AMR/data-raw/_pre_commit_hook.R

492 lines
21 KiB
R
Raw Normal View History

# ==================================================================== #
# TITLE #
2022-10-05 09:12:22 +02:00
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
2022-10-05 09:12:22 +02:00
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
2022-12-27 15:16:15 +01:00
# 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. #
2020-10-08 11:16:03 +02:00
# #
# 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:
2022-08-28 10:31:50 +02:00
# source("data-raw/_pre_commit_hook.R")
2020-09-24 00:30:11 +02:00
library(dplyr, warn.conflicts = FALSE)
devtools::load_all(quiet = TRUE)
2022-08-28 22:38:08 +02:00
suppressMessages(set_AMR_locale("English"))
2022-08-19 12:33:14 +02:00
old_globalenv <- ls(envir = globalenv())
2021-04-07 08:37:42 +02:00
# Save internal data to R/sysdata.rda -------------------------------------
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
2022-08-28 10:31:50 +02:00
EUCAST_RULES_DF <- utils::read.delim(
file = "data-raw/eucast_rules.tsv",
2022-11-14 15:20:39 +01:00
skip = 9,
2022-08-28 10:31:50 +02:00
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
strip.white = TRUE,
na = c(NA, "", NULL)
) %>%
2020-09-24 00:30:11 +02:00
# take the order of the reference.rule_group column in the original data file
2022-08-28 10:31:50 +02:00
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
) %>%
2022-08-26 22:25:15 +02:00
mutate(reference.rule_group = as.character(reference.rule_group)) %>%
2020-09-24 00:30:11 +02:00
select(-sorting_rule)
2022-08-28 10:31:50 +02:00
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 = ""
)
2022-08-26 22:25:15 +02:00
2022-08-28 10:31:50 +02:00
LANGUAGES_SUPPORTED_NAMES <- c(
list(en = list(exonym = "English", endonym = "English")),
lapply(
TRANSLATIONS[, which(nchar(colnames(TRANSLATIONS)) == 2), drop = FALSE],
function(x) list(exonym = x[1], endonym = x[2])
)
)
2022-08-26 22:25:15 +02:00
LANGUAGES_SUPPORTED <- names(LANGUAGES_SUPPORTED_NAMES)
# vectors of CoNS and CoPS, improves speed in as.mo()
2021-05-30 22:14:38 +02:00
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$genus == "Staphylococcus"), , drop = FALSE]
if (type == "CoNS") {
2023-01-23 15:01:21 +01:00
MO_staph[
which(MO_staph$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"
) |
# 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
2022-08-28 10:31:50 +02:00
]
2021-05-30 22:14:38 +02:00
} else if (type == "CoPS") {
2023-01-23 15:01:21 +01:00
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$subspecies == "coagulans")),
"mo",
drop = TRUE
2022-08-28 10:31:50 +02:00
]
2021-05-30 22:14:38 +02:00
}
}
MO_CONS <- create_species_cons_cops("CoNS")
MO_COPS <- create_species_cons_cops("CoPS")
MO_STREP_ABCG <- AMR::microorganisms$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"
2022-10-05 09:12:22 +02:00
))]
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(_|$))")]
2022-08-28 10:31:50 +02:00
MO_PREVALENT_GENERA <- c(
2022-12-19 15:32:41 +01:00
"Absidia", "Acanthamoeba", "Acremonium", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus",
"Anisakis", "Anopheles", "Apophysomyces", "Aspergillus", "Aureobasidium", "Basidiobolus", "Beauveria",
