(v2.1.1.9087) update unit tests

data-raw/_pre_commit_checks.R

@@ -159,15 +159,18 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
   ))]
 pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
 pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
-  # World Health Organization's (WHO) Priority Pathogen List
+  # World Health Organization's (WHO) Priority Pathogen List (some are from the group Enterobacteriaceae)
   "Acinetobacter",
   "Aspergillus",
   "Blastomyces",
   "Campylobacter",
   "Candida",
+  "Citrobacter",
   "Clostridioides",
   "Coccidioides",
   "Cryptococcus",
+  "Edwardsiella",
+  "Enterobacter",
   "Enterococcus",
   "Escherichia",
   "Fusarium",
@@ -175,15 +178,20 @@ pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
   "Helicobacter",
   "Histoplasma",
   "Klebsiella",
+  "Morganella",
   "Mycobacterium",
   "Neisseria",
   "Paracoccidioides",
   "Pneumocystis",
+  "Proteus",
+  "Providencia",
   "Pseudomonas",
   "Salmonella",
+  "Serratia",
   "Shigella",
   "Staphylococcus",
-  "Streptococcus"
+  "Streptococcus",
+  "Yersinia"
 )
 pre_commit_lst$MO_RELEVANT_GENERA <- c(
   "Absidia",

data-raw/gpt_training_input.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+# Define the output file, located in ./data-raw
+output_file="gpt_training_text.txt"
+
+# Clear the output file if it exists
+echo "This files contains all context you must know about the AMR package for R."> "$output_file"
+echo -e "\n\n\n\n" >> "$output_file"
+
+# Function to remove header block (delimited by # ======)
+remove_header() {
+  sed '/# =\{6,\}/,/# =\{6,\}/d' "$1"
+}
+
+# Process all .R files in the '../R' folder
+for file in ../R/*.R; do
+  echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+  echo -e "\n\n" >> "$output_file"
+  remove_header "$file" >> "$output_file"
+  echo -e "\n\n" >> "$output_file"
+done
+
+# Process all .Rmd files in the '../vignettes' folder
+for file in ../vignettes/*.Rmd; do
+  echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+  echo -e "\n\n" >> "$output_file"
+  remove_header "$file" >> "$output_file"
+  echo -e "\n\n" >> "$output_file"
+done
+
+# Process important metadata files (DESCRIPTION, NAMESPACE, README.md)
+for file in ../DESCRIPTION ../NAMESPACE ../README.md; do
+  if [[ -f $file ]]; then
+    echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+    echo -e "\n\n" >> "$output_file"
+    cat "$file" >> "$output_file"
+    echo -e "\n\n" >> "$output_file"
+  fi
+done
+
+# Process test files (if available) in the '../tests' folder
+for file in ../tests/*.R; do
+  echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+  echo -e "\n\n" >> "$output_file"
+  remove_header "$file" >> "$output_file"
+  echo -e "\n\n" >> "$output_file"
+done
+
+# Process all .Rd files from the '../man' folder
+for file in ../man/*.Rd; do
+  echo "THE NEXT PART CONTAINS CONTENTS FROM FILE $file" >> "$output_file"
+  echo -e "\n\n" >> "$output_file"
+  remove_header "$file" >> "$output_file"
+  echo -e "\n\n" >> "$output_file"
+done

inst/tinytest/test-first_isolate.R

@@ -206,7 +206,7 @@ expect_equal(
     ),
     na.rm = TRUE
   ),
-  1376
+  1390
 )
 
 # unknown MOs
@@ -214,23 +214,23 @@ test_unknown <- example_isolates
 test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
 expect_equal(
   sum(first_isolate(test_unknown, include_unknown = FALSE)),
-  1106
+  1116
 )
 expect_equal(
   sum(first_isolate(test_unknown, include_unknown = TRUE)),
-  1589
+  1599
 )
 
 test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
 expect_equal(
   sum(first_isolate(test_unknown)),
-  1106
+  1116
 )
 
 # empty sir results
 expect_equal(
   sum(first_isolate(example_isolates, include_untested_sir = FALSE)),
-  1360
+  1374
 )
 
 # shortcuts