From 461793dc34501ffe51962d41b830eafe61a94c57 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <berendsms@gmail.com>
Date: Mon, 8 Mar 2021 01:24:37 +0100
Subject: [PATCH] (v1.5.0.9038) quick test

---
 DESCRIPTION |  2 +-
 R/ab.R      | 34 +++++++++++++++++-----------------
 R/rsi.R     | 23 +++++++----------------
 3 files changed, 25 insertions(+), 34 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6688e9fd..bd1d00d5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.5.0.9037
+Version: 1.5.0.9038
 Date: 2021-03-07
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
diff --git a/R/ab.R b/R/ab.R
index 2379b41c..57271ee7 100755
--- a/R/ab.R
+++ b/R/ab.R
@@ -109,23 +109,23 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
   x <- toupper(x)
   x_nonNA <- x[!is.na(x)]
   
-  if (all(x_nonNA %in% antibiotics$ab, na.rm = TRUE)) {
-    # all valid AB codes, but not yet right class
-    return(set_clean_class(x,
-                           new_class = c("ab", "character")))
-  }
-  if (all(x_nonNA %in% toupper(antibiotics$name), na.rm = TRUE)) {
-    # all valid AB names
-    out <- antibiotics$ab[match(x, toupper(antibiotics$name))]
-    out[is.na(x)] <- NA_character_
-    return(out)
-  }
-  if (all(x_nonNA %in% antibiotics$atc, na.rm = TRUE)) {
-    # all valid ATC codes
-    out <- antibiotics$ab[match(x, antibiotics$atc)]
-    out[is.na(x)] <- NA_character_
-    return(out)
-  }
+  # if (all(x_nonNA %in% antibiotics$ab, na.rm = TRUE)) {
+  #   # all valid AB codes, but not yet right class
+  #   return(set_clean_class(x,
+  #                          new_class = c("ab", "character")))
+  # }
+  # if (all(x_nonNA %in% toupper(antibiotics$name), na.rm = TRUE)) {
+  #   # all valid AB names
+  #   out <- antibiotics$ab[match(x, toupper(antibiotics$name))]
+  #   out[is.na(x)] <- NA_character_
+  #   return(out)
+  # }
+  # if (all(x_nonNA %in% antibiotics$atc, na.rm = TRUE)) {
+  #   # all valid ATC codes
+  #   out <- antibiotics$ab[match(x, antibiotics$atc)]
+  #   out[is.na(x)] <- NA_character_
+  #   return(out)
+  # }
   
   # remove diacritics
   x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
diff --git a/R/rsi.R b/R/rsi.R
index d341f319..8a17ea28 100755
--- a/R/rsi.R
+++ b/R/rsi.R
@@ -337,6 +337,8 @@ as.rsi.mic <- function(x,
   meet_criteria(reference_data, allow_class = "data.frame")
   check_reference_data(reference_data)
   
+  pkg_env$strange <- list(before = ab)
+  
   # for dplyr's across()
   cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
   if (!is.null(cur_column_dplyr)) {
@@ -345,6 +347,8 @@ as.rsi.mic <- function(x,
                    error = function(e) ab)
   }
   
+  pkg_env$strange$afteracross <- ab
+  
   # for auto-determining mo
   mo_var_found <- ""
   if (is.null(mo)) {
@@ -369,6 +373,7 @@ as.rsi.mic <- function(x,
   }
   
   ab_coerced <- suppressWarnings(as.ab(ab))
+  pkg_env$strange$coerced <- ab_coerced
   mo_coerced <- suppressWarnings(as.mo(mo))
   guideline_coerced <- get_guideline(guideline, reference_data)
   if (is.na(ab_coerced)) {
@@ -704,6 +709,8 @@ exec_as.rsi <- function(method,
                         conserve_capped_values, 
                         add_intrinsic_resistance,
                         reference_data) {
+  pkg_env$strange$exec <- ab
+  pkg_env$strange$names <- names(pkg_env$strange)
   
   metadata_mo <- get_mo_failures_uncertainties_renamed()
   
@@ -812,22 +819,6 @@ exec_as.rsi <- function(method,
     get_record <- get_record[1L, , drop = FALSE]
     
     if (NROW(get_record) > 0) {
-      pkg_env$strange <- list(x_dbl = as.double(x[i]),
-                              x_chr = as.character(x[i]),
-                              get_record = get_record,
-                              guideline_coerced = guideline_coerced,
-                              lookup = c(lookup_mo[i],
-                                         lookup_genus[i],
-                                         lookup_family[i],
-                                         lookup_order[i],
-                                         lookup_becker[i],
-                                         lookup_lancefield[i],
-                                         lookup_other[i]),
-                              is_intrinsic_r = is_intrinsic_r,
-                              c1 = x[i] <= get_record$breakpoint_S,
-                              c2 = guideline_coerced %like% "EUCAST" & x[i] > get_record$breakpoint_R,
-                              c2 = guideline_coerced %like% "CLSI" & x[i] >= get_record$breakpoint_R)
-
       if (is.na(x[i]) | (is.na(get_record$breakpoint_S) & is.na(get_record$breakpoint_R))) {
         new_rsi[i] <- NA_character_
       } else if (method == "mic") {