(v2.1.1.9070) fix for mo_current mo (no-verify)

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9068
+Version: 2.1.1.9070
-Date: 2024-07-17
+Date: 2024-07-19
 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

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9068
+# AMR 2.1.1.9070
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 

R/mo.R

@@ -1258,14 +1258,14 @@ synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE, dataset = AMR
     
     # make sure to get the latest name, e.g. Fusarium pulicaris robiniae was first renamed to Fusarium roseum, then to Fusarium sambucinum
     # we need the MO of Fusarium pulicaris robiniae to return the MO of Fusarium sambucinum
-    idx <- !is.na(is_still_synonym) & is_still_synonym
+    must_be_corrected <- !is.na(is_still_synonym) & is_still_synonym
-    x_gbif <- dataset$gbif_renamed_to[match(out[idx], dataset$mo)]
+    x_gbif <- dataset$gbif_renamed_to[match(out, dataset$mo)]
-    x_mycobank <- dataset$mycobank_renamed_to[match(out[idx], dataset$mo)]
+    x_mycobank <- dataset$mycobank_renamed_to[match(out, dataset$mo)]
-    x_lpsn <- dataset$lpsn_renamed_to[match(out[idx], dataset$mo)]
+    x_lpsn <- dataset$lpsn_renamed_to[match(out, dataset$mo)]
 
-    out[idx][!is.na(x_gbif)] <- dataset$mo[match(x_gbif[idx][!is.na(x_gbif)], dataset$gbif)]
+    out[must_be_corrected & !is.na(x_gbif)] <- dataset$mo[match(x_gbif[must_be_corrected & !is.na(x_gbif)], dataset$gbif)]
-    out[idx][!is.na(x_mycobank)] <- dataset$mo[match(x_mycobank[idx][!is.na(x_mycobank)], dataset$mycobank)]
+    out[must_be_corrected & !is.na(x_mycobank)] <- dataset$mo[match(x_mycobank[must_be_corrected & !is.na(x_mycobank)], dataset$mycobank)]
-    out[idx][!is.na(x_lpsn)] <- dataset$mo[match(x_lpsn[idx][!is.na(x_lpsn)], dataset$lpsn)]
+    out[must_be_corrected & !is.na(x_lpsn)] <- dataset$mo[match(x_lpsn[must_be_corrected & !is.na(x_lpsn)], dataset$lpsn)]
 
     is_still_synonym <- dataset$status[match(out, dataset$mo)] == "synonym"
   }

R/mo_property.R

@@ -928,7 +928,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
   # overwrite with LPSN:
   u[!is.na(x.lpsn)] <- paste0(TAXONOMY_VERSION$LPSN$url, "/", x.rank[!is.na(x.lpsn)], "/", gsub(" ", "-", tolower(x.name[!is.na(x.lpsn)]), fixed = TRUE))
   # overwrite with MycoBank (bacteria from LPSN will not be overwritten since MycoBank has no bacteria)
-  u[!is.na(x.mycobank)] <- paste0(TAXONOMY_VERSION$MycoBank$url, "/name/", gsub(" ", "%20", tolower(x.name[!is.na(x.mycobank)]), fixed = TRUE))
+  u[!is.na(x.mycobank)] <- paste0(TAXONOMY_VERSION$MycoBank$url, "/mb/", gsub(" ", "%20", tolower(x.mycobank[!is.na(x.mycobank)]), fixed = TRUE))
 
   names(u) <- x.name
 

inst/tinytest/test-mo_property.R

@@ -113,7 +113,8 @@ expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
 expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
 expect_equal(mo_year("Escherichia coli"), 1919)
 
-expect_true(mo_url("Candida albicans") %like% "gbif.org")
+expect_true(mo_url("Amoeba dysenteriae") %like% "gbif.org")
+expect_true(mo_url("Candida albicans") %like% "mycobank.org")
 expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
 
 # test integrity of getting back full names

inst/tinytest/test-sir.R

@@ -326,7 +326,6 @@ expect_identical(out_vet$PRA, rep(NA_sir_, 11))
 expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
 
 sir_history <- sir_interpretation_history()
-print(sir_history$host)
 expect_identical(sort(sir_history$host),
                  c("cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
                    "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",