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synced 2025-07-12 19:41:58 +02:00
(v2.1.1.9228) repo cleaning
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@ -514,84 +514,84 @@ clin_break <- clinical_breakpoints %>%
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mutate(mo_name = microorganisms$fullname[match(mo, microorganisms$mo)], .after = mo) %>%
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mutate(ab_name = antimicrobials$name[match(ab, antimicrobials$ab)], .after = ab)
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if (changed_md5(clin_break)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('clinical_breakpoints')} to {usethis::ui_value('data-raw/')}"))
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usethis::ui_info(paste0("Saving {usethis::ui_value('clinical_breakpoints')} to {usethis::ui_value('data-raw/datasets/')}"))
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write_md5(clin_break)
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try(saveRDS(clin_break, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(clinical_breakpoints, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(clin_break, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
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try(haven::write_dta(clin_break, "data-raw/clinical_breakpoints.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(clin_break, "data-raw/clinical_breakpoints.xlsx"), silent = TRUE)
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try(arrow::write_feather(clin_break, "data-raw/clinical_breakpoints.feather"), silent = TRUE)
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try(arrow::write_parquet(clin_break, "data-raw/clinical_breakpoints.parquet"), silent = TRUE)
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try(saveRDS(clin_break, "data-raw/datasets/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(clinical_breakpoints, "data-raw/datasets/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(clin_break, "data-raw/datasets/clinical_breakpoints.sav"), silent = TRUE)
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try(haven::write_dta(clin_break, "data-raw/datasets/clinical_breakpoints.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(clin_break, "data-raw/datasets/clinical_breakpoints.xlsx"), silent = TRUE)
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try(arrow::write_feather(clin_break, "data-raw/datasets/clinical_breakpoints.feather"), silent = TRUE)
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try(arrow::write_parquet(clin_break, "data-raw/datasets/clinical_breakpoints.parquet"), silent = TRUE)
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}
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if (changed_md5(microorganisms)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('data-raw/')}"))
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('data-raw/datasets/')}"))
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write_md5(microorganisms)
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try(saveRDS(microorganisms, "data-raw/microorganisms.rds", version = 2, compress = "xz"), silent = TRUE)
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try(saveRDS(microorganisms, "data-raw/datasets/microorganisms.rds", version = 2, compress = "xz"), silent = TRUE)
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max_50_snomed <- sapply(microorganisms$snomed, function(x) paste(x[seq_len(min(50, length(x), na.rm = TRUE))], collapse = " "))
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mo <- microorganisms
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mo$snomed <- max_50_snomed
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mo <- dplyr::mutate_if(mo, ~ !is.numeric(.), as.character)
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try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
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try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
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try(haven::write_sav(mo, "data-raw/datasets/microorganisms.sav"), silent = TRUE)
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try(haven::write_dta(mo, "data-raw/datasets/microorganisms.dta"), silent = TRUE)
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mo_all_snomed <- microorganisms %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
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try(write.table(mo_all_snomed, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(openxlsx2::write_xlsx(mo_all_snomed, "data-raw/microorganisms.xlsx"), silent = TRUE)
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try(arrow::write_feather(microorganisms, "data-raw/microorganisms.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms, "data-raw/microorganisms.parquet"), silent = TRUE)
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try(write.table(mo_all_snomed, "data-raw/datasets/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(openxlsx2::write_xlsx(mo_all_snomed, "data-raw/datasets/microorganisms.xlsx"), silent = TRUE)
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try(arrow::write_feather(microorganisms, "data-raw/datasets/microorganisms.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms, "data-raw/datasets/microorganisms.parquet"), silent = TRUE)
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}
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if (changed_md5(microorganisms.codes)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.codes')} to {usethis::ui_value('data-raw/')}"))
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.codes')} to {usethis::ui_value('data-raw/datasets/')}"))
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write_md5(microorganisms.codes)
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try(saveRDS(microorganisms.codes, "data-raw/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.codes, "data-raw/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(microorganisms.codes, "data-raw/microorganisms.codes.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.codes, "data-raw/microorganisms.codes.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/microorganisms.codes.xlsx"), silent = TRUE)
