AMR/data-raw/_pre_commit_checks.R

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R

# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# 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. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# Run this file to update the package using:
# source("data-raw/_pre_commit_checks.R")
library(dplyr, warn.conflicts = FALSE)
try(detach("package:data.table", unload = TRUE), silent = TRUE) # to prevent like() to precede over AMR::like
devtools::load_all(quiet = TRUE)
suppressMessages(set_AMR_locale("English"))
pre_commit_lst <- list()
# Save internal data to R/sysdata.rda -------------------------------------
usethis::ui_info(paste0("Updating internal package data"))
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
pre_commit_lst$EUCAST_RULES_DF <- utils::read.delim(
file = "data-raw/eucast_rules.tsv",
skip = 9,
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
strip.white = TRUE,
na = c(NA, "", NULL)
) %>%
# take the order of the reference.rule_group column in the original data file
mutate(
reference.rule_group = factor(reference.rule_group,
levels = unique(reference.rule_group),
ordered = TRUE
),
sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)
) %>%
arrange(
reference.rule_group,
reference.version,
sorting_rule,
reference.rule
) %>%
mutate(reference.rule_group = as.character(reference.rule_group)) %>%
select(-sorting_rule)
pre_commit_lst$TRANSLATIONS <- utils::read.delim(
file = "data-raw/translations.tsv",
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
blank.lines.skip = TRUE,
fill = TRUE,
strip.white = TRUE,
encoding = "UTF-8",
fileEncoding = "UTF-8",
na.strings = c(NA, "", NULL),
allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
quote = ""
)
pre_commit_lst$LANGUAGES_SUPPORTED_NAMES <- c(
list(en = list(exonym = "English", endonym = "English")),
lapply(
TRANSLATIONS[, which(nchar(colnames(pre_commit_lst$TRANSLATIONS)) == 2), drop = FALSE],
function(x) list(exonym = x[1], endonym = x[2])
)
)
pre_commit_lst$LANGUAGES_SUPPORTED <- names(pre_commit_lst$LANGUAGES_SUPPORTED_NAMES)
# vectors of CoNS and CoPS, improves speed in as.mo()
create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
# Determination of which staphylococcal species are CoNS/CoPS according to:
# - Becker et al. 2014, PMID 25278577
# - Becker et al. 2019, PMID 30872103
# - Becker et al. 2020, PMID 32056452
# this function returns class <mo>
MO_staph <- AMR::microorganisms
MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
if (type == "CoNS") {
MO_staph[
which(MO_staph$species %in% c(
"coagulase-negative", "argensis", "arlettae",
"auricularis", "borealis", "caeli", "capitis", "caprae",
"carnosus", "casei", "caseolyticus", "chromogenes", "cohnii", "condimenti",
"croceilyticus",
"debuckii", "devriesei", "edaphicus", "epidermidis",
"equorum", "felis", "fleurettii", "gallinarum",
"haemolyticus", "hominis", "jettensis", "kloosii",
"lentus", "lugdunensis", "massiliensis", "microti",
"muscae", "nepalensis", "pasteuri", "petrasii",
"pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus",
"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
"sciuri", "simulans", "stepanovicii", "succinus",
"ureilyticus",
"vitulinus", "vitulus", "warneri", "xylosus",
"caledonicus", "canis",
"durrellii", "lloydii",
"ratti", "taiwanensis", "veratri", "urealyticus",
"americanisciuri", "marylandisciuri", "shinii", "brunensis"
) |
# old, now renamed to S. schleiferi (but still as synonym in our data of course):
(MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
"mo",
drop = TRUE
]
} else if (type == "CoPS") {
MO_staph[
which(MO_staph$species %in% c(
"coagulase-positive", "coagulans",
"agnetis", "argenteus",
