bold(paste('\n=> EUCAST rules', paste0(wouldve, 'affected'),
|
||||
amount_affected_rows %>% length() %>% format(big.mark = big.mark, decimal.mark = decimal.mark),
|
||||
number_affected_rows %>% length() %>% format(big.mark = big.mark, decimal.mark = decimal.mark),
|
||||
'out of', nrow(tbl_original) %>% format(big.mark = big.mark, decimal.mark = decimal.mark),
|
||||
'rows ->',
|
||||
colour(paste0(wouldve, 'changed'),
|
||||
amount_changed %>% format(big.mark = big.mark, decimal.mark = decimal.mark), 'test results.\n\n'))))
|
||||
number_changed %>% format(big.mark = big.mark, decimal.mark = decimal.mark), 'test results.\n\n'))))
|
||||
}
|
||||
|
||||
if (verbose == TRUE) {
|
||||
|
||||
76
R/guess_ab.R
Normal file
76
R/guess_ab.R
Normal file
@@ -0,0 +1,76 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://gitlab.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# #
|
||||
# This R package was created for academic research and was publicly #
|
||||
# released in the hope that it will be useful, but it comes WITHOUT #
|
||||
# ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitab.io/AMR. #
|
||||
# ==================================================================== #
|
||||
|
||||
#' Guess antibiotic column
|
||||
#'
|
||||
#' This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set.
|
||||
#' @param tbl a \code{data.frame}
|
||||
#' @param col a character to look for
|
||||
#' @param verbose a logical to indicate whether additional info should be printed
|
||||
#' @importFrom dplyr %>% select filter_all any_vars
|
||||
#' @export
|
||||
#' @inheritSection AMR Read more on our website!
|
||||
# @examples
|
||||
#
|
||||
guess_ab <- function(tbl = NULL, col = NULL, verbose = FALSE) {
|
||||
if (is.null(tbl) & is.null(col)) {
|
||||
return(as.name("guess_ab"))
|
||||
}
|
||||
#stop("This function should not be called directly.")
|
||||
if (length(col) > 1) {
|
||||
warning("argument 'col' has length > 1 and only the first element will be used")
|
||||
col <- col[1]
|
||||
}
|
||||
if (!is.data.frame(tbl)) {
|
||||
stop("`tbl` must be a data.frame")
|
||||
}
|
||||
tbl_names <- colnames(tbl)
|
||||
ab_result <- antibiotics %>%
|
||||
select(atc:trade_name) %>%
|
||||
filter_all(any_vars(tolower(.) == tolower(col)))
|
||||
if (nrow(ab_result) > 1) {
|
||||
# get most likely one
|
||||
if (col %in% ab_result$atc) {
|
||||
ab_result <- ab_result %>% filter(atc == col)
|
||||
} else if (col %in% ab_result$certe) {
|
||||
ab_result <- ab_result %>% filter(certe == col)
|
||||
} else if (col %in% ab_result$umcg) {
|
||||
ab_result <- ab_result %>% filter(umcg == col)
|
||||
} else if (col %in% ab_result$umcg) {
|
||||
ab_result <- ab_result %>% filter(official == col)
|
||||
} else {
|
||||
ab_result <- ab_result[1,]
|
||||
}
|
||||
}
|
||||
tbl_result <- tbl_names[tbl_names %in% ab_result]
|
||||
if (length(tbl_result) > 1) {
|
||||
tbl_result <- tbl_result[1]
|
||||
warning('using column `', tbl_result, '` for col "', col, '"', call. = FALSE)
|
||||
} else if (length(tbl_result) == 0) {
|
||||
if (verbose == TRUE) {
|
||||
message('no result found for col "', col, '"')
|
||||
}
|
||||
return(NULL)
|
||||
} else if (verbose == TRUE) {
|
||||
message('using column `', tbl_result, '` for col "', col, '"')
|
||||
}
|
||||
tbl_result
|
||||
}
|
||||
@@ -78,24 +78,24 @@
|
||||
#' # FALSE, because I is not ignored and so the 4th value differs
|
||||
key_antibiotics <- function(tbl,
|
||||
col_mo = NULL,
|
||||
universal_1 = "amox",
|
||||
universal_2 = "amcl",
|
||||
universal_3 = "cfur",
|
||||
universal_4 = "pita",
|
||||
universal_5 = "cipr",
|
||||
universal_6 = "trsu",
|
||||
GramPos_1 = "vanc",
|
||||
GramPos_2 = "teic",
|
||||
GramPos_3 = "tetr",
|
||||
GramPos_4 = "eryt",
|
||||
GramPos_5 = "oxac",
|
||||
GramPos_6 = "rifa",
|
||||
GramNeg_1 = "gent",
|
||||
GramNeg_2 = "tobr",
|
||||
GramNeg_3 = "coli",
|
||||
GramNeg_4 = "cfot",
|
||||
GramNeg_5 = "cfta",
|
||||
GramNeg_6 = "mero",
|
||||
universal_1 = guess_ab(tbl, "amox"),
|
||||
universal_2 = guess_ab(tbl, "amcl"),
|
||||
universal_3 = guess_ab(tbl, "cfur"),
|
||||
universal_4 = guess_ab(tbl, "pita"),
|
||||
universal_5 = guess_ab(tbl, "cipr"),
|
||||
universal_6 = guess_ab(tbl, "trsu"),
|
||||
GramPos_1 = guess_ab(tbl, "vanc"),
|
||||
GramPos_2 = guess_ab(tbl, "teic"),
|
||||
GramPos_3 = guess_ab(tbl, "tetr"),
|
||||
GramPos_4 = guess_ab(tbl, "eryt"),
|
||||
GramPos_5 = guess_ab(tbl, "oxac"),
|
||||
GramPos_6 = guess_ab(tbl, "rifa"),
|
||||
GramNeg_1 = guess_ab(tbl, "gent"),
|
||||
GramNeg_2 = guess_ab(tbl, "tobr"),
|
||||
GramNeg_3 = guess_ab(tbl, "coli"),
|
||||
GramNeg_4 = guess_ab(tbl, "cfot"),
|
||||
GramNeg_5 = guess_ab(tbl, "cfta"),
|
||||
GramNeg_6 = guess_ab(tbl, "mero"),
|
||||
warnings = TRUE,
|
||||
...) {
|
||||
|
||||
@@ -114,6 +114,7 @@ key_antibiotics <- function(tbl,
|
||||
GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6,
|
||||
GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6)
|
||||
col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = warnings)
|
||||
print(col.list)
|
||||
universal_1 <- col.list[universal_1]
|
||||
universal_2 <- col.list[universal_2]
|
||||
universal_3 <- col.list[universal_3]
|
||||
@@ -139,12 +140,12 @@ key_antibiotics <- function(tbl,
|
||||
gram_positive = c(universal,
|
||||
GramPos_1, GramPos_2, GramPos_3,
|
||||
GramPos_4, GramPos_5, GramPos_6)
|
||||
gram_positive <- gram_positive[!is.na(gram_positive)]
|
||||
gram_positive <- gram_positive[!is.null(gram_positive)]
|
||||
|
||||
gram_negative = c(universal,
|
||||
GramNeg_1, GramNeg_2, GramNeg_3,
|
||||
GramNeg_4, GramNeg_5, GramNeg_6)
|
||||
gram_negative <- gram_negative[!is.na(gram_negative)]
|
||||
gram_negative <- gram_negative[!is.null(gram_negative)]
|
||||
|
||||
# join to microorganisms data set
|
||||
tbl <- tbl %>%
|
||||
@@ -152,6 +153,9 @@ key_antibiotics <- function(tbl,
|
||||
left_join_microorganisms(by = col_mo) %>%
|
||||
mutate(key_ab = NA_character_)
|
||||
|
||||
print(as.character(gram_positive))
|
||||
print(gram_negative)
|
||||
|
||||
# Gram +
|
||||
tbl <- tbl %>% mutate(key_ab =
|
||||
if_else(gramstain == "Gram positive",
|
||||
|
||||
192
R/mdro.R
192
R/mdro.R
@@ -46,66 +46,66 @@ mdro <- function(tbl,
|
||||
country = NULL,
|
||||
col_mo = NULL,
|
||||
info = TRUE,
|
||||
amcl = 'amcl',
|
||||
amik = 'amik',
|
||||
amox = 'amox',
|
||||
ampi = 'ampi',
|
||||
azit = 'azit',
|
||||
aztr = 'aztr',
|
||||
cefa = 'cefa',
|
||||
cfra = 'cfra',
|
||||
