ecoPD: Ecologically-informed phylodiversity metrics
Version 0.2

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

AuthorJim Regetz, Marc Cadotte, Jonathan Davies
Date of publicationNone
MaintainerJim Regetz <regetz@nceas.ucsb.edu>
LicenseGPL
Version0.2
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ecoPD", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

aed: Abundance-weighted evolutionary distinctiveness
caterpillar: Caterpillar plots
ecoPD-package: Ecologically-informed phylodiversity metrics in R
pd: Calculate phylogenetic diversity
shannon: Shannon diversity index
siteBySpecies: Generate site-by-species matrix
Supertree: Reference plant phylogeny
See all...

All man pages Function index File listing

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

Functions

Families Man page
LookupTL Man page
Supertree Man page
abundance Man page Source code
abundance<- Man page
aed Man page
aed,phylo4com-method Man page
aed,phylo4d-method Man page
aed-methods Man page
caterpillar Man page Source code
communities Man page Source code
dijkstra Source code
eaed Man page
eaed,phylo4com-method Man page
eaed,phylo4d-method Man page
eaed-methods Man page
ecoPD Man page
ecoPD-package Man page
ed Man page
ed,phylo4com-method Man page
ed,phylo4d-method Man page
ed-methods Man page
eed Man page
eed,phylo4com-method Man page
eed,phylo4d-method Man page
eed-methods Man page
genera Man page
genera,phylo4-method Man page
genera,phylo4com-method Man page
genera-methods Man page
getMinTL Source code
getSubtrees Source code
haed Man page
haed,phylo4com-method Man page
haed,phylo4d-method Man page
haed-methods Man page
hed Man page
hed,phylo4com-method Man page
hed,phylo4d-method Man page
hed-methods Man page
iac Man page
iac,phylo4com-method Man page
iac,phylo4d-method Man page
iac-methods Man page
minTL Man page Source code
minTL<- Man page
pae Man page
pae,phylo4com-method Man page
pae,phylo4d-method Man page
pae-methods Man page
pairdist Man page Source code
pd Man page
pd,phylo4-method Man page
pd,phylo4com-method Man page
pd,phylo4d-method Man page
pd-methods Man page
phylo4,phylo4com-method Man page
phylo4com Man page
phylo4com,phylo,ANY-method Man page
phylo4com,phylo4,data.frame-method Man page
phylo4com,phylo4,matrix-method Man page
phylo4com,phylo4,numeric-method Man page
phylo4com,phylo4d,missing-method Man page
phylo4com-class Man page
phylo4com-methods Man page
phylo4d,phylo4com-method Man page
presence Man page Source code
richness Man page Source code
shannon Man page
shannon,phylo4com-method Man page
shannon,phylo4d-method Man page
shannon-methods Man page
simpson Man page
simpson,phylo4com-method Man page
simpson,phylo4d-method Man page
simpson-methods Man page
siteBySpecies Man page Source code
tipLength Man page Source code
value Man page
value,phylo4com-method Man page
value,phylo4d-method Man page
value-methods Man page
weeds Man page
weeds.data Man page
weeds.tree Man page
weightByAbund Source code

Files

data
data/weeds.data.rda
data/weeds.tree.rda
data/weeds.rda
R
R/genera.R
R/pd.R
R/phylo4com.R
R/utilities.R
R/community.R
R/simpson.R
R/plots.R
R/iac.R
R/indices.R
R/coerce.R
R/aed.R
R/shannon.R
R/pae.R
R/sysdata.rda
NAMESPACE
tests
tests/doRUnit.R
inst
inst/unitTests
inst/unitTests/runit.indices.R
inst/unitTests/Makefile
inst/unitTests/runit.phylo.R
inst/unitTests/runit.ecophylo.R
DESCRIPTION
man
man/aed.Rd
man/phylo4com.Rd
man/communities.Rd
man/pae.Rd
man/iac.Rd
man/weeds.Rd
man/Families.Rd
man/minTL.Rd
man/tipLength.Rd
man/pairdist.Rd
man/abundance.Rd
man/caterpillar.Rd
man/LookupTL.Rd
man/pd.Rd
man/phylo4com-class.Rd
man/ecoPD-package.Rd
man/siteBySpecies.Rd
man/Supertree.Rd
man/richness.Rd
man/coerce.Rd
man/genera.Rd
man/simpson.Rd
man/shannon.Rd
ecoPD documentation built on May 21, 2017, 1:18 a.m.

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