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Replace RSI with SIR

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This commit is contained in:
Dr. Matthijs Berends
2023-01-21 23:47:20 +01:00
committed by GitHub
parent 24b12024ce
commit 98e62c9af2
127 changed files with 1746 additions and 1648 deletions
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10
data-raw/reproduction_of_microorganisms.R
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@ -1333,7 +1333,7 @@ rm(microorganisms)
# and check: these codes should not be missing (will otherwise throw a unit test error):
AMR::microorganisms.codes %>% filter(!mo %in% taxonomy$mo)
AMR::rsi_translation %>% filter(!mo %in% taxonomy$mo)
AMR::clinical_breakpoints %>% filter(!mo %in% taxonomy$mo)
AMR::example_isolates %>% filter(!mo %in% taxonomy$mo)
AMR::intrinsic_resistant %>% filter(!mo %in% taxonomy$mo)
@ -1342,10 +1342,10 @@ devtools::load_all(".")
# reset previously changed mo codes
if (!identical(rsi_translation$mo, as.mo(rsi_translation$mo, language = NULL))) {
rsi_translation$mo <- as.mo(rsi_translation$mo, language = NULL)
usethis::use_data(rsi_translation, overwrite = TRUE, version = 2, compress = "xz")
rm(rsi_translation)
if (!identical(clinical_breakpoints$mo, as.mo(clinical_breakpoints$mo, language = NULL))) {
clinical_breakpoints$mo <- as.mo(clinical_breakpoints$mo, language = NULL)
usethis::use_data(clinical_breakpoints, overwrite = TRUE, version = 2, compress = "xz")
rm(clinical_breakpoints)
}
if (!identical(microorganisms.codes$mo, as.mo(microorganisms.codes$mo, language = NULL))) {