mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 08:06:12 +01:00
fix txt export of microorganisms
This commit is contained in:
parent
6ad7857d39
commit
afdc48db1e
@ -1,5 +1,5 @@
|
||||
Package: AMR
|
||||
Version: 1.8.2.9034
|
||||
Version: 1.8.2.9035
|
||||
Date: 2022-10-29
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
|
2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
|
||||
# AMR 1.8.2.9034
|
||||
# AMR 1.8.2.9035
|
||||
|
||||
This version will eventually become v2.0! We're happy to reach a new major milestone soon!
|
||||
|
||||
|
15
R/rsi.R
15
R/rsi.R
@ -622,7 +622,7 @@ as.rsi.data.frame <- function(x,
|
||||
# only print message if class not already set
|
||||
message_("=> Assigning class 'rsi' to already clean column '", font_bold(ab), "' (",
|
||||
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
|
||||
ab_name(ab_coerced, tolower = TRUE), ")... ",
|
||||
ab_name(ab_coerced, tolower = TRUE, language = NULL), ")... ",
|
||||
appendLF = FALSE,
|
||||
as_note = FALSE
|
||||
)
|
||||
@ -877,7 +877,8 @@ as_rsi_method <- function(method_short,
|
||||
warning_("No ", method_param, " breakpoints available for ",
|
||||
font_italic(suppressMessages(suppressWarnings(mo_shortname(mo[i], language = NULL, keep_synonyms = FALSE)))),
|
||||
paste0(" / "),
|
||||
suppressMessages(suppressWarnings(ab_name(ab, language = NULL, tolower = TRUE))))
|
||||
suppressMessages(suppressWarnings(ab_name(ab_param, language = NULL, tolower = TRUE))),
|
||||
" (", ab_param, ")")
|
||||
rise_warning <- TRUE
|
||||
next
|
||||
}
|
||||
@ -899,18 +900,18 @@ as_rsi_method <- function(method_short,
|
||||
# uti not set as TRUE, but there are only a UTI breakpoints available, so throw warning
|
||||
warning_("in `as.rsi()`: interpretation of ", font_bold(ab_name(ab_param, tolower = TRUE)), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms, thus assuming `uti = TRUE`. See ?as.rsi.")
|
||||
rise_warning <- TRUE
|
||||
} else if (nrow(records_same_mo) > 1 && length(unique(records_same_mo$site)) > 1 && uti[i] == FALSE && all(c(TRUE, FALSE) %in% records_same_mo$uti, na.rm = TRUE) && message_not_thrown_before("as.rsi", "siteUTI", records_same_mo$mo[1], records_same_mo$ab[1])) {
|
||||
} else if (nrow(records_same_mo) > 1 && length(unique(records_same_mo$site)) > 1 && is.na(uti[i]) && all(c(TRUE, FALSE) %in% records_same_mo$uti, na.rm = TRUE) && message_not_thrown_before("as.rsi", "siteUTI", records_same_mo$mo[1], ab_param)) {
|
||||
# uti not set and both UTI and non-UTI breakpoints available, so throw warning
|
||||
warning_("in `as.rsi()`: breakpoints for UTI ", font_underline("and"), " non-UTI available for ",
|
||||
font_italic(suppressMessages(suppressWarnings(mo_shortname(records_same_mo$mo[1], language = NULL, keep_synonyms = FALSE)))),
|
||||
paste0(" / "),
|
||||
suppressMessages(suppressWarnings(ab_name(records_same_mo$ab[1], language = NULL, tolower = TRUE))),
|
||||
paste0(" - assuming non-UTI. Use argument `uti` to set which isolates are from urine. See ?as.rsi. '"),
|
||||
" / ",
|
||||
suppressMessages(suppressWarnings(ab_name(ab_param, language = NULL, tolower = TRUE))),
|
||||
" (", ab_param, ") - assuming non-UTI. Use argument `uti` to set which isolates are from urine. See ?as.rsi.",
|
||||
call = FALSE)
|
||||
get_record <- get_record %pm>%
|
||||
pm_filter(uti == FALSE)
|
||||
rise_warning <- TRUE
|
||||
} else if (nrow(records_same_mo) > 1 && length(unique(records_same_mo$site)) > 1 && all(records_same_mo$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "site", records_same_mo$mo[1], records_same_mo$ab[1])) {
|
||||
} else if (nrow(records_same_mo) > 1 && length(unique(records_same_mo$site)) > 1 && all(records_same_mo$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "siteOther", records_same_mo$mo[1], ab_param)) {
|
||||
# breakpoints for multiple body sites available, so throw warning
|
||||
site <- get_record[1L, "site", drop = FALSE]
|
||||
if (is.na(site)) {
|
||||
|
@ -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)
|
||||
}
|
||||
|
File diff suppressed because one or more lines are too long
@ -125,6 +125,8 @@ This data set is in R available as `microorganisms`, after you load the `AMR` pa
|
||||
|
||||
**NOTE: The exported files for Excel, SAS, SPSS and Stata contain only the first 50 SNOMED codes per record, as their file size would otherwise exceed 100 MB; the file size limit of GitHub.** Advice? Use R instead.
|
||||
|
||||
The tab-separated text file contains all SNOMED codes as comma separated values.
|
||||
|
||||
### Source
|
||||
|
||||
This data set contains the full microbial taxonomy of `r AMR:::nr2char(length(unique(AMR::microorganisms$kingdom[!AMR::microorganisms$kingdom %like% "unknown"])))` kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF):
|
||||
|
Loading…
Reference in New Issue
Block a user