dealing with NA in summary for runBenchmarks

florianhartig · Nov 13, 2024 · 1166e1d · 1166e1d
1 parent be7efc8
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diff --git a/DHARMa/NEWS.md b/DHARMa/NEWS.md
@@ -1,5 +1,12 @@
 NOTE: for more news about the package, see https://github.com/florianhartig/DHARMa/releases
 
+# DHARMa 0.4.8
+
+
+## Minor changes
+
+* fixing error in runBenchmarks
+
 
 # DHARMa 0.4.7
 

diff --git a/DHARMa/R/runBenchmarks.R b/DHARMa/R/runBenchmarks.R
@@ -96,17 +96,21 @@ runBenchmarks <- function(calculateStatistics, controlValues = NULL, nRep = 10,
   summary = list()
 
   # function for aggregation
-  aggreg <- function(f) {
+  aggreg <- function(f,...) {
     ret <- aggregate(x[,- c(ncol(x) - 1, ncol(x))], by = list(x$controlValues), f)
     colnames(ret)[1] = "controlValues"
     return(ret)
   }
 
-  sig <- function(x) mean(x < alpha)
+  if(length(is.na(x)>0)){
+    warning("NA values in the output, this might be a problem for the summaries.")
+  }
+
+  sig <- function(x) mean(x < alpha, na.rm=T)
   isUnif <- function(x) ks.test(x, "punif")$p.value
 
   summary$propSignificant = aggreg(sig)
-  summary$meanP = aggreg(mean)
+  summary$meanP = aggreg(mean, na.rm=T)
   summary$isUnifP = aggreg(isUnif)
 
   out = list()