"Blastocystis", "Blastomyces", "Candida", "Capillaria", "Chaetomium", "Chrysonilia", "Cladophialophora",
"Cladosporium", "Conidiobolus", "Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex",
"Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Echinostoma", "Entamoeba", "Enterobius",
"Exophiala", "Exserohilum", "Fasciola", "Fonsecaea", "Fusarium", "Giardia", "Haloarcula", "Halobacterium",
"Halococcus", "Hendersonula", "Heterophyes", "Histomonas", "Histoplasma", "Hymenolepis", "Hypomyces",
"Hysterothylacium", "Leishmania", "Malassezia", "Malbranchea", "Metagonimus", "Meyerozyma", "Microsporidium",
"Microsporum", "Mortierella", "Mucor", "Mycocentrospora", "Necator", "Nectria", "Ochroconis", "Oesophagostomum",
"Oidiodendron", "Opisthorchis", "Pediculus", "Phlebotomus", "Phoma", "Pichia", "Piedraia", "Pithomyces",
"Pityrosporum", "Pneumocystis", "Pseudallescheria", "Pseudoterranova", "Pulex", "Rhizomucor", "Rhizopus",
"Rhodotorula", "Saccharomyces", "Sarcoptes", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra",
"Sporobolomyces", "Stachybotrys", "Strongyloides", "Syngamus", "Taenia", "Toxocara", "Trichinella", "Trichobilharzia",
"Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium",
"Trombicula", "Trypanosoma", "Tunga", "Wuchereria"
2022-08-28 10:31:50 +02:00
)
2021-04-07 08:37:42 +02:00
# antibiotic groups
# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
globalenv_before_ab <- c(ls(envir = globalenv()), "globalenv_before_ab")
2022-08-28 10:31:50 +02:00
AB_AMINOGLYCOSIDES <- antibiotics %>%
filter(group %like% "aminoglycoside") %>%
pull(ab)
AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX"))
2022-10-14 13:02:50 +02:00
AB_ANTIFUNGALS <- AMR_env$AB_lookup %>%
2022-08-28 10:31:50 +02:00
filter(group %like% "antifungal") %>%
pull(ab)
2022-10-14 13:02:50 +02:00
AB_ANTIMYCOBACTERIALS <- AMR_env$AB_lookup %>%
2022-08-28 10:31:50 +02:00
filter(group %like% "antimycobacterial") %>%
pull(ab)
AB_CARBAPENEMS <- antibiotics %>%
filter(group %like% "carbapenem") %>%
pull(ab)
AB_CEPHALOSPORINS <- antibiotics %>%
filter(group %like% "cephalosporin") %>%
pull(ab)
AB_CEPHALOSPORINS_1ST <- antibiotics %>%
filter(group %like% "cephalosporin.*1") %>%
pull(ab)
AB_CEPHALOSPORINS_2ND <- antibiotics %>%
filter(group %like% "cephalosporin.*2") %>%
pull(ab)
AB_CEPHALOSPORINS_3RD <- antibiotics %>%
filter(group %like% "cephalosporin.*3") %>%
pull(ab)
AB_CEPHALOSPORINS_4TH <- antibiotics %>%
filter(group %like% "cephalosporin.*4") %>%
pull(ab)
AB_CEPHALOSPORINS_5TH <- antibiotics %>%
filter(group %like% "cephalosporin.*5") %>%
pull(ab)
AB_CEPHALOSPORINS_EXCEPT_CAZ <- AB_CEPHALOSPORINS[AB_CEPHALOSPORINS != "CAZ"]
2022-08-28 10:31:50 +02:00
AB_FLUOROQUINOLONES <- antibiotics %>%
filter(atc_group2 %like% "fluoroquinolone" | (group %like% "quinolone" & is.na(atc_group2))) %>%
pull(ab)
AB_GLYCOPEPTIDES <- antibiotics %>%
filter(group %like% "glycopeptide") %>%
pull(ab)
AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
AB_GLYCOPEPTIDES_EXCEPT_LIPO <- AB_GLYCOPEPTIDES[!AB_GLYCOPEPTIDES %in% AB_LIPOGLYCOPEPTIDES]
2022-08-28 10:31:50 +02:00
AB_LINCOSAMIDES <- antibiotics %>%
filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2))) %>%
pull(ab)
AB_MACROLIDES <- antibiotics %>%
filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2))) %>%
pull(ab)
AB_OXAZOLIDINONES <- antibiotics %>%
filter(group %like% "oxazolidinone") %>%
pull(ab)
AB_PENICILLINS <- antibiotics %>%
filter(group %like% "penicillin") %>%
pull(ab)
AB_POLYMYXINS <- antibiotics %>%
filter(group %like% "polymyxin") %>%
pull(ab)
AB_QUINOLONES <- antibiotics %>%
filter(group %like% "quinolone") %>%
pull(ab)
AB_STREPTOGRAMINS <- antibiotics %>%
filter(atc_group2 %like% "streptogramin") %>%
pull(ab)
AB_TETRACYCLINES <- antibiotics %>%
filter(group %like% "tetracycline") %>%
pull(ab)
AB_TETRACYCLINES_EXCEPT_TGC <- AB_TETRACYCLINES[AB_TETRACYCLINES != "TGC"]
2022-08-28 10:31:50 +02:00
AB_TRIMETHOPRIMS <- antibiotics %>%
filter(group %like% "trimethoprim") %>%
pull(ab)
AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
AB_BETALACTAMS <- c(AB_PENICILLINS, AB_CEPHALOSPORINS, AB_CARBAPENEMS)
# this will be used for documentation:
2021-04-07 08:37:42 +02:00
DEFINED_AB_GROUPS <- ls(envir = globalenv())
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
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(
2023-01-23 15:01:21 +01:00
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
2022-08-28 10:31:50 +02:00
)),
function(x) {
x <- generalise_antibiotic_name(unname(unlist(x)))
x[x != ""]
}
))
new_df[, colnames(new_df)[colnames(new_df) %like% "^generalised"]]
2022-03-14 16:36:10 +01:00
}
AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
AV_LOOKUP <- create_AB_AV_lookup(AMR::antivirals)
2021-04-07 08:37:42 +02:00
2019-06-01 20:40:49 +02:00
# Export to package as internal data ----
2022-10-05 09:12:22 +02:00
usethis::ui_info(paste0("Updating internal package data"))
2022-08-27 20:49:37 +02:00
suppressMessages(usethis::use_data(EUCAST_RULES_DF,
2022-08-28 10:31:50 +02:00
TRANSLATIONS,
LANGUAGES_SUPPORTED_NAMES,
LANGUAGES_SUPPORTED,
MO_CONS,
MO_COPS,
MO_STREP_ABCG,
MO_LANCEFIELD,
2022-08-28 10:31:50 +02:00
MO_PREVALENT_GENERA,
AB_LOOKUP,
AV_LOOKUP,
2022-08-28 10:31:50 +02:00
AB_AMINOGLYCOSIDES,
AB_AMINOPENICILLINS,
AB_ANTIFUNGALS,
AB_ANTIMYCOBACTERIALS,
AB_CARBAPENEMS,
AB_CEPHALOSPORINS,
AB_CEPHALOSPORINS_1ST,
AB_CEPHALOSPORINS_2ND,
AB_CEPHALOSPORINS_3RD,
AB_CEPHALOSPORINS_4TH,
AB_CEPHALOSPORINS_5TH,
AB_CEPHALOSPORINS_EXCEPT_CAZ,
AB_FLUOROQUINOLONES,
AB_LIPOGLYCOPEPTIDES,
AB_GLYCOPEPTIDES,
AB_GLYCOPEPTIDES_EXCEPT_LIPO,
AB_LINCOSAMIDES,
AB_MACROLIDES,
AB_OXAZOLIDINONES,
AB_PENICILLINS,
AB_POLYMYXINS,
AB_QUINOLONES,
AB_STREPTOGRAMINS,
AB_TETRACYCLINES,
AB_TETRACYCLINES_EXCEPT_TGC,
AB_TRIMETHOPRIMS,
AB_UREIDOPENICILLINS,
AB_BETALACTAMS,
DEFINED_AB_GROUPS,
internal = TRUE,
overwrite = TRUE,
version = 2,
compress = "xz"
))
2019-06-01 20:40:49 +02:00
# Export data sets to the repository in different formats -----------------
2022-08-26 22:25:15 +02:00
for (pkg in c("haven", "openxlsx", "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"
}
2020-09-14 12:21:23 +02:00
write_md5 <- function(object) {
2020-09-24 00:30:11 +02:00
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
2022-08-26 22:25:15 +02:00
writeLines(md5(object), conn)
2020-09-24 00:30:11 +02:00
close(conn)
2020-09-14 12:21:23 +02:00
}
changed_md5 <- function(object) {
2022-08-28 10:31:50 +02:00
