Nothing
## ---- setup, echo=FALSE-------------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
## ---- eval = FALSE------------------------------------------------------------
# library(EvoPhylo)
## ---- include=FALSE-----------------------------------------------------------
devtools::load_all(".")
## -----------------------------------------------------------------------------
trees_file <- system.file("extdata", "ex_offset.trees", package = "EvoPhylo")
log_file <- system.file("extdata", "ex_offset.log", package = "EvoPhylo")
## Transform the trees to add a dummy tip
converted_trees <- offset.to.dummy.metadata(trees_file, log_file)
## ---- eval=FALSE--------------------------------------------------------------
# ## Transform the trees to add a dummy tip and save to file
# converted_trees <- offset.to.dummy.metadata(trees_file, log_file,
# output.file = "transformed_offset.trees")
## -----------------------------------------------------------------------------
## Find the example MCC tree from the package
tree_file <- system.file("extdata", "ex_offset.MCC.tre", package = "EvoPhylo")
## Then remove the dummy tip
final_tree <- drop.dummy.beast(tree_file)
## The output contains the final tree and the offset
final_tree$offset
final_tree$tree
## ---- eval=FALSE--------------------------------------------------------------
# ## Remove the dummy tip and save to file
# final_tree <- drop.dummy.beast(tree_file, output.file = "ex_final_mcc.tre")
## -----------------------------------------------------------------------------
## Find the example MCC tree from the package
tree_file_mb <- system.file("extdata", "tree_mb_dummy.tre", package = "EvoPhylo")
## Remove the dummy tip and save to file
final_tree_mb <- drop.dummy.mb(tree_file_mb, output.file = "tree_mb_final.tre")
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