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(v1.4.0.9052) replaced all sapply's with type-safe vapply's

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dr. M.S. (Matthijs) Berends
2020-12-28 22:24:33 +01:00
parent ccf13dd6c0
commit 526f8afb08
37 changed files with 155 additions and 117 deletions
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49
R/mdro.R
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@ -193,28 +193,28 @@ mdro <- function(x,
guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
guideline$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
guideline$version <- NA
guideline$source <- "Clinical Microbiology and Infection 18:3, 2012. DOI: 10.1111/j.1469-0691.2011.03570.x"
guideline$source_url <- "Clinical Microbiology and Infection 18:3, 2012. DOI: 10.1111/j.1469-0691.2011.03570.x"
guideline$type <- "MDRs/XDRs/PDRs"
} else if (guideline$code == "eucast3.1") {
guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Exceptional Phenotypes Tables\""
guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
guideline$version <- "3.1, 2016"
guideline$source <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf"
guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf"
guideline$type <- "EUCAST Exceptional Phenotypes"
} else if (guideline$code == "eucast3.2") {
guideline$name <- "EUCAST Expert Rules, \"Intrinsic Resistance and Unusual Phenotypes\""
guideline$author <- "EUCAST (European Committee on Antimicrobial Susceptibility Testing)"
guideline$version <- "3.2, 2020"
guideline$source <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf"
guideline$source_url <- "https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf"
guideline$type <- "EUCAST Unusual Phenotypes"
} else if (guideline$code == "tb") {
guideline$name <- "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis"
guideline$author <- "WHO (World Health Organization)"
guideline$version <- "WHO/HTM/TB/2014.11, 2014"
guideline$source <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
guideline$source_url <- "https://www.who.int/tb/publications/pmdt_companionhandbook/en/"
guideline$type <- "MDR-TB's"
# support per country:
@ -222,14 +222,14 @@ mdro <- function(x,
guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
guideline$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
guideline$version <- NA
guideline$source <- "Antimicrobial Resistance and Infection Control 4:7, 2015. DOI: 10.1186/s13756-015-0047-6"
guideline$source_url <- "Antimicrobial Resistance and Infection Control 4:7, 2015. DOI: 10.1186/s13756-015-0047-6"
guideline$type <- "MRGNs"
} else if (guideline$code == "brmo") {
guideline$name <- "WIP-Richtlijn Bijzonder Resistente Micro-organismen (BRMO)"
guideline$author <- "RIVM (Rijksinstituut voor de Volksgezondheid)"
guideline$version <- "Revision as of December 2017"
guideline$source <- "https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH"
guideline$source_url <- "https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH"
guideline$type <- "BRMOs"
} else {
stop("This guideline is currently unsupported: ", guideline$code, call. = FALSE)
@ -413,6 +413,7 @@ mdro <- function(x,
...)
}
# nolint start
AMC <- cols_ab["AMC"]
AMK <- cols_ab["AMK"]
AMP <- cols_ab["AMP"]
@ -555,6 +556,7 @@ mdro <- function(x,
abx_tb <- c(CAP, ETH, GAT, INH, PZA, RIF, RIB, RFP)
abx_tb <- abx_tb[!is.na(abx_tb)]
stop_if(guideline$code == "tb" & length(abx_tb) == 0, "no antimycobacterials found in data set")
# nolint end
if (combine_SI == TRUE) {
search_result <- "R"
@ -574,8 +576,8 @@ mdro <- function(x,
ifelse(!is.na(guideline$version),
paste0(word_wrap(paste0(font_bold("Version: "), guideline$version), extra_indent = 11, as_note = FALSE), "\n"),
""),
word_wrap(paste0(font_bold("Source: "), guideline$source), extra_indent = 11, as_note = FALSE), "\n",