tryCatch(
{
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
compared <- md5(object) != readLines(con = conn)
close(conn)
compared
},
error = function(e) TRUE
)
2020-09-14 12:21:23 +02:00
}
2020-02-14 19:54:13 +01:00
# give official names to ABs and MOs
2023-01-21 23:47:20 +01:00
clin_break <- clinical_breakpoints %>%
2022-10-05 09:12:22 +02:00
mutate(mo_name = mo_name(mo, language = NULL, keep_synonyms = TRUE, info = FALSE), .after = mo) %>%
2022-05-11 10:26:58 +02:00
mutate(ab_name = ab_name(ab, language = NULL), .after = ab)
2023-01-21 23:47:20 +01:00
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(clin_break, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
try(haven::write_sas(clin_break, "data-raw/clinical_breakpoints.sas"), 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(openxlsx::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)
2020-09-14 12:21:23 +02:00
}
2022-08-26 22:25:15 +02:00
if (changed_md5(microorganisms)) {
2022-08-27 20:49:37 +02:00
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('data-raw/')}"))
2022-08-26 22:25:15 +02:00
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
2022-08-28 10:31:50 +02:00
mo <- dplyr::mutate_if(mo, ~ !is.numeric(.), as.character)
2022-08-26 22:25:15 +02:00
try(haven::write_sas(mo, "data-raw/microorganisms.sas"), silent = TRUE)
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
2022-10-29 16:08:18 +02:00
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(openxlsx::write.xlsx(mo_all_snomed, "data-raw/microorganisms.xlsx"), silent = TRUE)
2022-08-26 22:25:15 +02:00
try(arrow::write_feather(microorganisms, "data-raw/microorganisms.feather"), silent = TRUE)
try(arrow::write_parquet(microorganisms, "data-raw/microorganisms.parquet"), silent = TRUE)
2020-09-14 12:21:23 +02:00
}
2022-08-28 10:31:50 +02:00
ab <- dplyr::mutate_if(antibiotics, ~ !is.numeric(.), as.character)
2020-09-14 12:21:23 +02:00
if (changed_md5(ab)) {
2022-08-27 20:49:37 +02:00
usethis::ui_info(paste0("Saving {usethis::ui_value('antibiotics')} to {usethis::ui_value('data-raw/')}"))
2020-09-14 12:21:23 +02:00
write_md5(ab)
2022-08-26 22:25:15 +02:00
try(saveRDS(antibiotics, "data-raw/antibiotics.rds", version = 2, compress = "xz"), silent = TRUE)
2020-09-14 12:21:23 +02:00
try(haven::write_sas(ab, "data-raw/antibiotics.sas"), 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(openxlsx::write.xlsx(ab_lists, "data-raw/antibiotics.xlsx"), silent = TRUE)
2022-08-26 22:25:15 +02:00
try(arrow::write_feather(antibiotics, "data-raw/antibiotics.feather"), silent = TRUE)
try(arrow::write_parquet(antibiotics, "data-raw/antibiotics.parquet"), silent = TRUE)
2020-09-14 12:21:23 +02:00
}
2022-08-28 10:31:50 +02:00
av <- dplyr::mutate_if(antivirals, ~ !is.numeric(.), as.character)
2020-09-14 12:21:23 +02:00
if (changed_md5(av)) {
2022-08-27 20:49:37 +02:00
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
2020-09-14 12:21:23 +02:00
write_md5(av)
2022-08-26 22:25:15 +02:00
try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
2020-09-14 12:21:23 +02:00
try(haven::write_sas(av, "data-raw/antivirals.sas"), 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(openxlsx::write.xlsx(av_lists, "data-raw/antivirals.xlsx"), silent = TRUE)
