styled, unit test fix

R/zzz.R

@@ -9,7 +9,7 @@
 # (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
-# Diagnostics & Advice, and University Medical Center Groningen.       # 
+# Diagnostics & Advice, and University Medical Center Groningen.       #
 #                                                                      #
 # This R package is free software; you can freely use and distribute   #
 # it for both personal and commercial purposes under the terms of the  #
@@ -26,16 +26,19 @@
 # set up package environment, used by numerous AMR functions
 pkg_env <- new.env(hash = FALSE)
 pkg_env$mo_failed <- character(0)
-pkg_env$mo_field_abbreviations <- c("AIEC", "ATEC", "BORSA", "CRSM", "DAEC", "EAEC",
-                                    "EHEC", "EIEC", "EPEC", "ETEC", "GISA", "MRPA",
-                                    "MRSA", "MRSE", "MSSA", "MSSE", "NMEC", "PISP",
-                                    "PRSP", "STEC", "UPEC", "VISA", "VISP", "VRE",
-                                    "VRSA", "VRSP")
+pkg_env$mo_field_abbreviations <- c(
+  "AIEC", "ATEC", "BORSA", "CRSM", "DAEC", "EAEC",
+  "EHEC", "EIEC", "EPEC", "ETEC", "GISA", "MRPA",
+  "MRSA", "MRSE", "MSSA", "MSSE", "NMEC", "PISP",
+  "PRSP", "STEC", "UPEC", "VISA", "VISP", "VRE",
+  "VRSA", "VRSP"
+)
 
 # determine info icon for messages
 utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
 is_latex <- tryCatch(import_fn("is_latex_output", "knitr", error_on_fail = FALSE)(),
-                     error = function(e) FALSE)
+  error = function(e) FALSE
+)
 if (utf8_supported && !is_latex) {
   # \u2139 is a symbol officially named 'information source'
   pkg_env$info_icon <- "\u2139"
@@ -45,8 +48,8 @@ if (utf8_supported && !is_latex) {
 
 .onLoad <- function(...) {
   # Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
-  # without the need to depend on other packages. This was suggested by the 
-  # developers of the vctrs package: 
+  # without the need to depend on other packages. This was suggested by the
+  # developers of the vctrs package:
   # https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
   s3_register("pillar::pillar_shaft", "ab")
   s3_register("pillar::pillar_shaft", "mo")
@@ -93,19 +96,22 @@ if (utf8_supported && !is_latex) {
   s3_register("vctrs::vec_ptype2", "disk.integer")
   s3_register("vctrs::vec_ptype2", "integer.disk")
   s3_register("vctrs::vec_cast", "integer.disk")
-  
+
   # if mo source exists, fire it up (see mo_source())
-  try({
-    if (file.exists(getOption("AMR_mo_source", "~/mo_source.rds"))) {
-      invisible(get_mo_source())
-    }
-  }, silent = TRUE)
-  
+  try(
+    {
+      if (file.exists(getOption("AMR_mo_source", "~/mo_source.rds"))) {
+        invisible(get_mo_source())
+      }
+    },
+    silent = TRUE
+  )
+
   # be sure to print tibbles as tibbles
   if (pkg_is_available("tibble", also_load = FALSE)) {
     loadNamespace("tibble")
   }
-  
+
   # reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
   # they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
   assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
@@ -123,7 +129,7 @@ create_AB_lookup <- function() {
 
 create_MO_lookup <- function() {
   MO_lookup <- AMR::microorganisms
-  
+
   MO_lookup$kingdom_index <- NA_real_
   MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
   MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
@@ -131,18 +137,18 @@ create_MO_lookup <- function() {
   MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
   # all the rest
   MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
-  
+
   # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
   if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
     MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
   } else {
     MO_lookup$fullname_lower <- ""
-    warning("MO table updated - Run: source(\"data-raw/pre-commit-hook.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
   MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
-  
+
   # so arrange data on prevalence first, then kingdom, then full name
   MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), , drop = FALSE]
 }
@@ -150,10 +156,10 @@ create_MO_lookup <- function() {
 create_MO.old_lookup <- function() {
   MO.old_lookup <- AMR::microorganisms.old
   MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
-  
+
   # add a column with only "e coli"-like combinations
   MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
-  
+
   # so arrange data on prevalence first, then full name
   MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), , drop = FALSE]
 }