saveTreeMan: Save a TreeMan object in serialization format

In treeman: Phylogenetic Tree Manipulation Class and Methods

Description

TreeMan equivalent to save() but able to handle node matrices.

Usage

saveTreeMan(tree, file)

Arguments

tree	TreeMan object
file	file path

Details

It is not possible to use save() on TreeMan objects with node matrices. Node matrices are bigmemory matrices and are therefore outside the R environment, see bigmemory documentation for more information. Saving and loading a bigmemory matrix may cause memory issues in R and cause R to crash.

This function can safely store a TreeMan object with and without a node matrix. This function stores the tree using the serialization format and the node matrix as a hidden .csv. Both parts of the tree can be reloaded to an R environment with loadTreeMan(). The hidden node matrix filename is based on the file argument: file + _ndmtrx

Reading and writing trees with saveTreeMan() and loadTreeMan is faster than any of the other read and write functions.

See Also

loadTreeMan, readTree,writeTree, readTrmn, writeTrmn

Examples

library(treeman)
tree <- randTree(100, wndmtrx=TRUE)
saveTreeMan(tree, file='test.RData')
rm(tree)
tree <- loadTreeMan(file='test.RData')
file.remove('test.RData', 'testRData_ndmtrx')

treeman documentation built on July 8, 2020, 7:28 p.m.