allow multi-furcating starting trees, no RF warnings for multi-furcat…

…ing trees
KlausVigo · Feb 13, 2019 · 1223171 · 1223171
1 parent 487c960
commit 1223171
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/R/parsimony.R b/R/parsimony.R
@@ -522,7 +522,7 @@ pratchet <- function(data, start = NULL, method = "fitch", maxit = 1000,
     while (length(trees) > 0) {
 #      rf <- sapply(trees, RF.dist, res, FALSE)
       class(trees) <- "multiPhylo"
-      rf <- RF.dist(res, trees, FALSE)
+      rf <- suppressWarnings( RF.dist(res, trees, FALSE) )
 # end new code
       if (any(rf == 0)) trees <- trees[-which(rf == 0)]
       if (length(trees) > 0) {
@@ -542,6 +542,9 @@ pratchet <- function(data, start = NULL, method = "fitch", maxit = 1000,
     if(is.null(start)) start <- optim.parsimony(nj(dist.hamming(data)), data,
                                         trace = trace, method = method,
                                         rearrangements = rearrangements, ...)
+    else{
+      if(!is.binary(start)) start <- multi2di(start)
+    }
     tree <- start
     data <- subset(data, tree$tip.label)
     attr(tree, "pscore") <- parsimony(tree, data, method = method, ...)