From 3829311dd3baffabc194aec16f8cfd2b723e3d2c Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Sat, 8 Jul 2023 21:00:49 +0200
Subject: [PATCH] random() fix

---
 DESCRIPTION  |  2 +-
 NEWS.md      |  2 +-
 R/random.R   | 15 ++++++++-------
 _pkgdown.yml |  1 +
 4 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0ebfc264..de5ce2da 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.0.0.9027
+Version: 2.0.0.9028
 Date: 2023-07-08
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 90f5f997..0757cc22 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.0.0.9027
+# AMR 2.0.0.9028
 
 ## 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
diff --git a/R/random.R b/R/random.R
index 31f0f245..c9d14a89 100755
--- a/R/random.R
+++ b/R/random.R
@@ -94,13 +94,14 @@ random_sir <- function(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...) {
   sample(as.sir(c("S", "I", "R")), size = size, replace = TRUE, prob = prob_SIR)
 }
 
-random_exec <- function(type, size, mo = NULL, ab = NULL) {
+random_exec <- function(method_type, size, mo = NULL, ab = NULL) {
   df <- AMR::clinical_breakpoints %pm>%
     pm_filter(guideline %like% "EUCAST") %pm>%
     pm_arrange(pm_desc(guideline)) %pm>%
     subset(guideline == max(guideline) &
-      method == type)
-
+      method == method_type &
+      type == "human")
+  
   if (!is.null(mo)) {
     mo_coerced <- as.mo(mo)
     mo_include <- c(
@@ -114,7 +115,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
     if (nrow(df_new) > 0) {
       df <- df_new
     } else {
-      warning_("in `random_", tolower(type), "()`: no rows found that match mo '", mo, "', ignoring argument `mo`")
+      warning_("in `random_", tolower(method_type), "()`: no rows found that match mo '", mo, "', ignoring argument `mo`")
     }
   }
 
@@ -125,11 +126,11 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
     if (nrow(df_new) > 0) {
       df <- df_new
     } else {
-      warning_("in `random_", tolower(type), "()`: no rows found that match ab '", ab, "', ignoring argument `ab`")
+      warning_("in `random_", tolower(method_type), "()`: no rows found that match ab '", ab, "' (", ab_name(ab_coerced, tolower = TRUE, language = NULL), "), ignoring argument `ab`")
     }
   }
 
-  if (type == "MIC") {
+  if (method_type == "MIC") {
     # set range
     mic_range <- c(0.001, 0.002, 0.005, 0.010, 0.025, 0.0625, 0.125, 0.250, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256)
 
@@ -156,7 +157,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
       out[out == max(out)] <- paste0(">=", out[out == max(out)])
     }
     return(out)
-  } else if (type == "DISK") {
+  } else if (method_type == "DISK") {
     set_range <- seq(
       from = as.integer(min(df$breakpoint_R, na.rm = TRUE) / 1.25),
       to = as.integer(max(df$breakpoint_S, na.rm = TRUE) * 1.25),
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 685e23e6..e8f62468 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -233,6 +233,7 @@ reference:
     - "`example_isolates`"
     - "`microorganisms`"
     - "`microorganisms.codes`"
+    - "`microorganisms.groups`"
     - "`antibiotics`"
     - "`intrinsic_resistant`"
     - "`dosage`"