cfep = 'cfep',
|
||||
cfot = 'cfot',
|
||||
cfox = 'cfox',
|
||||
cfta = 'cfta',
|
||||
cftr = 'cftr',
|
||||
cfur = 'cfur',
|
||||
chlo = 'chlo',
|
||||
cipr = 'cipr',
|
||||
clar = 'clar',
|
||||
clin = 'clin',
|
||||
clox = 'clox',
|
||||
coli = 'coli',
|
||||
czol = 'czol',
|
||||
dapt = 'dapt',
|
||||
doxy = 'doxy',
|
||||
erta = 'erta',
|
||||
eryt = 'eryt',
|
||||
fosf = 'fosf',
|
||||
fusi = 'fusi',
|
||||
gent = 'gent',
|
||||
imip = 'imip',
|
||||
kana = 'kana',
|
||||
levo = 'levo',
|
||||
linc = 'linc',
|
||||
line = 'line',
|
||||
mero = 'mero',
|
||||
metr = 'metr',
|
||||
mino = 'mino',
|
||||
moxi = 'moxi',
|
||||
nali = 'nali',
|
||||
neom = 'neom',
|
||||
neti = 'neti',
|
||||
nitr = 'nitr',
|
||||
novo = 'novo',
|
||||
norf = 'norf',
|
||||
oflo = 'oflo',
|
||||
peni = 'peni',
|
||||
pipe = 'pipe',
|
||||
pita = 'pita',
|
||||
poly = 'poly',
|
||||
qida = 'qida',
|
||||
rifa = 'rifa',
|
||||
roxi = 'roxi',
|
||||
siso = 'siso',
|
||||
teic = 'teic',
|
||||
tetr = 'tetr',
|
||||
tica = 'tica',
|
||||
tige = 'tige',
|
||||
tobr = 'tobr',
|
||||
trim = 'trim',
|
||||
trsu = 'trsu',
|
||||
vanc = 'vanc') {
|
||||
amcl = guess_ab(),
|
||||
amik = guess_ab(),
|
||||
amox = guess_ab(),
|
||||
ampi = guess_ab(),
|
||||
azit = guess_ab(),
|
||||
aztr = guess_ab(),
|
||||
cefa = guess_ab(),
|
||||
cfra = guess_ab(),
|
||||
cfep = guess_ab(),
|
||||
cfot = guess_ab(),
|
||||
cfox = guess_ab(),
|
||||
cfta = guess_ab(),
|
||||
cftr = guess_ab(),
|
||||
cfur = guess_ab(),
|
||||
chlo = guess_ab(),
|
||||
cipr = guess_ab(),
|
||||
clar = guess_ab(),
|
||||
clin = guess_ab(),
|
||||
clox = guess_ab(),
|
||||
coli = guess_ab(),
|
||||
czol = guess_ab(),
|
||||
dapt = guess_ab(),
|
||||
doxy = guess_ab(),
|
||||
erta = guess_ab(),
|
||||
eryt = guess_ab(),
|
||||
fosf = guess_ab(),
|
||||
fusi = guess_ab(),
|
||||
gent = guess_ab(),
|
||||
imip = guess_ab(),
|
||||
kana = guess_ab(),
|
||||
levo = guess_ab(),
|
||||
linc = guess_ab(),
|
||||
line = guess_ab(),
|
||||
mero = guess_ab(),
|
||||
metr = guess_ab(),
|
||||
mino = guess_ab(),
|
||||
moxi = guess_ab(),
|
||||
nali = guess_ab(),
|
||||
neom = guess_ab(),
|
||||
neti = guess_ab(),
|
||||
nitr = guess_ab(),
|
||||
novo = guess_ab(),
|
||||
norf = guess_ab(),
|
||||
oflo = guess_ab(),
|
||||
peni = guess_ab(),
|
||||
pipe = guess_ab(),
|
||||
pita = guess_ab(),
|
||||
poly = guess_ab(),
|
||||
qida = guess_ab(),
|
||||
rifa = guess_ab(),
|
||||
roxi = guess_ab(),
|
||||
siso = guess_ab(),
|
||||
teic = guess_ab(),
|
||||
tetr = guess_ab(),
|
||||
tica = guess_ab(),
|
||||
tige = guess_ab(),
|
||||
tobr = guess_ab(),
|
||||
trim = guess_ab(),
|
||||
trsu = guess_ab(),
|
||||
vanc = guess_ab()) {
|
||||
|
||||
if (!is.data.frame(tbl)) {
|
||||
stop("`tbl` must be a data frame.", call. = FALSE)
|
||||
@@ -169,12 +169,77 @@ mdro <- function(tbl,
|
||||
}
|
||||
|
||||
# check columns
|
||||
if (identical(amcl, as.name("guess_ab"))) { amcl <- guess_ab(tbl, "amcl", verbose = info) }
|
||||
if (identical(amik, as.name("guess_ab"))) { amik <- guess_ab(tbl, "amik", verbose = info) }
|
||||
if (identical(amox, as.name("guess_ab"))) { amox <- guess_ab(tbl, "amox", verbose = info) }
|
||||
if (identical(ampi, as.name("guess_ab"))) { ampi <- guess_ab(tbl, "ampi", verbose = info) }
