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guess_ab

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This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-01-03 23:56:19 +01:00
parent 6b2d464f8c
commit 80ea555663
14 changed files with 533 additions and 270 deletions
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3
.gitlab-ci.yml
View File

@ -41,7 +41,8 @@ before_script:
cache:
key: "$CI_COMMIT_REF_SLUG"
paths:
- /usr/lib/R/library/
- /usr/local/lib/R/
- /usr/lib/R/
R 3:
stage: build

1
NAMESPACE
View File

@ -76,6 +76,7 @@ export(g.test)
export(geom_rsi)
export(get_locale)
export(ggplot_rsi)
export(guess_ab)
export(guess_atc)
export(guess_mo)
export(header)

1
NEWS.md
View File

@ -7,6 +7,7 @@
* Contains the complete manual of this package and all of its functions with an explanation of their parameters
* Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis
* Support for [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
* Function `guess_ab` to find an antibiotic column in a table
* 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.
* Function `mo_renamed()` to get a list of all returned values from `as.mo()` that have had taxonomic renaming
* Function `age()` to calculate the (patients) age in years

344
R/eucast_rules.R
View File

@ -30,7 +30,7 @@
#' @param ... parameters that are passed on to \code{eucast_rules}
#' @inheritParams first_isolate
#' @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})
#'
@ -158,69 +158,69 @@ eucast_rules <- function(tbl,
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_VERSION_BREAKPOINTS <- "8.1, 2018"
EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
@ -268,12 +268,80 @@ eucast_rules <- function(tbl,
}
# check columns
if (identical(amcl, as.name("guess_ab"))) { amcl <- guess_ab(tbl, "amcl", verbose = verbose) }
if (identical(amik, as.name("guess_ab"))) { amik <- guess_ab(tbl, "amik", verbose = verbose) }
if (identical(amox, as.name("guess_ab"))) { amox <- guess_ab(tbl, "amox", verbose = verbose) }
if (identical(ampi, as.name("guess_ab"))) { ampi <- guess_ab(tbl, "ampi", verbose = verbose) }
if (identical(azit, as.name("guess_ab"))) { azit <- guess_ab(tbl, "azit", verbose = verbose) }
if (identical(azlo, as.name("guess_ab"))) { azlo <- guess_ab(tbl, "azlo", verbose = verbose) }
if (identical(aztr, as.name("guess_ab"))) { aztr <- guess_ab(tbl, "aztr", verbose = verbose) }
if (identical(cefa, as.name("guess_ab"))) { cefa <- guess_ab(tbl, "cefa", verbose = verbose) }
if (identical(cfep, as.name("guess_ab"))) { cfep <- guess_ab(tbl, "cfep", verbose = verbose) }
if (identical(cfot, as.name("guess_ab"))) { cfot <- guess_ab(tbl, "cfot", verbose = verbose) }
if (identical(cfox, as.name("guess_ab"))) { cfox <- guess_ab(tbl, "cfox", verbose = verbose) }
if (identical(cfra, as.name("guess_ab"))) { cfra <- guess_ab(tbl, "cfra", verbose = verbose) }
if (identical(cfta, as.name("guess_ab"))) { cfta <- guess_ab(tbl, "cfta", verbose = verbose) }
if (identical(cftr, as.name("guess_ab"))) { cftr <- guess_ab(tbl, "cftr", verbose = verbose) }
if (identical(cfur, as.name("guess_ab"))) { cfur <- guess_ab(tbl, "cfur", verbose = verbose) }
if (identical(chlo, as.name("guess_ab"))) { chlo <- guess_ab(tbl, "chlo", verbose = verbose) }
if (identical(cipr, as.name("guess_ab"))) { cipr <- guess_ab(tbl, "cipr", verbose = verbose) }
if (identical(clar, as.name("guess_ab"))) { clar <- guess_ab(tbl, "clar", verbose = verbose) }
if (identical(clin, as.name("guess_ab"))) { clin <- guess_ab(tbl, "clin", verbose = verbose) }
if (identical(clox, as.name("guess_ab"))) { clox <- guess_ab(tbl, "clox", verbose = verbose) }
if (identical(coli, as.name("guess_ab"))) { coli <- guess_ab(tbl, "coli", verbose = verbose) }
if (identical(czol, as.name("guess_ab"))) { czol <- guess_ab(tbl, "czol", verbose = verbose) }
if (identical(dapt, as.name("guess_ab"))) { dapt <- guess_ab(tbl, "dapt", verbose = verbose) }
