(v1.0.0.9005) info printing only in interactive mode

R/eucast_rules.R

@@ -197,7 +197,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #' }
 eucast_rules <- function(x,
                          col_mo = NULL,
-                         info = TRUE,
+                         info = interactive(),
                          rules = c("breakpoints", "expert", "other", "all"),
                          verbose = FALSE,
                          ...) {

R/first_isolate.R

@@ -148,7 +148,7 @@ first_isolate <- function(x,
                           type = "keyantibiotics",
                           ignore_I = TRUE,
                           points_threshold = 2,
-                          info = TRUE,
+                          info = interactive(),
                           include_unknown = FALSE,
                           ...) {
   

R/mdro.R

@@ -84,7 +84,7 @@
 mdro <- function(x,
                  guideline = "CMI2012",
                  col_mo = NULL,
-                 info = TRUE,
+                 info = interactive(),
                  pct_required_classes = 0.5,
                  combine_SI = TRUE,
                  verbose = FALSE,

R/misc.R

@@ -125,6 +125,7 @@ search_type_in_df <- function(x, type) {
       found <- colnames(x)[colnames(x) %like% "(urine|urinary)"][1]
     }
     if (!is.null(found)) {
+      # this column should contain logicals
       if (!is.logical(x[, found, drop = TRUE])) {
         message(red(paste0("NOTE: Column `", bold(found), "` found as input for `col_", type,
                            "`, but this column does not contain 'logical' values (TRUE/FALSE) and was ignored.")))

R/resistance_predict.R

@@ -121,7 +121,7 @@ resistance_predict <- function(x,
                                model = NULL,
                                I_as_S = TRUE,
                                preserve_measurements = TRUE,
-                               info = TRUE,
+                               info = interactive(),
                                ...) {
 
   if (nrow(x) == 0) {