getPrevalence, NA values

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.11.3
+Version: 1.11.4
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "[email protected]",

NEWS

@@ -97,3 +97,4 @@ Changes in version 1.9.x
 Changes in version 1.11.x
 + loadFromMetaphlan: support strain rank
 + agglomerateByRank: agglomerate tree fix
++ getPrevalence: bugfix, if assay contains NA values, it does not end up to NA anymore.

R/getPrevalence.R

@@ -204,12 +204,15 @@ setMethod("getPrevalence", signature = c(x = "ANY"),
             stop("'sort' must be TRUE or FALSE.", call. = FALSE)
         }
         #
-
         if (include_lowest) {
             prev <- x >= detection
         } else {
             prev <- x > detection
         }
+        # If there were taxa with NA values, convert NA values to FALSE -->
+        # not detected.
+        prev[ is.na(prev) ] <- FALSE
+        # Calculate prevalence for each taxa
         prev <- rowSums(prev)
         # Always return prevalence as a relative frequency.
         # This helps to avoid confusion with detection limit