## ----style, echo=FALSE, results="asis", message=FALSE-------------------- knitr::opts_chunk$set(tidy = FALSE, message = FALSE) ## ----echo=FALSE, results="hide", message=FALSE--------------------------- library('jsonlite') library("treeio") ## ----comment=NA---------------------------------------------------------- nhxfile <- system.file("extdata/NHX", "phyldog.nhx", package="treeio") nhx <- read.nhx(nhxfile) # write.beast(nhx, file = "phyldog.tree") write.beast(nhx) ## ----comment=NA---------------------------------------------------------- mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio") ml <- read.codeml_mlc(mlcfile) # write.beast(ml, file = "codeml.tree") write.beast(ml) ## ----comment=NA---------------------------------------------------------- phylo <- as.phylo(nhx) ## print the newick text write.tree(phylo) N <- Nnode2(phylo) fake_data <- data_frame(node = 1:N, fake_trait = rnorm(N), another_trait = runif(N)) fake_tree <- treedata(phylo = phylo, data = fake_data) write.beast(fake_tree) ## ------------------------------------------------------------------------ ## combine tree object with data tree_with_data <- full_join(nhx, fake_data, by = "node") tree_with_data ## merge two tree object tree2 <- merge_tree(nhx, fake_tree) tree2 identical(tree_with_data, tree2) ## ----comment=NA---------------------------------------------------------- write.beast(tree2) ## ------------------------------------------------------------------------ outfile <- tempfile(fileext = ".tree") write.beast(tree2, file = outfile) read.beast(outfile) ## ----comment=NA---------------------------------------------------------- write.jtree(tree2) ## ----comment=NA---------------------------------------------------------- jtree_file <- tempfile(fileext = '.jtree') write.jtree(tree2, file = jtree_file) jsonlite::fromJSON(jtree_file) ## ------------------------------------------------------------------------ read.jtree(jtree_file)