(v2.1.1.9045) fix host in animal guidelines

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9044
-Date: 2024-06-10
+Version: 2.1.1.9045
+Date: 2024-06-12
 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 2.1.1.9044
+# AMR 2.1.1.9045
 
 *(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!)*
 

R/sir.R

@@ -545,6 +545,13 @@ as.sir.data.frame <- function(x,
   }
 
   # -- host
+  if (missing(breakpoint_type) && any(host %in% AMR_env$host_preferred_order, na.rm = TRUE)) {
+    message_("Assuming `breakpoint_type = \"animal\"` since `host` contains animal species.")
+    breakpoint_type <- "animal"
+  } else if (any(!convert_host(host) %in% c("human", "ECOFF"), na.rm = TRUE)) {
+    message_("Assuming `breakpoint_type = \"animal\"`.")
+    breakpoint_type <- "animal"
+  }
   if (breakpoint_type == "animal") {
     if (is.null(host)) {
       host <- search_type_in_df(x = x, type = "host", add_col_prefix = FALSE)
@@ -936,6 +943,7 @@ as_sir_method <- function(method_short,
   }
   if (length(ab) == 1) {
     ab <- rep(ab, length(x))
+    ab.bak <- rep(ab.bak, length(ab))
   }
   if (length(host) == 1) {
     host <- rep(host, length(x))
@@ -952,7 +960,7 @@ as_sir_method <- function(method_short,
       warning_("in `as.sir()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
     }
   }
-
+  
   agent_formatted <- paste0("'", font_bold(ab.bak, collapse = NULL), "'")
   agent_name <- ab_name(ab, tolower = TRUE, language = NULL)
   same_ab <- generalise_antibiotic_name(ab) == generalise_antibiotic_name(agent_name)
@@ -966,7 +974,7 @@ as_sir_method <- function(method_short,
                                                     ")")
   # this intro text will also be printed in the progress bar if the `progress` package is installed
   intro_txt <- paste0("Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
-                      ifelse(length(unique(agent_formatted)) == 1, unique(agent_formatted), paste0("for ", vector_and(ab, quotes = FALSE, sort = FALSE))),
+                      ifelse(length(unique(agent_formatted)) == 1, unique(agent_formatted), paste0(vector_and(agent_formatted, quotes = FALSE, sort = FALSE))),
                       mo_var_found,
                       ifelse(identical(reference_data, AMR::clinical_breakpoints),
                              paste0(", ", font_bold(guideline_coerced)),
@@ -1042,17 +1050,6 @@ as_sir_method <- function(method_short,
   }
 
   msgs <- character(0)
-  if (nrow(breakpoints) == 0) {
-    # apparently no breakpoints found
-    message(
-      paste0(font_rose_bg(" WARNING "), "\n"),
-      font_black(paste0("  ", AMR_env$bullet_icon, " No ", guideline_coerced, " ", method_coerced, " breakpoints available for ",
-        suppressMessages(suppressWarnings(ab_name(ab_coerced, language = NULL, tolower = TRUE))),
-        " (", ab_coerced, ").")))
-
-    load_mo_uncertainties(metadata_mo)
-    return(rep(NA_sir_, nrow(df)))
-  }
 
   if (guideline_coerced %like% "EUCAST") {
     any_is_intrinsic_resistant <- FALSE
@@ -1067,6 +1064,18 @@ as_sir_method <- function(method_short,
   has_progress_bar <- !is.null(import_fn("progress_bar", "progress", error_on_fail = FALSE)) && nrow(df_unique) >= 10
   on.exit(close(p))
 
+  if (nrow(breakpoints) == 0) {
+    # apparently no breakpoints found
+    message(
+      paste0(font_rose_bg(" WARNING "), "\n"),
+      font_black(paste0("  ", AMR_env$bullet_icon, " No ", guideline_coerced, " ", method_coerced, " breakpoints available for ",
+                        suppressMessages(suppressWarnings(ab_name(unique(ab_coerced), language = NULL, tolower = TRUE))),
+                        " (", unique(ab_coerced), ")."), collapse = "\n"))
+
+    load_mo_uncertainties(metadata_mo)
+    return(rep(NA_sir_, nrow(df)))
+  }
+
   # run the rules (df_unique is a row combination per mo/ab/uti/host)
   for (i in seq_len(nrow(df_unique))) {
     p$tick()
@@ -1106,7 +1115,6 @@ as_sir_method <- function(method_short,
       suppressMessages(suppressWarnings(ab_name(ab_current, language = NULL, tolower = TRUE))),
       " (", ab_current, ")"
     )
-
 
     # gather all available breakpoints for current MO
     breakpoints_current <- breakpoints %pm>%
@@ -1151,7 +1159,7 @@ as_sir_method <- function(method_short,
           subset(host_match == TRUE)
       } else {
         # no breakpoint found for this host, so sort on mostly available guidelines
-        msgs <- c(msgs, paste0("No ", guideline_coerced, " breakpoints for ", font_bold(host_current), " available for ", ab_formatted, " in ", mo_formatted, " - using ", font_bold(breakpoints_current$host[1]), " breakpoints instead."))
+        msgs <- c(msgs, paste0("No breakpoints available for ", font_bold(host_current), " for ", ab_formatted, " in ", mo_formatted, " - using ", font_bold(breakpoints_current$host[1]), " instead."))
       }
     }
 

index.md

@@ -1,7 +1,5 @@
 # The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
 
-<img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120" />
-
 * Provides an **all-in-one solution** for AMR data analysis in a One Health approach
 * Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
 * Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
@@ -15,6 +13,8 @@
 <p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small></p>
 </div>
 
+<a href="./reference/clinical_breakpoints.html#response-from-clsi-and-eucast"><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120" /></a>
+
 ----
 
 ### Introduction

inst/tinytest/test-sir.R

@@ -292,6 +292,7 @@ expect_message(as.sir(data.frame(
 
 sir_history <- sir_interpretation_history(clean = TRUE)
 
+mics <- as.mic(2 ^ c(-4:6)) # 0.0625 to 64 in factors of 2
 vet <- data.frame(animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine", "horse", "cattle", "bird"),
                   PRA = mics,
                   FLR = mics,
@@ -313,12 +314,9 @@ expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA,
 sir_history <- sir_interpretation_history()
 expect_identical(sir_history$host,
                  c("cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
-                   "cattle", "cattle", "cattle", "cattle", "cattle", "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", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
-                   "cats"  , "cats"  , "cats"  , "dogs"  , "dogs"  , "dogs"  , "cattle", "cattle", "cattle", "cattle", "cats",
-                   "cats"  , "cats"  , "cats"  , "cats"  , "cats"  , "cats"))
+                   "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs", "dogs", "cattle", "cattle", "cats",
+                   "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
+                   "dogs", "cattle", "cattle", "cats", "cats"))
 
 # ECOFF -------------------------------------------------------------------
 

pkgdown/extra.css

@@ -89,13 +89,19 @@
   box-shadow: none !important;
 }
 
-.endorse_img {
-  width: 0% !important;
-}
-
 .template-home img.logo {
   width: 200px;
 }
+.template-home .endorse_img {
+  width: 150px;
+}
+
+.template-reference-index .section-desc {
+  font-style: italic;
+  text-align: justify;
+  font-size: 16px;
+}
+
 @media (max-width: 575.98px) {
   .template-home img.logo {
     width: 140px;