(v2.1.1.9053) add verbose to as.sir(), unit test fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9052
-Date: 2024-06-16
+Version: 2.1.1.9053
+Date: 2024-06-17
 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

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9052
+# AMR 2.1.1.9053
 
 *(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/aa_helper_functions.R

@@ -1340,23 +1340,24 @@ progress_ticker <- function(n = 1, n_min = 0, print = TRUE, clear = TRUE, title
     }
     set_clean_class(pb, new_class = "txtProgressBar")
   } else if (n >= n_min) {
-    # use `progress`, which also has a timer
+    title <- trimws2(title)
+    if (title != "") {
+      title <- paste0(title, " ")
+    }
     progress_bar <- import_fn("progress_bar", "progress", error_on_fail = FALSE)
     if (!is.null(progress_bar)) {
       # so we use progress::progress_bar
       # a close()-method was also added, see below for that
-      title <- trimws2(title)
-      if (title != "") {
-        title <- paste0(title, " ")
-      }
       pb <- progress_bar$new(
+        show_after = 0,
         format = paste0(title,
                         ifelse(only_bar_percent == TRUE, "[:bar] :percent", "[:bar] :percent (:current/:total,:eta)")),
         clear = clear,
         total = n
       )
     } else {
-      # use base R
+      # use base R's txtProgressBar
+      cat(title, "\n", sep = "")
       pb <- utils::txtProgressBar(max = n, style = 3)
       pb$tick <- function() {
         pb$up(pb$getVal() + 1)

R/zzz.R

@@ -58,14 +58,15 @@ AMR_env$av_previously_coerced <- data.frame(
 AMR_env$sir_interpretation_history <- data.frame(
   datetime = Sys.time()[0],
   index = integer(0),
-  ab_user = character(0),
-  mo_user = character(0),
+  ab_given = character(0),
+  mo_given = character(0),
+  host_given = character(0),
   ab = set_clean_class(character(0), c("ab", "character")),
   mo = set_clean_class(character(0), c("mo", "character")),
+  host = character(0),
   method = character(0),
   input = double(0),
   outcome = NA_sir_[0],
-  host = character(0),
   notes = character(0),
   guideline = character(0),
   ref_table = character(0),

inst/tinytest/test-sir.R

@@ -179,7 +179,7 @@ expect_equal(suppressMessages(
 
 expect_true(is.data.frame(sir_interpretation_history(clean = FALSE)))
 expect_true(is.data.frame(sir_interpretation_history(clean = TRUE)))
-expect_true(is.null(sir_interpretation_history()))
+expect_true(NROW(sir_interpretation_history()) == 0)
 
 # cutoffs at MIC = 8
 expect_equal(
@@ -319,10 +319,9 @@ 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", "cattle", "dogs", "dogs", "cattle", "cattle", "cats",
-                   "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
-                   "dogs", "cattle", "cattle", "cats", "cats"))
+                 c("poultry", "cattle", "poultry", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs", "horse", "dogs", "horse", "horse", "horse", "cattle", "horse", "cattle", "cattle", "cattle", 
+                   "cattle", "cattle", "cattle", "cattle", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "cattle", "dogs", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cats", "cats", 
+                   "cats", "cats", "cats", "cats", "cattle", "cats", "cattle", "cattle", "cats", "cattle", "cats", "cattle", "cattle"))
 
 # ECOFF -------------------------------------------------------------------