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try(arrow::write_feather(microorganisms.codes, "data-raw/microorganisms.codes.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms.codes, "data-raw/microorganisms.codes.parquet"), silent = TRUE)
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try(saveRDS(microorganisms.codes, "data-raw/datasets/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.codes, "data-raw/datasets/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(microorganisms.codes, "data-raw/datasets/microorganisms.codes.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.codes, "data-raw/datasets/microorganisms.codes.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/datasets/microorganisms.codes.xlsx"), silent = TRUE)
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try(arrow::write_feather(microorganisms.codes, "data-raw/datasets/microorganisms.codes.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms.codes, "data-raw/datasets/microorganisms.codes.parquet"), silent = TRUE)
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}
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if (changed_md5(microorganisms.groups)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.groups')} to {usethis::ui_value('data-raw/')}"))
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usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.groups')} to {usethis::ui_value('data-raw/datasets/')}"))
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write_md5(microorganisms.groups)
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try(saveRDS(microorganisms.groups, "data-raw/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.groups, "data-raw/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(microorganisms.groups, "data-raw/microorganisms.groups.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.groups, "data-raw/microorganisms.groups.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/microorganisms.groups.xlsx"), silent = TRUE)
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try(arrow::write_feather(microorganisms.groups, "data-raw/microorganisms.groups.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms.groups, "data-raw/microorganisms.groups.parquet"), silent = TRUE)
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try(saveRDS(microorganisms.groups, "data-raw/datasets/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(microorganisms.groups, "data-raw/datasets/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(microorganisms.groups, "data-raw/datasets/microorganisms.groups.sav"), silent = TRUE)
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try(haven::write_dta(microorganisms.groups, "data-raw/datasets/microorganisms.groups.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/datasets/microorganisms.groups.xlsx"), silent = TRUE)
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try(arrow::write_feather(microorganisms.groups, "data-raw/datasets/microorganisms.groups.feather"), silent = TRUE)
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try(arrow::write_parquet(microorganisms.groups, "data-raw/datasets/microorganisms.groups.parquet"), silent = TRUE)
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}
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ab <- dplyr::mutate_if(antimicrobials, ~ !is.numeric(.), as.character)
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if (changed_md5(ab)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('antimicrobials')} to {usethis::ui_value('data-raw/')}"))
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usethis::ui_info(paste0("Saving {usethis::ui_value('antimicrobials')} to {usethis::ui_value('data-raw/datasets/')}"))
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write_md5(ab)
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try(saveRDS(antimicrobials, "data-raw/antimicrobials.rds", version = 2, compress = "xz"), silent = TRUE)
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try(haven::write_sav(ab, "data-raw/antimicrobials.sav"), silent = TRUE)
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try(haven::write_dta(ab, "data-raw/antimicrobials.dta"), silent = TRUE)
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try(saveRDS(antimicrobials, "data-raw/datasets/antimicrobials.rds", version = 2, compress = "xz"), silent = TRUE)
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try(haven::write_sav(ab, "data-raw/datasets/antimicrobials.sav"), silent = TRUE)
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try(haven::write_dta(ab, "data-raw/datasets/antimicrobials.dta"), silent = TRUE)
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ab_lists <- antimicrobials %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
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try(write.table(ab_lists, "data-raw/antimicrobials.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(openxlsx2::write_xlsx(ab_lists, "data-raw/antimicrobials.xlsx"), silent = TRUE)
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try(arrow::write_feather(antimicrobials, "data-raw/antimicrobials.feather"), silent = TRUE)
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try(arrow::write_parquet(antimicrobials, "data-raw/antimicrobials.parquet"), silent = TRUE)
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try(write.table(ab_lists, "data-raw/datasets/antimicrobials.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(openxlsx2::write_xlsx(ab_lists, "data-raw/datasets/antimicrobials.xlsx"), silent = TRUE)
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try(arrow::write_feather(antimicrobials, "data-raw/datasets/antimicrobials.feather"), silent = TRUE)
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try(arrow::write_parquet(antimicrobials, "data-raw/datasets/antimicrobials.parquet"), silent = TRUE)
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}
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av <- dplyr::mutate_if(antivirals, ~ !is.numeric(.), as.character)
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if (changed_md5(av)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/')}"))
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usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/datasets/')}"))
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write_md5(av)
