Feather and Parquet files

R/aa_globals.R

@@ -24,7 +24,7 @@
 # ==================================================================== #
 
 # add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and rsi_translation
-# (sourcing "data-raw/_internals.R" will process the TSV file)
+# (sourcing "data-raw/pre-commit-hook.R" will process the TSV file)
 EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(version_txt = "v11.0",
                                                  year = 2021, 
                                                  title = "'EUCAST Clinical Breakpoint Tables'",

R/aa_helper_functions.R

@@ -596,7 +596,7 @@ create_eucast_ab_documentation <- function() {
   ab <- character()
   for (val in x) {
     if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-      # antibiotic group names, as defined in data-raw/_internals.R, such as `CARBAPENEMS`
+      # antibiotic group names, as defined in data-raw/pre-commit-hook.R, such as `CARBAPENEMS`
       val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
     } else if (val %in% AB_lookup$ab) {
       # separate drugs, such as `AMX`

R/ab_selectors.R

@@ -502,7 +502,7 @@ ab_select_exec <- function(function_name,
   }
   
   if (is.null(ab_class_args)) {
-    # their upper case equivalent are vectors with class <ab>, created in data-raw/_internals.R
+    # their upper case equivalent are vectors with class <ab>, created in data-raw/pre-commit-hook.R
     # carbapenems() gets its codes from AMR:::AB_CARBAPENEMS
     abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR"))  
     ab_group <- function_name

R/eucast_rules.R

@@ -543,7 +543,7 @@ eucast_rules <- function(x,
     # this allows: eucast_rules(x, eucast_rules_df = AMR:::EUCAST_RULES_DF %>% filter(is.na(have_these_values)))
     eucast_rules_df <- list(...)$eucast_rules_df
   } else {
-    # otherwise internal data file, created in data-raw/_internals.R
+    # otherwise internal data file, created in data-raw/pre-commit-hook.R
     eucast_rules_df <- EUCAST_RULES_DF
   }
   

R/guess_ab_col.R

@@ -311,7 +311,7 @@ get_ab_from_namespace <- function(x, cols_ab) {
   x_new <- character()
   for (val in x) {
     if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-      # antibiotic group names, as defined in data-raw/_internals.R, such as `AB_CARBAPENEMS`
+      # antibiotic group names, as defined in data-raw/pre-commit-hook.R, such as `AB_CARBAPENEMS`
       val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
     } else if (val %in% AB_lookup$ab) {
       # separate drugs, such as `AMX`

R/rsi.R

@@ -597,18 +597,18 @@ get_guideline <- function(guideline, reference_data) {
   guideline_param
 }
 
-as_rsi_method <- function(method_short = "mic",
-                          method_long = "MIC values",
-                          x = x,
-                          mo = NULL, 
-                          ab = deparse(substitute(x)), 
-                          guideline = "EUCAST", 
-                          uti = FALSE,
-                          conserve_capped_values = FALSE,
-                          add_intrinsic_resistance = FALSE,
-                          reference_data = AMR::rsi_translation,
+as_rsi_method <- function(method_short,
+                          method_long,
+                          x,
+                          mo,
+                          ab,
+                          guideline,
+                          uti,
+                          conserve_capped_values,
+                          add_intrinsic_resistance,
+                          reference_data,
                           ...) {
-  meet_criteria(x)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = c("ab", "character"))
   meet_criteria(guideline, allow_class = "character", has_length = 1)

R/zzz.R

@@ -133,7 +133,7 @@ create_MO_lookup <- function() {
     MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
   } else {
     MO_lookup$fullname_lower <- ""
-    warning("MO table updated - Run: source(\"data-raw/_internals.R\")", call. = FALSE)
+    warning("MO table updated - Run: source(\"data-raw/pre-commit-hook.R\")", call. = FALSE)
   }
   
   # add a column with only "e coli" like combinations