@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-Version: 1.7.1

+Version: 1.7.2

 Authors@R: c(

 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),

@@ -1,3 +1,8 @@

+CHANGES IN VERSION 1.7.2

+------------------------

+ o bug fixed of parsing tree text in beast file <2016-10-31, Mon>

+   + https://github.com/GuangchuangYu/ggtree/issues/84

+

 CHANGES IN VERSION 1.7.1

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

  o xlim_tree layer and test <2016-10-31, Mon>

@@ -1,7 +1,7 @@

 ##' read beast output

 ##'

-##' 

+##'

 ##' @title read.beast

 ##' @param file beast file

 ##' @return \code{beast} object

@@ -16,7 +16,7 @@ read.beast <- function(file) {

     treetext <- read.treetext_beast(file)

     stats <- read.stats_beast(file)

     phylo <- read.nexus(file)

-    

+

     if (length(treetext) == 1) {

         obj <- BEAST(file, treetext, translation, stats, phylo)

     } else {

@@ -31,12 +31,12 @@ read.beast <- function(file) {

 BEAST <- function(file, treetext, translation, stats, phylo) {

     stats$node %<>% gsub("\"*'*", "", .)

-    

+

     fields <- sub("_lower|_upper", "", names(stats)) %>% unique

     fields %<>% `[`(.!="node")

-        

+

     phylo <- remove_quote_in_tree_label(phylo)

-        

+

     obj <- new("beast",

                fields      = fields,

                treetext    = treetext,

@@ -53,7 +53,7 @@ remove_quote_in_tree_label <- function(phylo) {

         phylo$node.label %<>% gsub("\"*'*", "", .)

     }

     if ( !is.null(phylo$tip.label)) {

-        phylo$tip.label %<>% gsub("\"*'*", "", .) 

+        phylo$tip.label %<>% gsub("\"*'*", "", .)

     }

     return(phylo)

 }

@@ -70,29 +70,18 @@ setMethod("get.fields", signature(object="beast"),

 read.treetext_beast <- function(file) {

     beast <- readLines(file)

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

-    ii <- grep("^tree ", beast)

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

-        ii <- grep("[Bb]egin trees;", beast)

-    }

-    

+

+    ii <- grep("[Bb]egin trees;", beast)

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

     jj <- jj[jj > max(ii)][1]

-

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

-    ## if (length(tree) > 1) {

-    ##     tree <- paste0(tree)

-    ## }

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

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

-    ##         sub("[^(]*", "", .)

-    

     jj <- c(ii[-1], jj)

+

     trees <- sapply(seq_along(ii), function(i) {

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

-        if (length(tree) > 1) {

-            tree <- paste0(tree)

-        }

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

+        tree <- tree[grep("\\s*[Tt]ree", tree)]

+        ## if (length(tree) > 1) {

+        ##     tree <- paste0(tree, collapse='')

+        ## }

         sub("[^(]*", "", tree)

     })

@@ -134,17 +123,17 @@ read.stats_beast_internal <- function(beast, tree) {

     phylo <- read.tree(text = tree2)

     tree2 <- add_pseudo_nodelabel(phylo, tree2)

-    

+

     ## node name corresponding to stats

     nn <- strsplit(tree2, split=",") %>% unlist %>%

         strsplit(., split="\\)") %>% unlist %>%

         gsub("\\(*", "", .) %>%

-        gsub("[:;].*", "", .) 

-    

+        gsub("[:;].*", "", .)

+

     phylo <- read.tree(text = tree2)

     root <- getRoot(phylo)

     nnode <- phylo$Nnode

-    

+

     ## phylo2 <- read.nexus(file)

     ## treeinfo <- fortify.phylo(phylo)

     ## treeinfo2 <- fortify.phylo(phylo2)

@@ -178,7 +167,7 @@ read.stats_beast_internal <- function(beast, tree) {

     ## ## convert nn to node that encoded in phylo2

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

-    

+

     ####################################################

     ##                                                ##

     ##  after doing it in the hard way                ##

@@ -194,7 +183,7 @@ read.stats_beast_internal <- function(beast, tree) {

     } else {

         node <- as.character(treeinfo$node[match(nn, treeinfo$label)])

     }

-    

+

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

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

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

@@ -204,7 +193,7 @@ read.stats_beast_internal <- function(beast, tree) {

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

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

-        

+

     stats2 <- lapply(stats, function(x) {

         y <- unlist(strsplit(x, ","))

         sidx <- grep("=\\{", y)

@@ -215,18 +204,18 @@ read.stats_beast_internal <- function(beast, tree) {

             flag <- TRUE

             SETS <- sapply(seq_along(sidx), function(k) {

                 p <- y[sidx[k]:eidx[k]]

-                gsub(".*=\\{", "", p) %>% gsub("\\}$", "", .) %>% list                

+                gsub(".*=\\{", "", p) %>% gsub("\\}$", "", .) %>% list

             })

             names(SETS) <- gsub("=.*", "", y[sidx])

             kk <- sapply(seq_along(sidx), function(k) sidx[k]:eidx[k]) %>% unlist

             y <- y[-kk]

         }

-        

-        

+

+

         name <- gsub("=.*", "", y)

         val <- gsub(".*=", "", y) %>% gsub("^\\{", "", .) %>%

-            gsub("\\}$", "", .) 

+            gsub("\\}$", "", .)

         if (flag) {

@@ -234,7 +223,7 @@ read.stats_beast_internal <- function(beast, tree) {

         } else {

             nn <- name

         }

-        

+

         res <- character(length(nn))

         names(res) <- nn

@@ -247,7 +236,7 @@ read.stats_beast_internal <- function(beast, tree) {

                 res[i+j] <- SETS[i]

             }

         }

-        

+

         return(res)

     })

@@ -270,7 +259,7 @@ read.stats_beast_internal <- function(beast, tree) {

         colnames(stats3) <- nn

     }

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

-    

+

     ## stats3$node <- node

     stats3$node <- names(stats)

     return(stats3)