From 89a577805f1199e752b07a6e618757f0c563db9d Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Mon, 30 Jan 2023 12:26:48 +0100
Subject: [PATCH] prelim fix for g.test

---
 DESCRIPTION       | 4 ++--
 NEWS.md           | 2 +-
 R/g.test.R        | 2 +-
 R/mo.R            | 2 +-
 pkgdown/extra.css | 5 +++++
 5 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e3234804..f387dddc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9103
-Date: 2023-01-24
+Version: 1.8.2.9104
+Date: 2023-01-30
 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 c64a1c69..f04ee706 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9103
+# AMR 1.8.2.9104
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 
diff --git a/R/g.test.R b/R/g.test.R
index cde0c6e5..21deef6a 100755
--- a/R/g.test.R
+++ b/R/g.test.R
@@ -179,7 +179,7 @@ g.test <- function(x,
     V <- outer(sr, sc, v, n)
     dimnames(E) <- dimnames(x)
 
-    STATISTIC <- 2 * sum(x * log(x / E)) # sum((abs(x - E) - YATES)^2/E) for chisq.test
+    STATISTIC <- 2 * sum(x * log(x / E), na.rm = TRUE) # sum((abs(x - E) - YATES)^2/E) for chisq.test
     PARAMETER <- (nr - 1L) * (nc - 1L)
     PVAL <- pchisq(STATISTIC, PARAMETER, lower.tail = FALSE)
   } else {
diff --git a/R/mo.R b/R/mo.R
index 2a9b8e4e..7d7de8c7 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -210,7 +210,7 @@ as.mo <- function(x,
   # From known codes ----
   out[is.na(out) & toupper(x) %in% AMR::microorganisms.codes$code] <- AMR::microorganisms.codes$mo[match(toupper(x)[is.na(out) & toupper(x) %in% AMR::microorganisms.codes$code], AMR::microorganisms.codes$code)]
   # From SNOMED ----
-  if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(microorganisms$snomed), na.rm = TRUE)) {
+  if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed), na.rm = TRUE)) {
     # found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331
     out[is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed)] <- AMR_env$MO_lookup$mo[rep(seq_along(AMR_env$MO_lookup$snomed), vapply(FUN.VALUE = double(1), AMR_env$MO_lookup$snomed, length))[match(x[is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed)], unlist(AMR_env$MO_lookup$snomed))]]
   }
diff --git a/pkgdown/extra.css b/pkgdown/extra.css
index eb2fc57d..0995fd15 100644
--- a/pkgdown/extra.css
+++ b/pkgdown/extra.css
@@ -49,6 +49,11 @@
   content: 'Maintainers';
 }
 
+/* marked words for after using the search box */
+mark, .mark {
+  background: rgba(17, 143, 118, 0.25) !important;
+}
+
 
 /* SYNTAX */
 /* These are simple changes for the syntax highlighting */