(v1.3.0.9006) website update

data-raw/internals.R

@@ -74,47 +74,47 @@ usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
 devtools::load_all(quiet = TRUE)
 # give official names to ABs and MOs
 rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
-saveRDS(rsi, "data-raw/rsi_translation.rds", version = 2)
-write.table(rsi, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE)
-haven::write_sas(rsi, "data-raw/rsi_translation.sas")
-haven::write_sav(rsi, "data-raw/rsi_translation.sav")
-haven::write_dta(rsi, "data-raw/rsi_translation.dta")
-openxlsx::write.xlsx(rsi, "data-raw/rsi_translation.xlsx")
+try(saveRDS(rsi, "data-raw/rsi_translation.rds", version = 2), silent = TRUE)
+try(write.table(rsi, "data-raw/rsi_translation.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+try(haven::write_sas(rsi, "data-raw/rsi_translation.sas"), silent = TRUE)
+try(haven::write_sav(rsi, "data-raw/rsi_translation.sav"), silent = TRUE)
+try(haven::write_dta(rsi, "data-raw/rsi_translation.dta"), silent = TRUE)
+try(openxlsx::write.xlsx(rsi, "data-raw/rsi_translation.xlsx"), silent = TRUE)
 
 mo <- dplyr::mutate_if(microorganisms, ~!is.numeric(.), as.character)
-saveRDS(mo, "data-raw/microorganisms.rds", version = 2)
-write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE)
-haven::write_sas(mo, "data-raw/microorganisms.sas")
-haven::write_sav(mo, "data-raw/microorganisms.sav")
-haven::write_dta(mo, "data-raw/microorganisms.dta")
-openxlsx::write.xlsx(mo, "data-raw/microorganisms.xlsx")
+try(saveRDS(mo, "data-raw/microorganisms.rds", version = 2), silent = TRUE)
+try(write.table(mo, "data-raw/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+try(haven::write_sas(mo, "data-raw/microorganisms.sas"), silent = TRUE)
+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)
 
-saveRDS(microorganisms.old, "data-raw/microorganisms.old.rds", version = 2)
-write.table(microorganisms.old, "data-raw/microorganisms.old.txt", sep = "\t", na = "", row.names = FALSE)
-haven::write_sas(microorganisms.old, "data-raw/microorganisms.old.sas")
-haven::write_sav(microorganisms.old, "data-raw/microorganisms.old.sav")
-haven::write_dta(microorganisms.old, "data-raw/microorganisms.old.dta")
-openxlsx::write.xlsx(microorganisms.old, "data-raw/microorganisms.old.xlsx")
+try(saveRDS(microorganisms.old, "data-raw/microorganisms.old.rds", version = 2), silent = TRUE)
+try(write.table(microorganisms.old, "data-raw/microorganisms.old.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+try(haven::write_sas(microorganisms.old, "data-raw/microorganisms.old.sas"), silent = TRUE)
+try(haven::write_sav(microorganisms.old, "data-raw/microorganisms.old.sav"), silent = TRUE)
+try(haven::write_dta(microorganisms.old, "data-raw/microorganisms.old.dta"), silent = TRUE)
+try(openxlsx::write.xlsx(microorganisms.old, "data-raw/microorganisms.old.xlsx"), silent = TRUE)
 
 ab <- dplyr::mutate_if(antibiotics, ~!is.numeric(.), as.character)
-saveRDS(ab, "data-raw/antibiotics.rds", version = 2)
-write.table(ab, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE)
-haven::write_sas(ab, "data-raw/antibiotics.sas")
-haven::write_sav(ab, "data-raw/antibiotics.sav")
-haven::write_dta(ab, "data-raw/antibiotics.dta")
-openxlsx::write.xlsx(ab, "data-raw/antibiotics.xlsx")
+try(saveRDS(ab, "data-raw/antibiotics.rds", version = 2), silent = TRUE)
+try(write.table(ab, "data-raw/antibiotics.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+try(haven::write_sas(ab, "data-raw/antibiotics.sas"), silent = TRUE)
+try(haven::write_sav(ab, "data-raw/antibiotics.sav"), silent = TRUE)
+try(haven::write_dta(ab, "data-raw/antibiotics.dta"), silent = TRUE)
+try(openxlsx::write.xlsx(ab, "data-raw/antibiotics.xlsx"), silent = TRUE)
 
 av <- dplyr::mutate_if(antivirals, ~!is.numeric(.), as.character)
-saveRDS(av, "data-raw/antivirals.rds", version = 2)
-write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE)
-haven::write_sas(av, "data-raw/antivirals.sas")
-haven::write_sav(av, "data-raw/antivirals.sav")
-haven::write_dta(av, "data-raw/antivirals.dta")
-openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx")
+try(saveRDS(av, "data-raw/antivirals.rds", version = 2), silent = TRUE)
+try(write.table(av, "data-raw/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+try(haven::write_sas(av, "data-raw/antivirals.sas"), silent = TRUE)
+try(haven::write_sav(av, "data-raw/antivirals.sav"), silent = TRUE)
+try(haven::write_dta(av, "data-raw/antivirals.dta"), silent = TRUE)
+try(openxlsx::write.xlsx(av, "data-raw/antivirals.xlsx"), silent = TRUE)
 
-saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2)
-write.table(intrinsic_resistant, "data-raw/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE)
-haven::write_sas(intrinsic_resistant, "data-raw/intrinsic_resistant.sas")
-haven::write_sav(intrinsic_resistant, "data-raw/intrinsic_resistant.sav")
-haven::write_dta(intrinsic_resistant, "data-raw/intrinsic_resistant.dta")
-openxlsx::write.xlsx(intrinsic_resistant, "data-raw/intrinsic_resistant.xlsx")
+try(saveRDS(intrinsic_resistant, "data-raw/intrinsic_resistant.rds", version = 2), 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)