|
||||
if (identical(azit, as.name("guess_ab"))) { azit <- guess_ab(tbl, "azit", verbose = info) }
|
||||
if (identical(aztr, as.name("guess_ab"))) { aztr <- guess_ab(tbl, "aztr", verbose = info) }
|
||||
if (identical(cefa, as.name("guess_ab"))) { cefa <- guess_ab(tbl, "cefa", verbose = info) }
|
||||
if (identical(cfra, as.name("guess_ab"))) { cfra <- guess_ab(tbl, "cfra", verbose = info) }
|
||||
if (identical(cfep, as.name("guess_ab"))) { cfep <- guess_ab(tbl, "cfep", verbose = info) }
|
||||
if (identical(cfot, as.name("guess_ab"))) { cfot <- guess_ab(tbl, "cfot", verbose = info) }
|
||||
if (identical(cfox, as.name("guess_ab"))) { cfox <- guess_ab(tbl, "cfox", verbose = info) }
|
||||
if (identical(cfta, as.name("guess_ab"))) { cfta <- guess_ab(tbl, "cfta", verbose = info) }
|
||||
if (identical(cftr, as.name("guess_ab"))) { cftr <- guess_ab(tbl, "cftr", verbose = info) }
|
||||
if (identical(cfur, as.name("guess_ab"))) { cfur <- guess_ab(tbl, "cfur", verbose = info) }
|
||||
if (identical(chlo, as.name("guess_ab"))) { chlo <- guess_ab(tbl, "chlo", verbose = info) }
|
||||
if (identical(cipr, as.name("guess_ab"))) { cipr <- guess_ab(tbl, "cipr", verbose = info) }
|
||||
if (identical(clar, as.name("guess_ab"))) { clar <- guess_ab(tbl, "clar", verbose = info) }
|
||||
if (identical(clin, as.name("guess_ab"))) { clin <- guess_ab(tbl, "clin", verbose = info) }
|
||||
if (identical(clox, as.name("guess_ab"))) { clox <- guess_ab(tbl, "clox", verbose = info) }
|
||||
if (identical(coli, as.name("guess_ab"))) { coli <- guess_ab(tbl, "coli", verbose = info) }
|
||||
if (identical(czol, as.name("guess_ab"))) { czol <- guess_ab(tbl, "czol", verbose = info) }
|
||||
if (identical(dapt, as.name("guess_ab"))) { dapt <- guess_ab(tbl, "dapt", verbose = info) }
|
||||
if (identical(doxy, as.name("guess_ab"))) { doxy <- guess_ab(tbl, "doxy", verbose = info) }
|
||||
if (identical(erta, as.name("guess_ab"))) { erta <- guess_ab(tbl, "erta", verbose = info) }
|
||||
if (identical(eryt, as.name("guess_ab"))) { eryt <- guess_ab(tbl, "eryt", verbose = info) }
|
||||
if (identical(fosf, as.name("guess_ab"))) { fosf <- guess_ab(tbl, "fosf", verbose = info) }
|
||||
if (identical(fusi, as.name("guess_ab"))) { fusi <- guess_ab(tbl, "fusi", verbose = info) }
|
||||
if (identical(gent, as.name("guess_ab"))) { gent <- guess_ab(tbl, "gent", verbose = info) }
|
||||
if (identical(imip, as.name("guess_ab"))) { imip <- guess_ab(tbl, "imip", verbose = info) }
|
||||
if (identical(kana, as.name("guess_ab"))) { kana <- guess_ab(tbl, "kana", verbose = info) }
|
||||
if (identical(levo, as.name("guess_ab"))) { levo <- guess_ab(tbl, "levo", verbose = info) }
|
||||
if (identical(linc, as.name("guess_ab"))) { linc <- guess_ab(tbl, "linc", verbose = info) }
|
||||
if (identical(line, as.name("guess_ab"))) { line <- guess_ab(tbl, "line", verbose = info) }
|
||||
if (identical(mero, as.name("guess_ab"))) { mero <- guess_ab(tbl, "mero", verbose = info) }
|
||||
if (identical(metr, as.name("guess_ab"))) { metr <- guess_ab(tbl, "metr", verbose = info) }
|
||||
if (identical(mino, as.name("guess_ab"))) { mino <- guess_ab(tbl, "mino", verbose = info) }
|
||||
