From ba51c2d92f48df6b4d1a8a1f9c7b900c85f7c8c5 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Mon, 28 Nov 2022 19:39:52 +0100
Subject: [PATCH] add column to `as.mic()` and `as.disk()` warnings

---
 DESCRIPTION |  4 ++--
 NEWS.md     |  3 ++-
 R/disk.R    | 14 +++++++++-----
 R/mic.R     | 14 +++++++++-----
 4 files changed, 22 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0e307b06..4427ae5b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9053
-Date: 2022-11-24
+Version: 1.8.2.9054
+Date: 2022-11-28
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by
diff --git a/NEWS.md b/NEWS.md
index 6b5f8e3a..8802878b 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9053
+# AMR 1.8.2.9054
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 
@@ -69,6 +69,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles
 * Updated support for all WHONET 2022 microorganism codes 
 * Antimicrobial interpretation 'SDD' (susceptible dose-dependent, coined by CLSI) will be interpreted as 'I' to comply with EUCAST's 'I' in `as.rsi()`
 * Fix for `mo_shortname()` in case of higher taxonomic ranks (order, class, phylum)
+* Cleaning columns with `as.rsi()`, `as.mic()`, or `as.disk()` will now show the column name in the warning for invalid results
 
 ### Other
 * New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions
diff --git a/R/disk.R b/R/disk.R
index 91bc19c4..defc28dc 100644
--- a/R/disk.R
+++ b/R/disk.R
@@ -118,11 +118,15 @@ as.disk <- function(x, na.rm = FALSE) {
         unique() %pm>%
         sort() %pm>%
         vector_and(quotes = TRUE)
-      warning_(
-        "in `as.disk()`: ", na_after - na_before, " results truncated (",
-        round(((na_after - na_before) / length(x)) * 100),
-        "%) that were invalid disk zones: ",
-        list_missing
+      cur_col <- get_current_column()
+      warning_("in `as.disk()`: ", na_after - na_before, " result",
+               ifelse(na_after - na_before > 1, "s", ""),
+               ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
+               " truncated (",
+               round(((na_after - na_before) / length(x)) * 100),
+               "%) that were invalid disk zones: ",
+               list_missing,
+               call = FALSE
       )
     }
   }
diff --git a/R/mic.R b/R/mic.R
index 04f6577d..e282eb8a 100755
--- a/R/mic.R
+++ b/R/mic.R
@@ -228,11 +228,15 @@ as.mic <- function(x, na.rm = FALSE) {
         unique() %pm>%
         sort() %pm>%
         vector_and(quotes = TRUE)
-      warning_("in `as.mic()`: ", na_after - na_before, " results truncated (",
-        round(((na_after - na_before) / length(x)) * 100),
-        "%) that were invalid MICs: ",
-        list_missing,
-        call = FALSE
+      cur_col <- get_current_column()
+      warning_("in `as.mic()`: ", na_after - na_before, " result",
+               ifelse(na_after - na_before > 1, "s", ""),
+               ifelse(is.null(cur_col), "", paste0(" in column '", cur_col, "'")),
+               " truncated (",
+               round(((na_after - na_before) / length(x)) * 100),
+               "%) that were invalid MICs: ",
+               list_missing,
+               call = FALSE
       )
     }