if (identical(doxy, as.name("guess_ab"))) { doxy <- guess_ab(tbl, "doxy", verbose = verbose) }
if (identical(erta, as.name("guess_ab"))) { erta <- guess_ab(tbl, "erta", verbose = verbose) }
if (identical(eryt, as.name("guess_ab"))) { eryt <- guess_ab(tbl, "eryt", verbose = verbose) }
if (identical(fosf, as.name("guess_ab"))) { fosf <- guess_ab(tbl, "fosf", verbose = verbose) }
if (identical(fusi, as.name("guess_ab"))) { fusi <- guess_ab(tbl, "fusi", verbose = verbose) }
if (identical(gent, as.name("guess_ab"))) { gent <- guess_ab(tbl, "gent", verbose = verbose) }
if (identical(imip, as.name("guess_ab"))) { imip <- guess_ab(tbl, "imip", verbose = verbose) }
if (identical(kana, as.name("guess_ab"))) { kana <- guess_ab(tbl, "kana", verbose = verbose) }
if (identical(levo, as.name("guess_ab"))) { levo <- guess_ab(tbl, "levo", verbose = verbose) }
if (identical(linc, as.name("guess_ab"))) { linc <- guess_ab(tbl, "linc", verbose = verbose) }
if (identical(line, as.name("guess_ab"))) { line <- guess_ab(tbl, "line", verbose = verbose) }
if (identical(mero, as.name("guess_ab"))) { mero <- guess_ab(tbl, "mero", verbose = verbose) }
if (identical(mezl, as.name("guess_ab"))) { mezl <- guess_ab(tbl, "mezl", verbose = verbose) }
if (identical(mino, as.name("guess_ab"))) { mino <- guess_ab(tbl, "mino", verbose = verbose) }
if (identical(moxi, as.name("guess_ab"))) { moxi <- guess_ab(tbl, "moxi", verbose = verbose) }
if (identical(nali, as.name("guess_ab"))) { nali <- guess_ab(tbl, "nali", verbose = verbose) }
if (identical(neom, as.name("guess_ab"))) { neom <- guess_ab(tbl, "neom", verbose = verbose) }
if (identical(neti, as.name("guess_ab"))) { neti <- guess_ab(tbl, "neti", verbose = verbose) }
if (identical(nitr, as.name("guess_ab"))) { nitr <- guess_ab(tbl, "nitr", verbose = verbose) }
if (identical(norf, as.name("guess_ab"))) { norf <- guess_ab(tbl, "norf", verbose = verbose) }
if (identical(novo, as.name("guess_ab"))) { novo <- guess_ab(tbl, "novo", verbose = verbose) }
if (identical(oflo, as.name("guess_ab"))) { oflo <- guess_ab(tbl, "oflo", verbose = verbose) }
if (identical(oxac, as.name("guess_ab"))) { oxac <- guess_ab(tbl, "oxac", verbose = verbose) }
if (identical(peni, as.name("guess_ab"))) { peni <- guess_ab(tbl, "peni", verbose = verbose) }
if (identical(pipe, as.name("guess_ab"))) { pipe <- guess_ab(tbl, "pipe", verbose = verbose) }
if (identical(pita, as.name("guess_ab"))) { pita <- guess_ab(tbl, "pita", verbose = verbose) }
if (identical(poly, as.name("guess_ab"))) { poly <- guess_ab(tbl, "poly", verbose = verbose) }
if (identical(pris, as.name("guess_ab"))) { pris <- guess_ab(tbl, "pris", verbose = verbose) }
if (identical(qida, as.name("guess_ab"))) { qida <- guess_ab(tbl, "qida", verbose = verbose) }
if (identical(rifa, as.name("guess_ab"))) { rifa <- guess_ab(tbl, "rifa", verbose = verbose) }
if (identical(roxi, as.name("guess_ab"))) { roxi <- guess_ab(tbl, "roxi", verbose = verbose) }
if (identical(siso, as.name("guess_ab"))) { siso <- guess_ab(tbl, "siso", verbose = verbose) }
if (identical(teic, as.name("guess_ab"))) { teic <- guess_ab(tbl, "teic", verbose = verbose) }
if (identical(tetr, as.name("guess_ab"))) { tetr <- guess_ab(tbl, "tetr", verbose = verbose) }
if (identical(tica, as.name("guess_ab"))) { tica <- guess_ab(tbl, "tica", verbose = verbose) }
if (identical(tige, as.name("guess_ab"))) { tige <- guess_ab(tbl, "tige", verbose = verbose) }
if (identical(tobr, as.name("guess_ab"))) { tobr <- guess_ab(tbl, "tobr", verbose = verbose) }
if (identical(trim, as.name("guess_ab"))) { trim <- guess_ab(tbl, "trim", verbose = verbose) }
if (identical(trsu, as.name("guess_ab"))) { trsu <- guess_ab(tbl, "trsu", verbose = verbose) }
if (identical(vanc, as.name("guess_ab"))) { vanc <- guess_ab(tbl, "vanc", verbose = verbose) }
col.list <- c(amcl, amik, amox, ampi, azit, azlo, 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, mezl, mino, moxi, nali, neom, neti, nitr,
