Minor

R/interface.R

@@ -512,32 +512,20 @@ HaldDP <- R6::R6Class(
     {
       if (!is.data.frame(k))
         stop("k must be a data frame.")
-      k <- na.omit(k)
-
       if (!all(c("Value", "Source", "Time") %in% colnames(k)))
         stop("k must have columns named Value, Source and Time.")
-
-      k$Source <- as.factor(k$Source)
-      k$Time <- as.factor(k$Time)
-
-      if (all(paste(gtools::mixedsort(unique(k$Time))) != private$namesTimes))
+      if (!setequal(unique(k$Time), private$namesTimes))
         stop("The times in the Time column of k must be the same as those in the data.")
-      if (all(paste(gtools::mixedsort(unique(k$Source))) != private$namesSources))
+      if (!setequal(unique(k$Source), private$namesSources))
         stop("The sources in the Source column of k must be the same as those in the data.")
 
-      if (dim(unique(k[, c("Time", "Source")]))[1] != (private$nTimes * private$nSources))
-        stop("k must have a single number for each time, source combination.")
-
-      ## check all data values are positive, numeric, and whole numbers
-      if (!all(is.finite(k$Value)) |
-          !all(k$Value >= 0) | !all(k$Value <= 1))
-        stop("All prevalence values must be numbers between 0 and 1.")
-
       private$k = tryCatch(
         acast(k, Source ~ Time, value.var = 'Value'),
         condition = function(c)
-          stop('Malformed k.  Check Source/Time combinations for regularity.')
+          stop('k must have a single number for each time, source combination. Check Source/Time combinations for regularity.')
       )
+      if (!all(is.finite(private$k) & private$k >=0 & private$k <=1))
+        stop("Prevalence value outside [0,1].  Check each Source/Time combination has a value.")
     },
     set_a_q = function(a_q)
     {
@@ -722,9 +710,9 @@ HaldDP <- R6::R6Class(
         inits$r$Source <- as.factor(inits$r$Source)
         inits$r$Time <- as.factor(inits$r$Time)
 
-        if (!all(paste(gtools::mixedsort(unique(inits$r$Type))) == private$namesTypes) |
-            !all(paste(gtools::mixedsort(unique(inits$r$Time))) == private$namesTimes) |
-            !all(paste(gtools::mixedsort(unique(inits$r$Source))) == private$namesSources) |
+        if (!setequal(unique(inits$r$Type), private$namesTypes) |
+            !setequal(unique(inits$r$Time), private$namesTimes) |
+            !setequal(unique(inits$r$Source), private$namesSources) |
             dim(inits$r)[1] != (private$nTypes * private$nSources * private$nTimes))
           stop(
             "inits$r must be a data frame with columns called Type, Source, Time and Value with one row per combination of type, source and time."