if (identical(moxi, as.name("guess_ab"))) { moxi <- guess_ab(tbl, "moxi", verbose = info) }
|
||||
if (identical(nali, as.name("guess_ab"))) { nali <- guess_ab(tbl, "nali", verbose = info) }
|
||||
if (identical(neom, as.name("guess_ab"))) { neom <- guess_ab(tbl, "neom", verbose = info) }
|
||||
if (identical(neti, as.name("guess_ab"))) { neti <- guess_ab(tbl, "neti", verbose = info) }
|
||||
if (identical(nitr, as.name("guess_ab"))) { nitr <- guess_ab(tbl, "nitr", verbose = info) }
|
||||
if (identical(novo, as.name("guess_ab"))) { novo <- guess_ab(tbl, "novo", verbose = info) }
|
||||
if (identical(norf, as.name("guess_ab"))) { norf <- guess_ab(tbl, "norf", verbose = info) }
|
||||
if (identical(oflo, as.name("guess_ab"))) { oflo <- guess_ab(tbl, "oflo", verbose = info) }
|
||||
if (identical(peni, as.name("guess_ab"))) { peni <- guess_ab(tbl, "peni", verbose = info) }
|
||||
if (identical(pipe, as.name("guess_ab"))) { pipe <- guess_ab(tbl, "pipe", verbose = info) }
|
||||
if (identical(pita, as.name("guess_ab"))) { pita <- guess_ab(tbl, "pita", verbose = info) }
|
||||
if (identical(poly, as.name("guess_ab"))) { poly <- guess_ab(tbl, "poly", verbose = info) }
|
||||
if (identical(qida, as.name("guess_ab"))) { qida <- guess_ab(tbl, "qida", verbose = info) }
|
||||
if (identical(rifa, as.name("guess_ab"))) { rifa <- guess_ab(tbl, "rifa", verbose = info) }
|
||||
if (identical(roxi, as.name("guess_ab"))) { roxi <- guess_ab(tbl, "roxi", verbose = info) }
|
||||
if (identical(siso, as.name("guess_ab"))) { siso <- guess_ab(tbl, "siso", verbose = info) }
|
||||
if (identical(teic, as.name("guess_ab"))) { teic <- guess_ab(tbl, "teic", verbose = info) }
|
||||
if (identical(tetr, as.name("guess_ab"))) { tetr <- guess_ab(tbl, "tetr", verbose = info) }
|
||||
if (identical(tica, as.name("guess_ab"))) { tica <- guess_ab(tbl, "tica", verbose = info) }
|
||||
if (identical(tige, as.name("guess_ab"))) { tige <- guess_ab(tbl, "tige", verbose = info) }
|
||||
if (identical(tobr, as.name("guess_ab"))) { tobr <- guess_ab(tbl, "tobr", verbose = info) }
|
||||
if (identical(trim, as.name("guess_ab"))) { trim <- guess_ab(tbl, "trim", verbose = info) }
|
||||
if (identical(trsu, as.name("guess_ab"))) { trsu <- guess_ab(tbl, "trsu", verbose = info) }
|
||||
if (identical(vanc, as.name("guess_ab"))) { vanc <- guess_ab(tbl, "vanc", verbose = info) }
|
||||
col.list <- c(amcl, amik, amox, ampi, azit, aztr, cefa, cfra, cfep, cfot,
|
||||
cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
|
||||
czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
|
||||
levo, linc, line, mero, metr, mino, moxi, nali, neom, neti, nitr,
|
||||
novo, norf, oflo, peni, pita, poly, qida, rifa, roxi, siso,
|
||||
teic, tetr, tica, tige, tobr, trim, trsu, vanc)
|
||||
levo, linc, line, mero, metr, mino, moxi, nali, neom, neti,
|
||||
nitr, novo, norf, oflo, peni, pipe, pita, poly, qida, rifa,
|
||||
roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
|
||||
if (length(col.list) < 60) {
|
||||
warning('Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.',
|
||||
immediate. = TRUE,
|
||||
call. = FALSE)
|
||||
}
|
||||
col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
|
||||
amcl <- col.list[amcl]
|
||||
amik <- col.list[amik]
|
