unit test

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.0.0.9032
+Version: 2.0.0.9033
 Date: 2023-07-10
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.0.0.9032
+# AMR 2.0.0.9033
 
 ## New
 * Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations

data-raw/_pre_commit_hook.R

@@ -365,7 +365,7 @@ if (changed_md5(clin_break)) {
   usethis::ui_info(paste0("Saving {usethis::ui_value('clinical_breakpoints')} to {usethis::ui_value('data-raw/')}"))
   write_md5(clin_break)
   try(saveRDS(clin_break, "data-raw/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
-  try(write.table(clin_break, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
+  try(write.table(clinical_breakpoints, "data-raw/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
   try(haven::write_xpt(clin_break, "data-raw/clinical_breakpoints.xpt"), silent = TRUE)
   try(haven::write_sav(clin_break, "data-raw/clinical_breakpoints.sav"), silent = TRUE)
   try(haven::write_dta(clin_break, "data-raw/clinical_breakpoints.dta"), silent = TRUE)

data-raw/clin_break.md5

@@ -1 +1 @@
-7aeceefb444830af010fcc16f5ba4705
+18c1848bb7fc97b46ccb889aa7f48dd9

data-raw/reproduction_of_clinical_breakpoints.R

@@ -294,7 +294,7 @@ breakpoints_new[which(breakpoints_new$method == "MIC" &
 # raise these one higher valid MIC factor level:
 breakpoints_new[which(breakpoints_new$breakpoint_R == 129), "breakpoint_R"] <- 128
 breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- 256
-breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 513
+breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- 512
 breakpoints_new[which(breakpoints_new$breakpoint_R == 1025), "breakpoint_R"] <- 1024
 
 # WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales: