(v1.7.1.9073) as.rsi() fix for UTIs

data-raw/_internals.R

@@ -279,15 +279,19 @@ if (changed_md5(av)) {
   try(openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx"), silent = TRUE)
 }
 
-if (changed_md5(intrinsic_resistant)) {
+# give official names to ABs and MOs
+intrinsicR <- data.frame(microorganism = mo_name(intrinsic_resistant$mo),
+                         antibiotic = ab_name(intrinsic_resistant$ab),
+                         stringsAsFactors = FALSE)
+if (changed_md5(intrinsicR)) {
   usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('/data-raw/')}"))
-  write_md5(intrinsic_resistant)
-  try(saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
-  try(write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
-  try(haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas"), silent = TRUE)
-  try(haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
-  try(haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
-  try(openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
+  write_md5(intrinsicR)
+  try(saveRDS(intrinsicR, "data-raw/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
+  try(write.table(intrinsicR, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+  try(haven::write_sas(intrinsicR, "data-raw/intrinsic_resistant.sas"), silent = TRUE)
+  try(haven::write_sav(intrinsicR, "data-raw/intrinsic_resistant.sav"), silent = TRUE)
+  try(haven::write_dta(intrinsicR, "data-raw/intrinsic_resistant.dta"), silent = TRUE)
+  try(openxlsx::write.xlsx(intrinsicR, "data-raw/intrinsic_resistant.xlsx"), silent = TRUE)
 }
 
 if (changed_md5(dosage)) {

data-raw/intrinsicR.md5

@@ -0,0 +1 @@
+56b3cea0e28d8a54e0fcbd3e50af96fc

data-raw/reproduction_of_intrinsic_resistant.R

@@ -25,29 +25,27 @@
 
 library(AMR)
 library(dplyr)
-int_resis <- data.frame(microorganism = microorganisms$mo, stringsAsFactors = FALSE)
+int_resis <- data.frame(mo = microorganisms$mo, stringsAsFactors = FALSE)
 for (i in seq_len(nrow(antibiotics))) {
   int_resis$new <- as.rsi("S")
-  colnames(int_resis)[ncol(int_resis)] <- antibiotics$name[i]
+  colnames(int_resis)[ncol(int_resis)] <- antibiotics$ab[i]
 }
 
-int_resis <- eucast_rules(int_resis, 
+int_resis <- eucast_rules(int_resis,
                           eucast_rules_df = subset(AMR:::EUCAST_RULES_DF,
                                                    is.na(have_these_values) & reference.version == 3.3),
                           info = FALSE)
 
 int_resis2 <- int_resis[, sapply(int_resis, function(x) any(!is.rsi(x) | x == "R"))] %>% 
-  tidyr::pivot_longer(-microorganism) %>%
+  tidyr::pivot_longer(-mo) %>%
   filter(value == "R") %>% 
-  select(microorganism, antibiotic = name)
+  select(mo, ab = name)
 
 # remove lab drugs
-untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "name", drop = TRUE]
+untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
 int_resis2 <- int_resis2 %>% 
-  filter(!antibiotic %in% untreatable) %>% 
-  arrange(microorganism, antibiotic)
-  
-int_resis2$microorganism <- mo_name(int_resis2$microorganism, language = NULL)
+  filter(!ab %in% untreatable) %>% 
+  arrange(mo, ab)
 
 intrinsic_resistant <- as.data.frame(int_resis2, stringsAsFactors = FALSE)
 usethis::use_data(intrinsic_resistant, internal = FALSE, overwrite = TRUE, version = 2, compress = "xz")