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(v1.7.1.9000) ab_class update, unit tests

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dr. M.S. (Matthijs) Berends
2021-06-04 21:07:55 +02:00
parent 7e70403efb
commit 1908e7cc7a
34 changed files with 365 additions and 1368 deletions
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data-raw/AMR_latest.tar.gz
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16
data-raw/_internals.R
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@ -34,7 +34,7 @@ old_globalenv <- ls(envir = globalenv())
# Save internal data to R/sysdata.rda -------------------------------------
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
EUCAST_RULES_DF <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
skip = 10,
sep = "\t",
stringsAsFactors = FALSE,
@ -54,7 +54,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
select(-sorting_rule)
# Translations
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
TRANSLATIONS <- utils::read.delim(file = "data-raw/translations.tsv",
sep = "\t",
stringsAsFactors = FALSE,
header = TRUE,
@ -68,7 +68,7 @@ translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
quote = "")
# for checking input in `language` argument in e.g. mo_*() and ab_*() functions
LANGUAGES_SUPPORTED <- sort(c("en", colnames(translations_file)[nchar(colnames(translations_file)) == 2]))
LANGUAGES_SUPPORTED <- sort(c("en", colnames(TRANSLATIONS)[nchar(colnames(TRANSLATIONS)) == 2]))
# vectors of CoNS and CoPS, improves speed in as.mo()
create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
@ -121,6 +121,8 @@ CEPHALOSPORINS <- antibiotics %>% filter(group %like% "cephalosporin") %>% pull(
CEPHALOSPORINS_1ST <- antibiotics %>% filter(group %like% "cephalosporin.*1") %>% pull(ab)
CEPHALOSPORINS_2ND <- antibiotics %>% filter(group %like% "cephalosporin.*2") %>% pull(ab)
CEPHALOSPORINS_3RD <- antibiotics %>% filter(group %like% "cephalosporin.*3") %>% pull(ab)
CEPHALOSPORINS_4TH <- antibiotics %>% filter(group %like% "cephalosporin.*4") %>% pull(ab)
CEPHALOSPORINS_5TH <- antibiotics %>% filter(group %like% "cephalosporin.*5") %>% pull(ab)
CEPHALOSPORINS_EXCEPT_CAZ <- CEPHALOSPORINS[CEPHALOSPORINS != "CAZ"]
FLUOROQUINOLONES <- antibiotics %>% filter(atc_group2 %like% "fluoroquinolone") %>% pull(ab)
LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
@ -131,6 +133,7 @@ MACROLIDES <- antibiotics %>% filter(atc_group2 %like% "macrolide") %>% pull(ab)
OXAZOLIDINONES <- antibiotics %>% filter(group %like% "oxazolidinone") %>% pull(ab)
PENICILLINS <- antibiotics %>% filter(group %like% "penicillin") %>% pull(ab)
POLYMYXINS <- antibiotics %>% filter(group %like% "polymyxin") %>% pull(ab)
QUINOLONES <- antibiotics %>% filter(group %like% "quinolone") %>% pull(ab)
STREPTOGRAMINS <- antibiotics %>% filter(atc_group2 %like% "streptogramin") %>% pull(ab)
TETRACYCLINES <- antibiotics %>% filter(atc_group2 %like% "tetracycline") %>% pull(ab)
TETRACYCLINES_EXCEPT_TGC <- TETRACYCLINES[TETRACYCLINES != "TGC"]
@ -141,8 +144,8 @@ DEFINED_AB_GROUPS <- ls(envir = globalenv())
DEFINED_AB_GROUPS <- DEFINED_AB_GROUPS[!DEFINED_AB_GROUPS %in% globalenv_before_ab]
# Export to package as internal data ----
usethis::use_data(eucast_rules_file,
translations_file,
usethis::use_data(EUCAST_RULES_DF,
TRANSLATIONS,
LANGUAGES_SUPPORTED,
MO_CONS,
MO_COPS,
@ -153,6 +156,8 @@ usethis::use_data(eucast_rules_file,
CEPHALOSPORINS_1ST,
CEPHALOSPORINS_2ND,
CEPHALOSPORINS_3RD,
CEPHALOSPORINS_4TH,
CEPHALOSPORINS_5TH,
CEPHALOSPORINS_EXCEPT_CAZ,
FLUOROQUINOLONES,
LIPOGLYCOPEPTIDES,
@ -163,6 +168,7 @@ usethis::use_data(eucast_rules_file,
OXAZOLIDINONES,
PENICILLINS,
POLYMYXINS,
QUINOLONES,
STREPTOGRAMINS,
TETRACYCLINES,
TETRACYCLINES_EXCEPT_TGC,

2
data-raw/reproduction_of_intrinsic_resistant.R
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@ -32,7 +32,7 @@ for (i in seq_len(nrow(antibiotics))) {
}
int_resis <- eucast_rules(int_resis,
eucast_rules_df = subset(AMR:::eucast_rules_file,
eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
is.na(have_these_values) & reference.version == 3.2),
info = FALSE)