"cornubiensis",
"delphini", "lutrae",
"hyicus", "intermedius",
"pseudintermedius", "pseudointermedius",
"schweitzeri", "simiae",
"roterodami",
"singaporensis"
) |
# old, now renamed to S. coagulans (but still as synonym in our data of course):
(MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
"mo",
drop = TRUE
]
}
}
pre_commit_lst$MO_CONS <- create_species_cons_cops("CoNS")
pre_commit_lst$MO_COPS <- create_species_cons_cops("CoPS")
pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms$genus == "Streptococcus" &
tolower(AMR::microorganisms$species) %in% c(
"pyogenes", "agalactiae", "dysgalactiae", "equi", "canis",
"group a", "group b", "group c", "group g"
))]
pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
pre_commit_lst$MO_PREVALENT_GENERA <- c(
"Absidia",
"Acanthamoeba",
"Acremonium",
"Aedes",
"Alternaria",
"Amoeba",
"Ancylostoma",
"Angiostrongylus",
"Anisakis",
"Anopheles",
"Apophysomyces",
"Arthroderma",
"Aspergillus",
"Aureobasidium",
"Basidiobolus",
"Beauveria",
"Blastocystis",
"Blastomyces",
"Candida",
"Capillaria",
"Chaetomium",
"Chrysonilia",
"Chrysosporium",
"Cladophialophora",
"Cladosporium",
"Conidiobolus",
"Contracaecum",
"Cordylobia",
"Cryptococcus",
"Curvularia",
"Demodex",
"Dermatobia",
"Dientamoeba",
"Diphyllobothrium",
"Dirofilaria",
"Echinostoma",
"Entamoeba",
"Enterobius",
"Exophiala",
"Exserohilum",
"Fasciola",
"Fonsecaea",
"Fusarium",
"Geotrichum",
"Giardia",
"Haloarcula",
"Halobacterium",
"Halococcus",
"Hansenula",
"Hendersonula",
"Heterophyes",
"Histomonas",
"Histoplasma",
"Hymenolepis",
"Hypomyces",
"Hysterothylacium",
"Kloeckera",
"Kluyveromyces",
"Kodamaea",
"Leishmania",
"Lichtheimia",
"Lodderomyces",
"Lomentospora",
"Malassezia",
"Malbranchea",
"Metagonimus",
"Meyerozyma",
"Microsporidium",
"Microsporum",
"Millerozyma",
"Mortierella",
"Mucor",
"Mycocentrospora",
"Necator",
"Nectria",
"Ochroconis",
"Oesophagostomum",
"Oidiodendron",
"Opisthorchis",
"Paecilomyces",
"Pediculus",
"Penicillium",
"Phlebotomus",
"Phoma",
"Pichia",
"Piedraia",
"Pithomyces",
"Pityrosporum",
"Pneumocystis",
"Pseudallescheria",
"Pseudoscopulariopsis",
"Pseudoterranova",
"Pulex",
"Rhizomucor",
"Rhizopus",
"Rhodotorula",
"Saccharomyces",
"Saprochaete",
"Sarcoptes",
"Scedosporium",
"Scolecobasidium",
"Scopulariopsis",
"Scytalidium",
"Spirometra",
"Sporobolomyces",
"Sporotrichum",
"Stachybotrys",
"Strongyloides",
"Syngamus",
"Taenia",
"Talaromyces",
"Toxocara",
"Trichinella",
"Trichobilharzia",
"Trichoderma",
"Trichomonas",
"Trichophyton",
"Trichosporon",
"Trichostrongylus",
"Trichuris",
"Tritirachium",
"Trombicula",
"Trypanosoma",
"Tunga",
"Verticillium",
"Wuchereria"
)
# antibiotic groups
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
pre_commit_lst$AB_AMINOGLYCOSIDES <- antibiotics %>%
filter(group %like% "aminoglycoside") %>%
pull(ab)
pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
pre_commit_lst$AB_ANTIFUNGALS <- antibiotics %>%
filter(group %like% "antifungal") %>%
pull(ab)
pre_commit_lst$AB_ANTIMYCOBACTERIALS <- antibiotics %>%
filter(group %like% "antimycobacterial") %>%
pull(ab)
pre_commit_lst$AB_CARBAPENEMS <- antibiotics %>%
filter(group %like% "carbapenem") %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS <- antibiotics %>%
filter(group %like% "cephalosporin") %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS_1ST <- antibiotics %>%
filter(group %like% "cephalosporin.*1") %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS_2ND <- antibiotics %>%
filter(group %like% "cephalosporin.*2") %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS_3RD <- antibiotics %>%
filter(group %like% "cephalosporin.*3") %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS_4TH <- antibiotics %>%
