phyndr v0.1.0

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Matches Tip and Trait Data

Use topological or taxonomic information to maximize the overlap of phylogenetic and comparative data.

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phyndr

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Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data is available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data.

In this package we have implemented a simple solution to increase the overlap while avoiding potential the biases introduced by imputing data. If some external topological or taxonomic information is available, this can be used to maximize the overlap between the data and the phylogeny. The algorithms in phyndr replace a species lacking data with a species that has data. This swap can be made because for those two species, all phylogenetic relationships are exactly equivalent.

This project was developed by Matthew Pennell, Rich FitzJohn, and Will Cornwell.

Installation

The easiest way to install phyndr is to use devtools

install.packages("devtools")
devtools::install_github("richfitz/phyndr")

Eventually, this will be moved to CRAN but for now it is only available on github.

Functions in phyndr

Name Description
phyndr_sample Sample one distinct set of tip labels from a phyndr tree
phyndr_n_distinct Number of distinct trees
phyndr_taxonomy Phyndr taxonomic
phyndr_combn Generate all distinct sets of tip labels from a phyndr tree
phyndr_topology phyndr for topo trees
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Details

Date 2015-08-04
License BSD_2_clause + file LICENSE
LazyData true
NeedsCompilation yes
Packaged 2015-08-12 20:29:34 UTC; mwpennell
Repository CRAN
Date/Publication 2015-08-18 21:04:16

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