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try(saveRDS(antivirals, "data-raw/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
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try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
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try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
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try(saveRDS(antivirals, "data-raw/datasets/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
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try(haven::write_sav(av, "data-raw/datasets/antivirals.sav"), silent = TRUE)
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try(haven::write_dta(av, "data-raw/datasets/antivirals.dta"), silent = TRUE)
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av_lists <- antivirals %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
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try(write.table(av_lists, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(openxlsx2::write_xlsx(av_lists, "data-raw/antivirals.xlsx"), silent = TRUE)
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try(arrow::write_feather(antivirals, "data-raw/antivirals.feather"), silent = TRUE)
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try(arrow::write_parquet(antivirals, "data-raw/antivirals.parquet"), silent = TRUE)
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try(write.table(av_lists, "data-raw/datasets/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(openxlsx2::write_xlsx(av_lists, "data-raw/datasets/antivirals.xlsx"), silent = TRUE)
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try(arrow::write_feather(antivirals, "data-raw/datasets/antivirals.feather"), silent = TRUE)
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try(arrow::write_parquet(antivirals, "data-raw/datasets/antivirals.parquet"), silent = TRUE)
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}
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# give official names to ABs and MOs
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@ -601,27 +601,27 @@ intrinsicR <- data.frame(
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stringsAsFactors = FALSE
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)
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if (changed_md5(intrinsicR)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('data-raw/')}"))
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usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('data-raw/datasets/')}"))
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write_md5(intrinsicR)
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try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
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try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
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try(arrow::write_feather(intrinsicR, "data-raw/intrinsic_resistant.feather"), silent = TRUE)
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try(arrow::write_parquet(intrinsicR, "data-raw/intrinsic_resistant.parquet"), silent = TRUE)
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try(saveRDS(intrinsicR, "data-raw/datasets/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(intrinsicR, "data-raw/datasets/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(intrinsicR, "data-raw/datasets/intrinsic_resistant.sav"), silent = TRUE)
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try(haven::write_dta(intrinsicR, "data-raw/datasets/intrinsic_resistant.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(intrinsicR, "data-raw/datasets/intrinsic_resistant.xlsx"), silent = TRUE)
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try(arrow::write_feather(intrinsicR, "data-raw/datasets/intrinsic_resistant.feather"), silent = TRUE)
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try(arrow::write_parquet(intrinsicR, "data-raw/datasets/intrinsic_resistant.parquet"), silent = TRUE)
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}
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if (changed_md5(dosage)) {
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usethis::ui_info(paste0("Saving {usethis::ui_value('dosage')} to {usethis::ui_value('data-raw/')}"))
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usethis::ui_info(paste0("Saving {usethis::ui_value('dosage')} to {usethis::ui_value('data-raw/datasets/')}"))
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write_md5(dosage)
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try(saveRDS(dosage, "data-raw/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(dosage, "data-raw/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(dosage, "data-raw/dosage.sav"), silent = TRUE)
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try(haven::write_dta(dosage, "data-raw/dosage.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)
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try(arrow::write_feather(dosage, "data-raw/dosage.feather"), silent = TRUE)
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try(arrow::write_parquet(dosage, "data-raw/dosage.parquet"), silent = TRUE)
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try(saveRDS(dosage, "data-raw/datasets/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
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try(write.table(dosage, "data-raw/datasets/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
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try(haven::write_sav(dosage, "data-raw/datasets/dosage.sav"), silent = TRUE)
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try(haven::write_dta(dosage, "data-raw/datasets/dosage.dta"), silent = TRUE)
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try(openxlsx2::write_xlsx(dosage, "data-raw/datasets/dosage.xlsx"), silent = TRUE)
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try(arrow::write_feather(dosage, "data-raw/datasets/dosage.feather"), silent = TRUE)
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try(arrow::write_parquet(dosage, "data-raw/datasets/dosage.parquet"), silent = TRUE)
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}
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suppressMessages(reset_AMR_locale())
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