ecoPD: Ecologically-informed phylodiversity metrics

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A set of metrics and functions for combining ecological and phylogenetic information

Author
Jim Regetz, Marc Cadotte, Jonathan Davies
Date of publication
None
Maintainer
Jim Regetz <regetz@nceas.ucsb.edu>
License
GPL
Version
0.2

View on R-Forge

Man pages

abundance
Get or set species abundances
aed
Abundance-weighted evolutionary distinctiveness
caterpillar
Caterpillar plots
coerce
Extract phylo4com phylogenies
communities
List communities
ecoPD-package
Ecologically-informed phylodiversity metrics in R
Families
Plant family lookup vector
genera
Extract genus names
iac
Imbalance of Abundances at the Clade level
LookupTL
Family-based lookup table for minimum tip lengths
minTL
Get or set minimum tip lengths
pae
Phylogenetic-Abundance Evenness
pairdist
Calculate pairwise distances between nodes
pd
Calculate phylogenetic diversity
phylo4com
Create community phylogenies object
phylo4com-class
phylo4com class
richness
Calculate richness for each community
shannon
Shannon diversity index
simpson
Phylogenetic Simpson's diversity index
siteBySpecies
Generate site-by-species matrix
Supertree
Reference plant phylogeny
tipLength
Calculate distance to tips from ancestors
weeds
Weed phylogeny and community data

Files in this package

ecoPD
ecoPD/data
ecoPD/data/weeds.data.rda
ecoPD/data/weeds.tree.rda
ecoPD/data/weeds.rda
ecoPD/R
ecoPD/R/genera.R
ecoPD/R/pd.R
ecoPD/R/phylo4com.R
ecoPD/R/utilities.R
ecoPD/R/community.R
ecoPD/R/simpson.R
ecoPD/R/plots.R
ecoPD/R/iac.R
ecoPD/R/indices.R
ecoPD/R/coerce.R
ecoPD/R/aed.R
ecoPD/R/shannon.R
ecoPD/R/pae.R
ecoPD/R/sysdata.rda
ecoPD/NAMESPACE
ecoPD/tests
ecoPD/tests/doRUnit.R
ecoPD/inst
ecoPD/inst/unitTests
ecoPD/inst/unitTests/runit.indices.R
ecoPD/inst/unitTests/Makefile
ecoPD/inst/unitTests/runit.phylo.R
ecoPD/inst/unitTests/runit.ecophylo.R
ecoPD/DESCRIPTION
ecoPD/man
ecoPD/man/aed.Rd
ecoPD/man/phylo4com.Rd
ecoPD/man/communities.Rd
ecoPD/man/pae.Rd
ecoPD/man/iac.Rd
ecoPD/man/weeds.Rd
ecoPD/man/Families.Rd
ecoPD/man/minTL.Rd
ecoPD/man/tipLength.Rd
ecoPD/man/pairdist.Rd
ecoPD/man/abundance.Rd
ecoPD/man/caterpillar.Rd
ecoPD/man/LookupTL.Rd
ecoPD/man/pd.Rd
ecoPD/man/phylo4com-class.Rd
ecoPD/man/ecoPD-package.Rd
ecoPD/man/siteBySpecies.Rd
ecoPD/man/Supertree.Rd
ecoPD/man/richness.Rd
ecoPD/man/coerce.Rd
ecoPD/man/genera.Rd
ecoPD/man/simpson.Rd
ecoPD/man/shannon.Rd