||||
@@ -221,6 +286,7 @@ mdro <- function(tbl,
|
||||
norf <- col.list[norf]
|
||||
oflo <- col.list[oflo]
|
||||
peni <- col.list[peni]
|
||||
pipe <- col.list[pipe]
|
||||
pita <- col.list[pita]
|
||||
poly <- col.list[poly]
|
||||
qida <- col.list[qida]
|
||||
|
||||
2
R/misc.R
2
R/misc.R
@@ -80,7 +80,7 @@ check_available_columns <- function(tbl, col.list, info = TRUE) {
|
||||
} else if (tolower(col.list[i]) %in% colnames(tbl)) {
|
||||
col.list[i] <- tolower(col.list[i])
|
||||
} else if (!col.list[i] %in% colnames(tbl)) {
|
||||
col.list[i] <- NA
|
||||
col.list[i] <- NULL
|
||||
}
|
||||
}
|
||||
if (!all(col.list %in% colnames(tbl))) {
|
||||
|
||||
@@ -25,22 +25,27 @@
|
||||
\usage{
|
||||
eucast_rules(tbl, col_mo = NULL, info = TRUE,
|
||||
rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
|
||||
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
|
||||
azit = "azit", azlo = "azlo", aztr = "aztr", cefa = "cefa",
|
||||
cfep = "cfep", cfot = "cfot", cfox = "cfox", cfra = "cfra",
|
||||
cfta = "cfta", cftr = "cftr", cfur = "cfur", chlo = "chlo",
|
||||
cipr = "cipr", clar = "clar", clin = "clin", clox = "clox",
|
||||
coli = "coli", czol = "czol", dapt = "dapt", doxy = "doxy",
|
||||
erta = "erta", eryt = "eryt", fosf = "fosf", fusi = "fusi",
|
||||
gent = "gent", imip = "imip", kana = "kana", levo = "levo",
|
||||
linc = "linc", line = "line", mero = "mero", mezl = "mezl",
|
||||
mino = "mino", moxi = "moxi", nali = "nali", neom = "neom",
|
||||
neti = "neti", nitr = "nitr", norf = "norf", novo = "novo",
|
||||
oflo = "oflo", oxac = "oxac", peni = "peni", pipe = "pipe",
|
||||
pita = "pita", poly = "poly", pris = "pris", qida = "qida",
|
||||
rifa = "rifa", roxi = "roxi", siso = "siso", teic = "teic",
|
||||
tetr = "tetr", tica = "tica", tige = "tige", tobr = "tobr",
|
||||
trim = "trim", trsu = "trsu", vanc = "vanc")
|
||||
amcl = guess_ab(), amik = guess_ab(), amox = guess_ab(),
|
||||
ampi = guess_ab(), azit = guess_ab(), azlo = guess_ab(),
|
||||
aztr = guess_ab(), cefa = guess_ab(), cfep = guess_ab(),
|
||||
cfot = guess_ab(), cfox = guess_ab(), cfra = guess_ab(),
|
||||
cfta = guess_ab(), cftr = guess_ab(), cfur = guess_ab(),
|
||||
chlo = guess_ab(), cipr = guess_ab(), clar = guess_ab(),
|
||||
clin = guess_ab(), clox = guess_ab(), coli = guess_ab(),
|
||||
czol = guess_ab(), dapt = guess_ab(), doxy = guess_ab(),
|
||||
erta = guess_ab(), eryt = guess_ab(), fosf = guess_ab(),
|
||||
fusi = guess_ab(), gent = guess_ab(), imip = guess_ab(),
|
||||
kana = guess_ab(), levo = guess_ab(), linc = guess_ab(),
|
||||
line = guess_ab(), mero = guess_ab(), mezl = guess_ab(),
|
||||
mino = guess_ab(), moxi = guess_ab(), nali = guess_ab(),
|
||||
neom = guess_ab(), neti = guess_ab(), nitr = guess_ab(),
|
||||
norf = guess_ab(), novo = guess_ab(), oflo = guess_ab(),
|
||||
oxac = guess_ab(), peni = guess_ab(), pipe = guess_ab(),
|
||||
pita = guess_ab(), poly = guess_ab(), pris = guess_ab(),
|
||||
qida = guess_ab(), rifa = guess_ab(), roxi = guess_ab(),
|
||||
siso = guess_ab(), teic = guess_ab(), tetr = guess_ab(),
|
||||
tica = guess_ab(), tige = guess_ab(), tobr = guess_ab(),
|
||||
trim = guess_ab(), trsu = guess_ab(), vanc = guess_ab())
|
||||
|
||||
EUCAST_rules(...)
