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

man/as.sir.Rd

@@ -54,6 +54,7 @@ is_sir_eligible(x, threshold = 0.05)
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"),
   host = NULL,
+  verbose = FALSE,
   ...
 )
 
@@ -69,6 +70,7 @@ is_sir_eligible(x, threshold = 0.05)
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"),
   host = NULL,
+  verbose = FALSE,
   ...
 )
 
@@ -84,7 +86,8 @@ is_sir_eligible(x, threshold = 0.05)
   include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"),
-  host = NULL
+  host = NULL,
+  verbose = FALSE
 )
 
 sir_interpretation_history(clean = FALSE)
@@ -120,6 +123,8 @@ sir_interpretation_history(clean = FALSE)
 
 \item{host}{a vector (or column name) with \link{character}s to indicate the host. Only useful for veterinary breakpoints, as it requires \code{breakpoint_type = "animal"}. The values can be any text resembling the animal species, even in any of the 20 supported languages of this package. For foreign languages, be sure to set the language with \code{\link[=set_AMR_locale]{set_AMR_locale()}} (though it will be automatically guessed based on the system language).}
 
+\item{verbose}{a \link{logical} to indicate that all notes should be printed during interpretation of MIC values or disk diffusion values.}
+
 \item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
 \item{clean}{a \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results}