filter(group %like% "cephalosporin.*4") %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antibiotics %>%
filter(group %like% "cephalosporin.*5") %>%
pull(ab)
pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"]
pre_commit_lst$AB_FLUOROQUINOLONES <- antibiotics %>%
filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>%
pull(ab)
pre_commit_lst$AB_GLYCOPEPTIDES <- antibiotics %>%
filter(group %like% "glycopeptide") %>%
pull(ab)
pre_commit_lst$AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
pre_commit_lst$AB_GLYCOPEPTIDES_EXCEPT_LIPO <- pre_commit_lst$AB_GLYCOPEPTIDES[!pre_commit_lst$AB_GLYCOPEPTIDES %in% pre_commit_lst$AB_LIPOGLYCOPEPTIDES]
pre_commit_lst$AB_LINCOSAMIDES <- antibiotics %>%
filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>%
pull(ab)
pre_commit_lst$AB_MACROLIDES <- antibiotics %>%
filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2) & name %unlike% "screening|inducible")) %>%
pull(ab)
pre_commit_lst$AB_NITROFURANS <- antibiotics %>%
filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>%
pull(ab)
pre_commit_lst$AB_OXAZOLIDINONES <- antibiotics %>%
filter(group %like% "oxazolidinone") %>%
pull(ab)
pre_commit_lst$AB_PENICILLINS <- antibiotics %>%
filter(group %like% "penicillin") %>%
pull(ab)
pre_commit_lst$AB_POLYMYXINS <- antibiotics %>%
filter(group %like% "polymyxin") %>%
pull(ab)
pre_commit_lst$AB_QUINOLONES <- antibiotics %>%
filter(group %like% "quinolone") %>%
pull(ab)
pre_commit_lst$AB_RIFAMYCINS <- antibiotics %>%
filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
pull(ab)
pre_commit_lst$AB_STREPTOGRAMINS <- antibiotics %>%
filter(atc_group2 %like% "streptogramin") %>%
pull(ab)
pre_commit_lst$AB_TETRACYCLINES <- antibiotics %>%
filter(group %like% "tetracycline") %>%
pull(ab)
pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"]
pre_commit_lst$AB_TRIMETHOPRIMS <- antibiotics %>%
filter(group %like% "trimethoprim") %>%
pull(ab)
pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
pre_commit_lst$AB_BETALACTAMS <- c(pre_commit_lst$AB_PENICILLINS, pre_commit_lst$AB_CEPHALOSPORINS, pre_commit_lst$AB_CARBAPENEMS)
# this will be used for documentation:
pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
create_AB_AV_lookup <- function(df) {
new_df <- df
new_df$generalised_name <- generalise_antibiotic_name(new_df$name)
new_df$generalised_synonyms <- lapply(new_df$synonyms, generalise_antibiotic_name)
if ("abbreviations" %in% colnames(df)) {
new_df$generalised_abbreviations <- lapply(new_df$abbreviations, generalise_antibiotic_name)
}
new_df$generalised_loinc <- lapply(new_df$loinc, generalise_antibiotic_name)
new_df$generalised_all <- unname(lapply(
as.list(as.data.frame(
t(new_df[,
c(
colnames(new_df)[colnames(new_df) %in% c("ab", "av", "atc", "cid", "name")],
colnames(new_df)[colnames(new_df) %like% "generalised"]
),
drop = FALSE
]),
stringsAsFactors = FALSE
)),
function(x) {
x <- generalise_antibiotic_name(unname(unlist(x)))
x[x != ""]
}
))
new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
}
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
# Export to package as internal data ----
# usethis::use_data() must receive unquoted object names, which is not flexible at all.
# we'll use good old base::save() instead
save(list = names(pre_commit_lst),
file = "R/sysdata.rda",
envir = as.environment(pre_commit_lst),
compress = "xz",
version = 2,
ascii = FALSE)
usethis::ui_done("Saved to {usethis::ui_value('R/sysdata.rda')}")
# Export data sets to the repository in different formats -----------------
for (pkg in c("haven", "openxlsx2", "arrow")) {
if (!pkg %in% rownames(utils::installed.packages())) {
message("NOTE: package '", pkg, "' not installed! Ignoring export where this package is required.")