|
||||
|
||||
@@ -69,7 +74,7 @@ Apply susceptibility rules as defined by the European Committee on Antimicrobial
|
||||
}
|
||||
\section{Antibiotics}{
|
||||
|
||||
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.
|
||||
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.
|
||||
|
||||
Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
|
||||
|
||||
|
||||
24
man/guess_ab.Rd
Normal file
24
man/guess_ab.Rd
Normal file
@@ -0,0 +1,24 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/guess_ab.R
|
||||
\name{guess_ab}
|
||||
\alias{guess_ab}
|
||||
\title{Guess antibiotic column}
|
||||
\usage{
|
||||
guess_ab(tbl = NULL, col = NULL, verbose = FALSE)
|
||||
}
|
||||
\arguments{
|
||||
\item{tbl}{a \code{data.frame}}
|
||||
|
||||
\item{col}{a character to look for}
|
||||
|
||||
\item{verbose}{a logical to indicate whether additional info should be printed}
|
||||
}
|
||||
\description{
|
||||
This tries to find a column name in a data set based on information from the \code{\link{antibiotics}} data set.
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
|
||||
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.
|
||||
}
|
||||
|
||||
@@ -5,13 +5,17 @@
|
||||
\alias{key_antibiotics_equal}
|
||||
\title{Key antibiotics for first \emph{weighted} isolates}
|
||||
\usage{
|
||||
key_antibiotics(tbl, col_mo = NULL, universal_1 = "amox",
|
||||
universal_2 = "amcl", universal_3 = "cfur", universal_4 = "pita",
|
||||
universal_5 = "cipr", universal_6 = "trsu", GramPos_1 = "vanc",
|
||||
GramPos_2 = "teic", GramPos_3 = "tetr", GramPos_4 = "eryt",
|
||||
GramPos_5 = "oxac", GramPos_6 = "rifa", GramNeg_1 = "gent",
|
||||
GramNeg_2 = "tobr", GramNeg_3 = "coli", GramNeg_4 = "cfot",
|
||||
GramNeg_5 = "cfta", GramNeg_6 = "mero", warnings = TRUE, ...)
|
||||
key_antibiotics(tbl, col_mo = NULL, universal_1 = guess_ab(tbl,
|
||||
"amox"), universal_2 = guess_ab(tbl, "amcl"),
|
||||
universal_3 = guess_ab(tbl, "cfur"), universal_4 = guess_ab(tbl,
|
||||
"pita"), universal_5 = guess_ab(tbl, "cipr"),
|
||||
universal_6 = guess_ab(tbl, "trsu"), GramPos_1 = guess_ab(tbl,
|
||||
"vanc"), GramPos_2 = guess_ab(tbl, "teic"), GramPos_3 = guess_ab(tbl,
|
||||
"tetr"), GramPos_4 = guess_ab(tbl, "eryt"), GramPos_5 = guess_ab(tbl,
|
||||
"oxac"), GramPos_6 = guess_ab(tbl, "rifa"), GramNeg_1 = guess_ab(tbl,
|
||||
"gent"), GramNeg_2 = guess_ab(tbl, "tobr"), GramNeg_3 = guess_ab(tbl,
|
||||
"coli"), GramNeg_4 = guess_ab(tbl, "cfot"), GramNeg_5 = guess_ab(tbl,
|
||||
"cfta"), GramNeg_6 = guess_ab(tbl, "mero"), warnings = TRUE, ...)
