From 05d536ebb7e1897cf0606c1308ff9b3bbdf0239f Mon Sep 17 00:00:00 2001
From: Matthijs Berends <berendsms@gmail.com>
Date: Thu, 17 Nov 2022 15:23:29 +0100
Subject: [PATCH] complexes

---
 DESCRIPTION              | 4 ++--
 NEWS.md                  | 2 +-
 R/mo.R                   | 6 +++++-
 R/rsi.R                  | 7 ++++++-
 README.md                | 2 +-
 inst/tinytest/test-mo.R  | 2 ++
 inst/tinytest/test-rsi.R | 6 ++++++
 7 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 55008ba3..b6546527 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9051
-Date: 2022-11-14
+Version: 1.8.2.9052
+Date: 2022-11-17
 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 bc251510..20b07483 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9051
+# AMR 1.8.2.9052
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 
diff --git a/R/mo.R b/R/mo.R
index daaf67d1..7c1b851c 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -180,6 +180,10 @@ as.mo <- function(x,
   x <- replace_ignore_pattern(x, ignore_pattern)
 
   x_lower <- tolower(x)
+  
+  if (any(trimws2(x_lower) %like_case% "complex$", na.rm = TRUE)) {
+    warning_("in `as.mo()`: translation of complexes is not supported at the moment - the input text 'complex' was ignored.", call = FALSE)
+  }
 
   # WHONET: xxx = no growth
   x[x_lower %in% c("", "xxx", "na", "nan")] <- NA_character_
@@ -521,7 +525,7 @@ mo_cleaning_regex <- function() {
     "|",
     "([({]|\\[).+([})]|\\])",
     "|",
-    "(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|e?species)[.]*( |$))"
+    "(^| )(e?spp|e?ssp|e?ss|e?sp|e?subsp|sube?species|biovar|biotype|serovar|serogr.?up|e?species|complex)[.]*( |$))"
   )
 }
 
diff --git a/R/rsi.R b/R/rsi.R
index c8ca6588..7b98a3b0 100755
--- a/R/rsi.R
+++ b/R/rsi.R
@@ -285,7 +285,7 @@ as.rsi.default <- function(x, ...) {
 
   x.bak <- x
   x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
-
+  
   if (inherits(x.bak, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
     # support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
     lbls <- attributes(x.bak)$labels
@@ -298,6 +298,10 @@ as.rsi.default <- function(x, ...) {
       x[x.bak == 2] <- "I"
       x[x.bak == 3] <- "R"
     }
+  } else if (inherits(x.bak, "character") && all(x %in% c("1", "2", "3", "S", "I", "R", NA_character_))) {
+    x[x.bak == "1"] <- "S"
+    x[x.bak == "2"] <- "I"
+    x[x.bak == "3"] <- "R"
   } else if (!all(is.na(x)) && !identical(levels(x), c("R", "S", "I")) && !all(x %in% c("R", "S", "I", NA))) {
     if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
       # check if they are actually MICs or disks
@@ -312,6 +316,7 @@ as.rsi.default <- function(x, ...) {
     x <- trimws2(as.character(unlist(x)))
     x[x %in% c(NA, "", "-", "NULL")] <- NA_character_
     x.bak <- x
+    
     na_before <- length(x[is.na(x)])
 
     # correct for translations
diff --git a/README.md b/README.md
index 22667bef..c28e9582 100755
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 # `AMR` (for R)
 
-<a href="https://msberends.github.io/AMR/"><img src="https://msberends.github.io/AMR/AMR_intro.svg" align="center"></a>
+<a href="https://msberends.github.io/AMR/"><img src="https://msberends.github.io/AMR/AMR_intro.png" align="center"></a>
 
 ----
 
diff --git a/inst/tinytest/test-mo.R b/inst/tinytest/test-mo.R
index 66ca08a9..8cd2e83f 100644
--- a/inst/tinytest/test-mo.R
+++ b/inst/tinytest/test-mo.R
@@ -80,6 +80,8 @@ expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
 
 expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
 
+expect_warning(as.mo("Acinetobacter calcoaceticus/baumannii complex"))
+
 # prevalent MO
 expect_identical(
   suppressWarnings(as.character(
diff --git a/inst/tinytest/test-rsi.R b/inst/tinytest/test-rsi.R
index 6467c6aa..0a8c3f8e 100644
--- a/inst/tinytest/test-rsi.R
+++ b/inst/tinytest/test-rsi.R
@@ -81,6 +81,12 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_equal(sum(is.rsi(example_isolates)), 40)
 
   expect_stdout(print(tibble(ab = as.rsi("S"))))
+  
+  expect_true(example_isolates %>% 
+                select(AMC, MEM) %>% 
+                mutate(MEM = as.rsi(ifelse(AMC == "S", "S", MEM))) %>% 
+                pull(MEM) %>% 
+                is.rsi())
 }
 if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
   expect_inherits(