@@ -1,6 +1,6 @@

 Package: mia

 Type: Package

-Version: 1.13.39

+Version: 1.13.40

 Authors@R:

     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),

              email = "felix.gm.ernst@outlook.com",

@@ -311,20 +311,25 @@ NULL

             call. = FALSE)

     }

-    # Subset and rename rows of the assay to correspond node_labs

+    # Subset rows of the assay to correspond node_labs (if there are any NAs

+    # in node labels)

     if( !is.null(node.label) && any(is.na(node.label)) ){

-        # Subset

-        if( !any(is.na(node.label)) ){

-            warning(

-                "The tree named does not include all the ",

-                "rows. 'x' is subsetted.", call. = FALSE)

-            mat <- mat[ !is.na(node.label), ]

-            node.label <- node.label[ !is.na(node.label) ]

-        }

-        # Rename

+        warning(

+            "The tree named does not include all the ",

+            "rows. 'x' is subsetted.", call. = FALSE)

+        mat <- mat[ !is.na(node.label), ]

+        node.label <- node.label[ !is.na(node.label) ]

+    }

+    # If there are node labels (any TreeSE should have because they are rowLinks

+    # by default), rename the features in matrix to match with labels found in

+    # tree.

+    if( !is.null(node.label) ){

         rownames(mat) <- node.label

     }

-    # To calculate faith, the assay must have rownames

+    

+    # To calculate faith, the assay must have rownames. TreeSE has always

+    # rownames at this point, but if the object is SE, it might be that it is

+    # missing rownames.

     if( is.null(rownames(mat)) ){

         stop("'x' must have rownames.", call. = FALSE)

     }