@@ -1,5 +1,8 @@

 CHANGES IN VERSION 1.1.4

 ------------------------

+ o better performance of parsing beast tree  <2015-05-11, Mon>

+   + support beast tree begin with 'tree tree_1 = ' and other forms.

+   + support file that only contains one evidence for some of the nodes/tips

  o update add_colorbar to auto determine the position <2015-05-04, Mon>

  o add_colorbar function <2015-04-30, Thu>

@@ -158,14 +158,22 @@ setMethod("get.fields", signature(object="beast"),

 read.treetext_beast <- function(file) {

     beast <- readLines(file)

     ii <- grep("tree TREE1\\s+=", beast)

+    if (length(ii) == 0) {

+        ii <- grep("begin trees;", beast)

+    }

+    

     jj <- grep("[Ee]nd;", beast)

     jj <- jj[jj > ii][1]

     tree <- beast[ii:(jj-1)]

     if (length(tree) > 1) {

         tree <- paste0(tree)

     }

-    tree %<>% sub("tree TREE1\\s+=\\s+\\[&R\\]\\s+", "", .)

-    tree %<>% sub("[^(]*", "", .)

+    ## tree %<>% sub("tree TREE1\\s+=\\s+\\[&R\\]\\s+", "", .)

+    ## tree %<>% sub("[^(]*", "", .)

+    tree %<>% sub("[^=]+=", "", .) %>%

+        sub("\\s+\\[&R\\]\\s+", "", .) %>%

+            sub("[^(]*", "", .)

+

     return(tree)

 }

@@ -258,10 +266,13 @@ read.stats_beast <- function(file) {

                 root:(root+nnode-1))

     node <- label2[match(nn, treeinfo$label)]

+    ## stats <- unlist(strsplit(tree, "\\["))[-1]

+    ## stats <- sub(":.+$", "", stats

+    stats <- strsplit(tree, ":") %>% unlist

+    names(stats) <- node

+    stats <- stats[grep("\\[", stats)]

+    stats <- sub("[^\\[]+\\[", "", stats)

-    

-    stats <- unlist(strsplit(tree, "\\["))[-1]

-    stats <- sub(":.+$", "", stats)

     stats <- sub("^&", "", stats)

     stats <- sub("];*$", "", stats)

@@ -323,9 +334,17 @@ read.stats_beast <- function(file) {

     }))

     stats3 <- as.data.frame(stats3)

+    if (nrow(stats3) == 1) {

+        ## only has one evidence

+        ## transpose

+        stats3 <- data.frame(X=unlist(stats3[1,]))

+        colnames(stats3) <- nn

+    }

     colnames(stats3) <- gsub("(\\d+)%", "0.\\1", colnames(stats3))

-    stats3$node <- node

+    ## stats3$node <- node

+    stats3$node <- names(stats)

     return(stats3)

 }

+

@@ -185,9 +185,14 @@ fortify.beast <- function(model, data,

     idx   <- match(df$node, stats$node)

     stats <- stats[idx,]

-    stats <- stats[,colnames(stats) != "node"]

+    cn_stats <- colnames(stats)

+    stats <- stats[, cn_stats != "node"]

     df <- cbind(df, stats)

+    if (is(stats, "data.frame") == FALSE) {

+        colnames(df)[colnames(df) == "stats"] <- cn_stats[cn_stats != "node"]

+    }

+    

     df <- scaleY(phylo, df, yscale, layout, ...)

     if (time_scale) {