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fix txt export of microorganisms

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-29 16:08:18 +02:00
parent 6ad7857d39
commit afdc48db1e
6 changed files with 48898 additions and 12 deletions
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3
data-raw/_pre_commit_hook.R
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@ -391,7 +391,6 @@ 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)
try(write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), 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
@ -400,6 +399,8 @@ if (changed_md5(microorganisms)) {
try(haven::write_sav(mo, "data-raw/microorganisms.sav"), silent = TRUE)
try(haven::write_dta(mo, "data-raw/microorganisms.dta"), silent = TRUE)
try(openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx"), 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(arrow::write_feather(microorganisms, "data-raw/microorganisms.feather"), silent = TRUE)
try(arrow::write_parquet(microorganisms, "data-raw/microorganisms.parquet"), silent = TRUE)
}

48884
data-raw/microorganisms.txt
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