DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9073
+Version: 2.1.1.9071
 Date: 2024-09-19
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9073
+# AMR 2.1.1.9071
 
 *(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/sir.R

@@ -623,7 +623,7 @@ as.sir.data.frame <- function(x,
   }
   
   # -- host
-  if (missing(breakpoint_type) && any(host %in% clinical_breakpoints$host[!clinical_breakpoints$host %in% c("human", "ECOFF")], na.rm = TRUE)) {
+  if (missing(breakpoint_type) && any(host %in% AMR_env$host_preferred_order, na.rm = TRUE)) {
     message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
     breakpoint_type <- "animal"
   } else if (any(!suppressMessages(convert_host(host)) %in% c("human", "ECOFF"), na.rm = TRUE)) {
@@ -865,7 +865,16 @@ convert_host <- function(x, lang = get_AMR_locale()) {
   x_out[is.na(x_out) & (x %like% "sheep|ovine" | x %like% translate_AMR("sheep|sheeps|ovine", lang))] <- "sheep"
   x_out[is.na(x_out) & (x %like% "snake|serpentine" | x %like% translate_AMR("snake|snakes|serpentine", lang))] <- "snakes"
   x_out[is.na(x_out) & (x %like% "turkey|meleagrine" | x %like% translate_AMR("turkey|turkeys|meleagrine", lang))] <- "turkey"
-  
+  if (any(x_out %in% c(NA_character_, "animal"))) {
+    x_out[is.na(x_out) & x == "animal"] <- AMR_env$host_preferred_order[1]
+    if (message_not_thrown_before("as.sir", "convert_host_missing")) {
+      message_(ifelse(any(is.na(x_out) & !is.na(x), na.rm = TRUE),
+                      paste0("The following host(s) are invalid: ", vector_and(x[is.na(x_out) & !is.na(x)]), ". "),
+                      ""),
+               "For missing animal hosts, assuming \"", AMR_env$host_preferred_order[1], "\", since these have the highest breakpoint availability.")
+    x_out[is.na(x_out)] <- AMR_env$host_preferred_order[1]
+    }
+  }
   x_out[x_out == "ecoff"] <- "ECOFF"
   x_out
 }
@@ -920,9 +929,9 @@ as_sir_method <- function(method_short,
   # get host
   if (breakpoint_type == "animal") {
     if (is.null(host)) {
-      host <- "dogs"
+      host <- AMR_env$host_preferred_order[1]
       if (message_not_thrown_before("as.sir", "host_missing")) {
-        message_("Animal hosts not set in `host`, assuming `host = \"dogs\"`, since these have the highest breakpoint availability.\n\n")  
+        message_("Animal hosts not set in `host`, assuming `host = \"", host, "\"`, since these have the highest breakpoint availability.\n\n")  
       }
     }
   } else {

R/zzz.R

@@ -205,6 +205,8 @@ AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
   # they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
   AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
   AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
+  
+  AMR_env$host_preferred_order <- names(sort(table(AMR::clinical_breakpoints$host[!AMR::clinical_breakpoints$host %in% AMR::clinical_breakpoints$type]), decreasing = TRUE))
 }
 
 .onAttach <- function(lib, pkg) {

inst/tinytest/test-mo_property.R

@@ -97,7 +97,7 @@ expect_equal(names(mo_info("Escherichia coli")), c(
   "mo",
   "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
   "status", "synonyms", "gramstain", "oxygen_tolerance",
-  "url", "ref", "snomed", "lpsn", "mycobank", "gbif", "group_members"
+  "url", "ref", "snomed", "lpsn", "gbif", "group_members"
 ))
 expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
 expect_true(length(mo_group_members("B_HACEK")) > 1)

inst/tinytest/test-sir.R

@@ -312,14 +312,14 @@ vet <- data.frame(animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine",
                   FLR = mics,
                   mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1]))
 
-out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
+out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI")
 # host column name instead of values
 expect_identical(out_vet,
                  as.sir(vet, host = "animal", guideline = "CLSI 2023"))
 
 # check outcomes
-expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", NA, NA, "R", NA, NA, NA, "I", NA)))
-expect_identical(out_vet$FLR, as.sir(c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "R", NA)))
+expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", "R", NA, "R", "R", NA, "R", "R", NA)))
+expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
 
 out_vet <- as.sir(vet, host = "animal", guideline = "EUCAST 2023")
 expect_identical(out_vet$PRA, rep(NA_sir_, 11))
@@ -327,10 +327,9 @@ expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA,
 
 sir_history <- sir_interpretation_history()
 expect_identical(sort(sir_history$host),
-                 c("cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",   "cats",
-                   "cats",   "cats",   "cats",   "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
-                   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",
-                   "horse",  "horse",  "horse",  "horse",  "horse",  "horse",  "horse",  "horse",  "horse",  "poultry","poultry","poultry","poultry"))
+                 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",  
+                   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "dogs",   "horse",  "horse",  "horse",  "horse",  "horse",  "poultry","poultry"))
 
 # ECOFF -------------------------------------------------------------------
 

vignettes/datasets.Rmd

@@ -131,10 +131,10 @@ The tab-separated text file and Microsoft Excel workbook both contain all SNOMED
 
 This data set contains the full microbial taxonomy of `r AMR:::nr2char(length(unique(AMR::microorganisms$kingdom[!AMR::microorganisms$kingdom %like% "unknown"])))` kingdoms from the `r AMR:::TAXONOMY_VERSION$LPSN$name`, `r AMR:::TAXONOMY_VERSION$MycoBank$name`, and the `r AMR:::TAXONOMY_VERSION$GBIF$name`:
 
-* `r AMR:::TAXONOMY_VERSION$LPSN$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$LPSN$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$LPSN$accessed_date)`.
-* `r AMR:::TAXONOMY_VERSION$MycoBank$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$MycoBank$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$MycoBank$accessed_date)`.
-* `r AMR:::TAXONOMY_VERSION$GBIF$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$GBIF$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$GBIF$accessed_date)`.
-* `r AMR:::TAXONOMY_VERSION$BacDive$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$BacDive$url`> on `r AMR:::documentation_date(AMR:::TAXONOMY_VERSION$BacDive$accessed_date)`.
+* `r AMR:::TAXONOMY_VERSION$LPSN$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$LPSN$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$LPSN$accessed_date)`.
+* `r AMR:::TAXONOMY_VERSION$MycoBank$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$MycoBank$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$MycoBank$accessed_date)`.
+* `r AMR:::TAXONOMY_VERSION$GBIF$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$GBIF$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$GBIF$accessed_date)`.
+* `r AMR:::TAXONOMY_VERSION$BacDive$citation` Accessed from <`r AMR:::TAXONOMY_VERSION$BacDive$url`> on `r documentation_date(AMR:::TAXONOMY_VERSION$BacDive$accessed_date)`.
 * `r AMR:::TAXONOMY_VERSION$SNOMED$citation` URL: <`r AMR:::TAXONOMY_VERSION$SNOMED$url`>
 
 ### Example content