"\n", sep = "")
paste0(font_bold("Source: "), guideline$source_url),
"\n\n", sep = "")
}
ab_missing <- function(ab) {
@ -585,9 +587,8 @@ mdro <- function(x,
x[!is.na(x)]
}
verbose_df <- NULL
# antibiotic classes
# nolint start
aminoglycosides <- c(TOB, GEN)
cephalosporins <- c(CDZ, CAC, CEC, CFR, RID, MAN, CTZ, CZD, CZO, CDR, DIT, FEP, CAT, CFM, CMX, CMZ, DIZ, CID, CFP, CSL, CND, CTX, CTT, CTF, FOX, CPM, CPO, CPD, CPR, CRD, CFS, CPT, CAZ, CCV, CTL, CTB, CZX, BPR, CFM1, CEI, CRO, CXM, LEX, CEP, HAP, CED, LTM, LOR)
cephalosporins_1st <- c(CAC, CFR, RID, CTZ, CZD, CZO, CRD, CTL, LEX, CEP, HAP, CED)
@ -595,6 +596,7 @@ mdro <- function(x,
cephalosporins_3rd <- c(CDZ, CDR, DIT, CAT, CFM, CMX, DIZ, CFP, CSL, CTX, CPM, CPD, CFS, CAZ, CCV, CTB, CZX, CRO, LTM)
carbapenems <- c(DOR, ETP, IPM, MEM, MEV)
fluoroquinolones <- c(CIP, ENX, FLE, GAT, GEM, GRX, LVX, LOM, MFX, NOR, OFX, PAZ, PEF, PRU, RFL, SPX, TMX, TVA)
# nolint end
# helper function for editing the table
trans_tbl <- function(to, rows, cols, any_all) {
@ -604,9 +606,10 @@ mdro <- function(x,
x[, cols] <- as.data.frame(lapply(x[, cols, drop = FALSE],
function(col) as.rsi(col)),
stringsAsFactors = FALSE)
x[rows, "columns_nonsusceptible"] <<- sapply(rows,
x[rows, "columns_nonsusceptible"] <<- vapply(FUN.VALUE = character(1),
rows,
function(row, group_vct = cols) {
cols_nonsus <- sapply(x[row, group_vct, drop = FALSE],
cols_nonsus <- vapply(FUN.VALUE = logical(1), x[row, group_vct, drop = FALSE],
function(y) y %in% search_result)
paste(sort(c(unlist(strsplit(x[row, "columns_nonsusceptible", drop = TRUE], ", ")),
names(cols_nonsus)[cols_nonsus])),
@ -620,7 +623,7 @@ mdro <- function(x,
}
x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE]),
stringsAsFactors = FALSE))
row_filter <- sapply(x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
row_filter <- vapply(FUN.VALUE = logical(1), x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
row_filter <- x[which(row_filter), "row_number", drop = TRUE]
rows <- rows[rows %in% row_filter]
x[rows, "MDRO"] <<- to
@ -638,21 +641,27 @@ mdro <- function(x,
function(col) as.rsi(col)),
stringsAsFactors = FALSE)
x[rows, "classes_in_guideline"] <<- length(lst)
x[rows, "classes_available"] <<- sapply(rows,
x[rows, "classes_available"] <<- vapply(FUN.VALUE = double(1),
rows,
function(row, group_tbl = lst) {
sum(sapply(group_tbl, function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "I", "R"))))
sum(vapply(FUN.VALUE = logical(1),
group_tbl,
function(group) any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% c("S", "I", "R"))))
})
if (verbose == TRUE) {
x[rows, "columns_nonsusceptible"] <<- sapply(rows,
x[rows, "columns_nonsusceptible"] <<- vapply(FUN.VALUE = character(1),
rows,
function(row, group_vct = lst_vector) {
cols_nonsus <- sapply(x[row, group_vct, drop = FALSE], function(y) y %in% search_result)
cols_nonsus <- vapply(FUN.VALUE = logical(1), x[row, group_vct, drop = FALSE], function(y) y %in% search_result)
paste(sort(names(cols_nonsus)[cols_nonsus]), collapse = ", ")
})
}
x[rows, "classes_affected"] <<- sapply(rows,
x[rows, "classes_affected"] <<- vapply(FUN.VALUE = double(1),
rows,
function(row, group_tbl = lst) {
sum(sapply(group_tbl,
sum(vapply(FUN.VALUE = logical(1),
group_tbl,
function(group) {
any(unlist(x[row, group[!is.na(group)], drop = TRUE]) %in% search_result, na.rm = TRUE)
}),
@ -661,7 +670,7 @@ mdro <- function(x,
# for PDR; all agents are R (or I if combine_SI = FALSE)
x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE]),
stringsAsFactors = FALSE))
row_filter <- sapply(x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
row_filter <- vapply(FUN.VALUE = logical(1), x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
x[which(row_filter), "classes_affected"] <<- 999
}