README.md

In stoufferlab/phyloint: Phylogenetic components of food-web intervality

phyloint

This R package provides functions to calculate properties related to food-web intervality (Stouffer et al. 2006; Eklöf et al. 2013) while mixing species phylogenies with interaction matrices as described in:

Anna Eklöf and Daniel B. Stouffer (2016) "The phylogenetic component of food-web structure and intervality." Theoretical Ecology 9(1) 107-115 doi:10.1007/s12080-015-0273-9.

How to install directly from github

require(devtools)
install_github("stoufferlab/phyloint")

How to conduct key analyses in Eklöf & Stouffer

require(ape)
require(phyloint)

# load in some sample data
data(eklof)

# use steepest descent to minimize the number of phylogenetic gaps in the data
gaps.phylo <- minimize.phylo.gaps.sd(adj=eklof$network, phy=eklof$tree)

# calculate trait values when accounting for the expected covariance between species
corrected.traits <- phylo.correction(traits=eklof$traits, phy=eklof$tree)

# produce the overlap matrices based on the phylogentically corrected trait values 
overlap.matrices <- build.matrix.from.traits(eklof$network, corrected.traits)

# calculate the overlap values for all different combinations of traits and produce a result table 
combinations <- overlap.combinations(eklof$network, overlap.matrices)

stoufferlab/phyloint documentation built on May 30, 2019, 7:23 p.m.