}
}
if ("digest" %in% rownames(utils::installed.packages())) {
md5 <- function(object) digest::digest(object, "md5")
} else {
# will write all files anyway, since MD5 hash cannot be determined
md5 <- function(object) "unknown-md5-hash"
}
write_md5 <- function(object) {
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
writeLines(md5(object), conn)
close(conn)
}
changed_md5 <- function(object) {
tryCatch(
{
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
compared <- md5(object) != readLines(con = conn)
close(conn)
compared
},
error = function(e) TRUE
)
}
# give official names to ABs and MOs
clin_break <- clinical_breakpoints %>%
mutate(mo_name = mo_name(mo, language = NULL, keep_synonyms = TRUE, info = FALSE), .after = mo) %>%
mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
if (changed_md5(clin_break)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('clinical_breakpoints')} to {usethis::ui_value('data-raw/')}"))
write_md5(clin_break)
try(saveRDS(clin_break, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(clinical_breakpoints, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(clin_break, "data-raw/clinical_breakpoints.xpt"), silent = TRUE)
try(haven::write_sav(clin_break, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
try(haven::write_dta(clin_break, "data-raw/clinical_breakpoints.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(clin_break, "data-raw/clinical_breakpoints.xlsx"), silent = TRUE)
try(arrow::write_feather(clin_break, "data-raw/clinical_breakpoints.feather"), silent = TRUE)
try(arrow::write_parquet(clin_break, "data-raw/clinical_breakpoints.parquet"), silent = TRUE)
}
if (changed_md5(microorganisms)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('data-raw/')}"))
write_md5(microorganisms)
try(saveRDS(microorganisms, "data-raw/microorganisms.rds", version = 2, compress = "xz"), silent = TRUE)
max_50_snomed <- sapply(microorganisms$snomed, function(x) paste(x[seq_len(min(50, length(x), na.rm = TRUE))], collapse = " "))
mo <- microorganisms
mo$snomed <- max_50_snomed
mo <- dplyr::mutate_if(mo, ~ !is.numeric(.), as.character)
try(haven::write_xpt(mo, "data-raw/microorganisms.xpt"), silent = TRUE)
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
mo_all_snomed <- microorganisms %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
try(write.table(mo_all_snomed, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(openxlsx2::write_xlsx(mo_all_snomed, "data-raw/microorganisms.xlsx"), silent = TRUE)
try(arrow::write_feather(microorganisms, "data-raw/microorganisms.feather"), silent = TRUE)
try(arrow::write_parquet(microorganisms, "data-raw/microorganisms.parquet"), silent = TRUE)
}
if (changed_md5(microorganisms.codes)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.codes')} to {usethis::ui_value('data-raw/')}"))
write_md5(microorganisms.codes)
try(saveRDS(microorganisms.codes, "data-raw/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.codes, "data-raw/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(microorganisms.codes, "data-raw/microorganisms.codes.xpt"), silent = TRUE)
try(haven::write_sav(microorganisms.codes, "data-raw/microorganisms.codes.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.codes, "data-raw/microorganisms.codes.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/microorganisms.codes.xlsx"), silent = TRUE)
try(arrow::write_feather(microorganisms.codes, "data-raw/microorganisms.codes.feather"), silent = TRUE)
try(arrow::write_parquet(microorganisms.codes, "data-raw/microorganisms.codes.parquet"), silent = TRUE)
}
if (changed_md5(microorganisms.groups)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.groups')} to {usethis::ui_value('data-raw/')}"))
write_md5(microorganisms.groups)
try(saveRDS(microorganisms.groups, "data-raw/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(microorganisms.groups, "data-raw/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(microorganisms.groups, "data-raw/microorganisms.groups.xpt"), silent = TRUE)
