cleanup

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.0.0.9034
+Version: 2.0.0.9035
 Date: 2023-07-11
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.0.0.9034
+# AMR 2.0.0.9035
 
 ## New
 * Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for `as.sir()`. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations

R/ab.R

@@ -548,7 +548,7 @@ pillar_shaft.ab <- function(x, ...) {
   
   # add the names to the drugs as mouse-over!
   if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
-    out[!is.na(x)] <- font_url(url = ab_name(x[!is.na(x)], language = NULL),
+    out[!is.na(x)] <- font_url(url = ab_name(x[!is.na(x)]),
                                txt = out[!is.na(x)])
   }
   

R/disk.R

@@ -70,7 +70,7 @@
 #' # interpret whole data set, pretend to be all from urinary tract infections:
 #' as.sir(df, uti = TRUE)
 as.disk <- function(x, na.rm = FALSE) {
-  meet_criteria(x, allow_class = c("disk", "character", "numeric", "integer"), allow_NA = TRUE)
+  meet_criteria(x, allow_NA = TRUE)
   meet_criteria(na.rm, allow_class = "logical", has_length = 1)
 
   if (!is.disk(x)) {

R/mo.R

@@ -630,7 +630,7 @@ pillar_shaft.mo <- function(x, ...) {
   
   # add the names to the bugs as mouse-over!
   if (tryCatch(isTRUE(getExportedValue("ansi_has_hyperlink_support", ns = asNamespace("cli"))()), error = function(e) FALSE)) {
-    out[!x %in% c("UNKNOWN", NA)] <- font_url(url = mo_name(x[!x %in% c("UNKNOWN", NA)], language = NULL, keep_synonyms = TRUE),
+    out[!x %in% c("UNKNOWN", NA)] <- font_url(url = mo_name(x[!x %in% c("UNKNOWN", NA)], keep_synonyms = TRUE),
                                               txt = out[!x %in% c("UNKNOWN", NA)])
   }
   

R/sir.R

@@ -741,8 +741,10 @@ as_sir_method <- function(method_short,
   check_reference_data(reference_data, .call_depth = -2)
   meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1, .call_depth = -2)
 
+  guideline_coerced <- get_guideline(guideline, reference_data)
+  
   if (message_not_thrown_before("as.sir", "sir_interpretation_history")) {
-    message_("Run `sir_interpretation_history()` afterwards to retrieve a logbook with all the details of the breakpoint interpretations.\n\n")  
+    message_("Run `sir_interpretation_history()` afterwards to retrieve a logbook with all the details of the breakpoint interpretations. Note that some microorganisms might not have breakpoints for each antimicrobial drug in ", guideline_coerced, ".\n\n")  
   }
   
   # for dplyr's across()
@@ -798,7 +800,6 @@ as_sir_method <- function(method_short,
   }
   # be sure to take current taxonomy, as the 'clinical_breakpoints' data set only contains current taxonomy
   mo <- suppressWarnings(suppressMessages(as.mo(mo, keep_synonyms = FALSE, info = FALSE)))
-  guideline_coerced <- get_guideline(guideline, reference_data)
   if (is.na(ab)) {
     message_("Returning NAs for unknown antibiotic: '", font_bold(ab.bak),
       "'. Rename this column to a valid name or code, and check the output with `as.ab()`.",
@@ -919,7 +920,7 @@ as_sir_method <- function(method_short,
       paste0(font_rose_bg(" WARNING "), "\n"),
       font_black(paste0("  ", AMR_env$bullet_icon, " No ", method_coerced, " breakpoints available for ",
         suppressMessages(suppressWarnings(ab_name(ab_coerced, language = NULL, tolower = TRUE))),
-        " (", ab_coerced, ")")))
+        " (", ab_coerced, ").")))
     
     load_mo_uncertainties(metadata_mo)
     return(rep(NA_sir_, nrow(df)))
@@ -1017,8 +1018,11 @@ as_sir_method <- function(method_short,
     } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_coerced)) {
       # breakpoints for multiple body sites available
       msgs <- c(msgs, paste0("Multiple breakpoints available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, "."))
+    } else if (nrow(breakpoints_current) == 0) {
+      # # do not note - it's already in the header before the interpretation starts
+      next
     }
-
+    
     # first check if mo is intrinsic resistant
     if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_current, ab_coerced) %in% AMR_env$intrinsic_resistant) {
       msgs <- c(msgs, paste0("Intrinsic resistance applied for ", ab_formatted, " in ", mo_formatted, ""))
@@ -1031,10 +1035,10 @@ as_sir_method <- function(method_short,
       breakpoints_current <- breakpoints_current[1L, , drop = FALSE]
 
       if (any(breakpoints_current$mo == "UNKNOWN", na.rm = TRUE) | any(breakpoints_current$ref_tbl %like% "PK.*PD", na.rm = TRUE)) {
-        msgs <- c(msgs, "(Some) PK/PD breakpoints were applied - use `include_PKPD = FALSE` to prevent this")
+        msgs <- c(msgs, "Some PK/PD breakpoints were applied - use `include_PKPD = FALSE` to prevent this")
       }
       if (any(breakpoints_current$site %like% "screen", na.rm = TRUE) | any(breakpoints_current$ref_tbl %like% "screen", na.rm = TRUE)) {
-        msgs <- c(msgs, "(Some) screening breakpoints were applied - use `include_screening = FALSE` to prevent this")
+        msgs <- c(msgs, "Some screening breakpoints were applied - use `include_screening = FALSE` to prevent this")
       }
 
       if (method == "mic") {