novo, norf, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa,
roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
if (length(col.list) < 63) {
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]
@ -339,8 +407,8 @@ eucast_rules <- function(tbl,
trsu <- col.list[trsu]
vanc <- col.list[vanc]
amount_changed <- 0
amount_affected_rows <- integer(0)
number_changed <- 0
number_affected_rows <- integer(0)
verbose_info <- data.frame(rule_type = character(0),
rule_set = character(0),
force_to = character(0),
@ -352,7 +420,7 @@ eucast_rules <- function(tbl,
# helper function for editing the table
edit_rsi <- function(to, rule, rows, cols) {
cols <- unique(cols[!is.na(cols)])
cols <- unique(cols[!is.na(cols) & !is.null(cols)])
if (length(rows) > 0 & length(cols) > 0) {
before <- as.character(unlist(as.list(tbl_original[rows, cols])))
tryCatch(
@ -376,8 +444,8 @@ eucast_rules <- function(tbl,
tbl[rows, cols] <<- to
))
after <- as.character(unlist(as.list(tbl_original[rows, cols])))
amount_changed <<- amount_changed + sum(before != after, na.rm = TRUE)
amount_affected_rows <<- unique(c(amount_affected_rows, rows))
number_changed <<- number_changed + sum(before != after, na.rm = TRUE)
number_affected_rows <<- unique(c(number_affected_rows, rows))
changed_results <<- changed_results + sum(before != after, na.rm = TRUE) # will be reset at start of every rule
if (verbose == TRUE) {
@ -399,7 +467,7 @@ eucast_rules <- function(tbl,
}
}
na.rm <- function(col) {
if (is.na(col)) {
if (is.null(col)) {
""
} else {
col
@ -420,7 +488,7 @@ eucast_rules <- function(tbl,
}
# since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table)
if (!is.na(ampi) & !is.na(amox)) {
if (!is.null(ampi) & !is.null(amox)) {
if (verbose == TRUE) {
cat(bgGreen("\n VERBOSE: transforming",
length(which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R"))),
@ -435,7 +503,7 @@ eucast_rules <- function(tbl,
tbl[which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "S"
tbl[which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "I"
tbl[which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "R"
} else if (is.na(ampi) & !is.na(amox)) {
} else if (is.null(ampi) & !is.null(amox)) {
# ampicillin column is missing, but amoxicillin is available
message(blue(paste0("NOTE: Using column `", bold(amox), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it.")))
ampi <- amox
@ -471,21 +539,21 @@ eucast_rules <- function(tbl,
cat(rule)
}
if (!is.na(ampi)) {
if (!is.null(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$order == 'Enterobacteriales'
& tbl[, ampi] == 'S'),
cols = amox)
}
if (!is.na(ampi)) {
if (!is.null(ampi)) {
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$order == 'Enterobacteriales'
& tbl[, ampi] == 'I'),
cols = amox)
}
if (!is.na(ampi)) {
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
View 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
}

44
R/key_antibiotics.R
View File

@ -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
View File

@ -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
View File

@ -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))) {

39
man/eucast_rules.Rd
View File

@ -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
View 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.
}

18
man/key_antibiotics.Rd
View File

@ -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
View File

@ -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})

4
tests/testthat/test-eucast_rules.R
View File

@ -86,12 +86,14 @@ test_that("EUCAST rules work", {
# amox is inferred by benzylpenicillin in Kingella kingae
expect_equal(
suppressWarnings(
as.list(eucast_rules(
data.frame(mo = as.mo("Kingella kingae"),
peni = "S",
amox = "-",
stringsAsFactors = FALSE)
, info = FALSE))$amox,
, info = FALSE))$amox
),
"S")
# also test norf

8
tests/testthat/test-mdro.R
View File

@ -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)))