try(haven::write_sav(microorganisms.groups, "data-raw/microorganisms.groups.sav"), silent = TRUE)
try(haven::write_dta(microorganisms.groups, "data-raw/microorganisms.groups.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/microorganisms.groups.xlsx"), silent = TRUE)
try(arrow::write_feather(microorganisms.groups, "data-raw/microorganisms.groups.feather"), silent = TRUE)
try(arrow::write_parquet(microorganisms.groups, "data-raw/microorganisms.groups.parquet"), silent = TRUE)
}
ab <- dplyr::mutate_if(antibiotics, ~ !is.numeric(.), as.character)
if (changed_md5(ab)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
write_md5(ab)
try(saveRDS(antibiotics, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
try(haven::write_xpt(ab, "data-raw/antibiotics.xpt"), silent = TRUE)
try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
ab_lists <- antibiotics %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
try(write.table(ab_lists, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(openxlsx2::write_xlsx(ab_lists, "data-raw/antibiotics.xlsx"), silent = TRUE)
try(arrow::write_feather(antibiotics, "data-raw/antibiotics.feather"), silent = TRUE)
try(arrow::write_parquet(antibiotics, "data-raw/antibiotics.parquet"), silent = TRUE)
}
av <- dplyr::mutate_if(antivirals, ~ !is.numeric(.), as.character)
if (changed_md5(av)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
write_md5(av)
try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
try(haven::write_xpt(av, "data-raw/antivirals.xpt"), silent = TRUE)
try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
av_lists <- antivirals %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
try(write.table(av_lists, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(openxlsx2::write_xlsx(av_lists, "data-raw/antivirals.xlsx"), silent = TRUE)
try(arrow::write_feather(antivirals, "data-raw/antivirals.feather"), silent = TRUE)
try(arrow::write_parquet(antivirals, "data-raw/antivirals.parquet"), silent = TRUE)
}
# give official names to ABs and MOs
intrinsicR <- data.frame(
microorganism = mo_name(intrinsic_resistant$mo, language = NULL, keep_synonyms = TRUE, info = FALSE),
antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
stringsAsFactors = FALSE
)
if (changed_md5(intrinsicR)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('data-raw/')}"))
write_md5(intrinsicR)
try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(intrinsicR, "data-raw/intrinsic_resistant.xpt"), silent = TRUE)
try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
try(arrow::write_feather(intrinsicR, "data-raw/intrinsic_resistant.feather"), silent = TRUE)
try(arrow::write_parquet(intrinsicR, "data-raw/intrinsic_resistant.parquet"), silent = TRUE)
}
if (changed_md5(dosage)) {
usethis::ui_info(paste0("Saving {usethis::ui_value('dosage')} to {usethis::ui_value('data-raw/')}"))
write_md5(dosage)
try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_xpt(dosage, "data-raw/dosage.xpt"), silent = TRUE)
try(haven::write_sav(dosage, "data-raw/dosage.sav"), silent = TRUE)
try(haven::write_dta(dosage, "data-raw/dosage.dta"), silent = TRUE)
try(openxlsx2::write_xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)
try(arrow::write_feather(dosage, "data-raw/dosage.feather"), silent = TRUE)
try(arrow::write_parquet(dosage, "data-raw/dosage.parquet"), silent = TRUE)
}
suppressMessages(reset_AMR_locale())
devtools::load_all(quiet = TRUE)
suppressMessages(set_AMR_locale("English"))
# Update URLs -------------------------------------------------------------
usethis::ui_info("Checking URLs for redirects")
invisible(capture.output(urlchecker::url_update()))
# Document pkg ------------------------------------------------------------
usethis::ui_info("Documenting package")
suppressMessages(devtools::document(quiet = TRUE))
# Finished ----------------------------------------------------------------
usethis::ui_done("All done")
suppressMessages(reset_AMR_locale())