2022-08-26 22:25:15 +02:00
try(arrow::write_feather(antivirals, "data-raw/antivirals.feather"), silent = TRUE)
try(arrow::write_parquet(antivirals, "data-raw/antivirals.parquet"), silent = TRUE)
2020-09-14 12:21:23 +02:00
}
2021-12-14 21:47:14 +01:00
# give official names to ABs and MOs
2022-08-28 10:31:50 +02:00
intrinsicR <- data.frame(
2022-10-05 09:12:22 +02:00
microorganism = mo_name(intrinsic_resistant$mo, language = NULL, keep_synonyms = TRUE, info = FALSE),
2022-08-28 10:31:50 +02:00
antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
stringsAsFactors = FALSE
)
2021-12-14 21:47:14 +01:00
if (changed_md5(intrinsicR)) {
2022-08-27 20:49:37 +02:00
usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('data-raw/')}"))
2021-12-14 21:47:14 +01:00
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_sas(intrinsicR, "data-raw/intrinsic_resistant.sas"), 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(openxlsx::write.xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
2022-08-26 22:25:15 +02:00
try(arrow::write_feather(intrinsicR, "data-raw/intrinsic_resistant.feather"), silent = TRUE)
try(arrow::write_parquet(intrinsicR, "data-raw/intrinsic_resistant.parquet"), silent = TRUE)
2020-09-14 12:21:23 +02:00
}
if (changed_md5(dosage)) {
2022-08-27 20:49:37 +02:00
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_sas(dosage, "data-raw/dosage.sas"), 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(openxlsx::write.xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)
2022-08-26 22:25:15 +02:00
try(arrow::write_feather(dosage, "data-raw/dosage.feather"), silent = TRUE)
try(arrow::write_parquet(dosage, "data-raw/dosage.parquet"), silent = TRUE)
}
2022-08-27 20:49:37 +02:00
suppressMessages(reset_AMR_locale())
2022-08-19 12:33:14 +02:00
# remove leftovers from global env
current_globalenv <- ls(envir = globalenv())
rm(list = current_globalenv[!current_globalenv %in% old_globalenv])
rm(current_globalenv)
2022-08-26 22:25:15 +02:00
devtools::load_all(quiet = TRUE)
2022-08-28 22:38:08 +02:00
suppressMessages(set_AMR_locale("English"))
2022-08-28 10:31:50 +02:00
2022-08-28 19:17:12 +02:00
# Update URLs -------------------------------------------------------------
usethis::ui_info("Checking URLs for redirects")
invisible(capture.output(urlchecker::url_update()))
2022-08-28 10:31:50 +02:00
# Document pkg ------------------------------------------------------------
usethis::ui_info("Documenting package")
suppressMessages(devtools::document(quiet = TRUE))
# Style pkg ---------------------------------------------------------------
2023-01-05 14:46:44 +01:00
if (!"styler" %in% rownames(utils::installed.packages())) {
message("Package 'styler' not installed!")
} else if (interactive()) {
2023-01-23 15:01:21 +01:00
# only when sourcing this file ourselves
2023-01-05 14:46:44 +01:00
# usethis::ui_info("Styling package")
# styler::style_pkg(
# style = styler::tidyverse_style,
# filetype = c("R", "Rmd")
# )
}
2022-08-28 10:31:50 +02:00
# Finished ----------------------------------------------------------------
2022-08-28 11:17:53 +02:00
usethis::ui_done("All done")
2022-08-28 22:38:08 +02:00
suppressMessages(reset_AMR_locale())