|
||||
|
||||
key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
|
||||
ignore_I = TRUE, points_threshold = 2, info = FALSE)
|
||||
|
||||
37
man/mdro.Rd
37
man/mdro.Rd
@@ -8,21 +8,26 @@
|
||||
\title{Determine multidrug-resistant organisms (MDRO)}
|
||||
\usage{
|
||||
mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
|
||||
amcl = "amcl", amik = "amik", amox = "amox", ampi = "ampi",
|
||||
azit = "azit", aztr = "aztr", cefa = "cefa", cfra = "cfra",
|
||||
cfep = "cfep", cfot = "cfot", cfox = "cfox", cfta = "cfta",
|
||||
cftr = "cftr", cfur = "cfur", chlo = "chlo", cipr = "cipr",
|
||||
clar = "clar", clin = "clin", clox = "clox", coli = "coli",
|
||||
czol = "czol", dapt = "dapt", doxy = "doxy", erta = "erta",
|
||||
eryt = "eryt", fosf = "fosf", fusi = "fusi", gent = "gent",
|
||||
imip = "imip", kana = "kana", levo = "levo", linc = "linc",
|
||||
line = "line", mero = "mero", metr = "metr", mino = "mino",
|
||||
moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
|
||||
nitr = "nitr", novo = "novo", norf = "norf", oflo = "oflo",
|
||||
peni = "peni", pipe = "pipe", pita = "pita", poly = "poly",
|
||||
qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso",
|
||||
teic = "teic", tetr = "tetr", tica = "tica", tige = "tige",
|
||||
tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc")
|
||||
amcl = guess_ab(), amik = guess_ab(), amox = guess_ab(),
|
||||
ampi = guess_ab(), azit = guess_ab(), aztr = guess_ab(),
|
||||
cefa = guess_ab(), cfra = guess_ab(), cfep = guess_ab(),
|
||||
cfot = guess_ab(), cfox = guess_ab(), cfta = guess_ab(),
|
||||
cftr = guess_ab(), cfur = guess_ab(), chlo = guess_ab(),
|
||||
cipr = guess_ab(), clar = guess_ab(), clin = guess_ab(),
|
||||
clox = guess_ab(), coli = guess_ab(), czol = guess_ab(),
|
||||
dapt = guess_ab(), doxy = guess_ab(), erta = guess_ab(),
|
||||
eryt = guess_ab(), fosf = guess_ab(), fusi = guess_ab(),
|
||||
gent = guess_ab(), imip = guess_ab(), kana = guess_ab(),
|
||||
levo = guess_ab(), linc = guess_ab(), line = guess_ab(),
|
||||
mero = guess_ab(), metr = guess_ab(), mino = guess_ab(),
|
||||
moxi = guess_ab(), nali = guess_ab(), neom = guess_ab(),
|
||||
neti = guess_ab(), nitr = guess_ab(), novo = guess_ab(),
|
||||
norf = guess_ab(), oflo = guess_ab(), peni = guess_ab(),
|
||||
pipe = guess_ab(), pita = guess_ab(), poly = guess_ab(),
|
||||
qida = guess_ab(), rifa = guess_ab(), roxi = guess_ab(),
|
||||
siso = guess_ab(), teic = guess_ab(), tetr = guess_ab(),
|
||||
tica = guess_ab(), tige = guess_ab(), tobr = guess_ab(),
|
||||
trim = guess_ab(), trsu = guess_ab(), vanc = guess_ab())
|
||||
|
||||
brmo(..., country = "nl")
|
||||
|
||||
@@ -172,7 +177,7 @@ When \code{country} will be left blank, guidelines will be taken from EUCAST Exp
|
||||
}
|
||||
\section{Antibiotics}{
|
||||
|
||||
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.
|
||||
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.
|
||||
|
||||
Abbrevations of the column containing antibiotics in the form: \strong{abbreviation}: generic name (\emph{ATC code})
|
||||
|
||||
|
||||
@@ -86,12 +86,14 @@ test_that("EUCAST rules work", {
|
||||
|
||||
# amox is inferred by benzylpenicillin in Kingella kingae
|
||||
expect_equal(
|
||||
as.list(eucast_rules(
|
||||
data.frame(mo = as.mo("Kingella kingae"),
|
||||
peni = "S",
|
||||
amox = "-",
|
||||
stringsAsFactors = FALSE)
|
||||
, info = FALSE))$amox,
|
||||
suppressWarnings(
|
||||
as.list(eucast_rules(
|
||||
data.frame(mo = as.mo("Kingella kingae"),
|
||||
peni = "S",
|
||||
amox = "-",
|
||||
stringsAsFactors = FALSE)
|
||||
, info = FALSE))$amox
|
||||
),
|
||||
"S")
|
||||
|
||||
# also test norf
|
||||
|
||||
@@ -42,7 +42,13 @@ test_that("mdro works", {
|
||||
expect_equal(outcome %>% freq() %>% pull(count),
|
||||
c(1989, 9, 2)) # 1989 neg, 9 pos, 2 unconfirmed
|
||||
|
||||
expect_equal(brmo(septic_patients, info = FALSE), mdro(septic_patients, "nl", info = FALSE))
|
||||
expect_equal(
|
||||
suppressWarnings(
|
||||
brmo(septic_patients, info = FALSE)),
|
||||
suppressWarnings(
|
||||
mdro(septic_patients, "nl", info = FALSE)
|
||||
)
|
||||
)
|
||||
|
||||
# still working on German guidelines
|
||||
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
|
||||
|
||||
Reference in New Issue
Block a user