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Methods in Comparative Plant Population Ecology, Second Edition$

David J. Gibson

Print publication date: 2014

Print ISBN-13: 9780199671465

Published to Oxford Scholarship Online: January 2015

DOI: 10.1093/acprof:oso/9780199671465.001.0001

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(p.247) Appendix

(p.247) Appendix

Source:
Methods in Comparative Plant Population Ecology, Second Edition
Publisher:
Oxford University Press

R Packages for Analysis of Plant Population Ecology Data

R (R Development Core Team 2011) is a freely available, open source statistical environment that is increasing in popularity and use. While many conventional statistical analyses can be accomplished with ‘standard’ R modules, a large number of packages have been developed for implementing specific analyses. Be warned, R packages are ‘a bit of a moving feast’ (Rob Freckleton, personal communication)! R packages that are useful for plant population ecology are provided here. Most are available for free download from the Comprehensive R Archive Network at 〈http://cran.r-project.org/web/packages/〉. If you are not familiar with R then there is a cottage industry of books and online sources available to help including Bolker (2008), Beckerman and Petchey (2012), and Crawley (2012), and R manuals available at 〈http://www.R-project.org〉 (see Chapter 7 for more details). (p.248)

Package name

Application

Reference and description and download site if not CRAN

Population dynamics

demoniche

Simulates stochastic population dynamics in multiple populations of a species

Nenzén et al. (2012), 〈https://r-forge.r-project.org/projects/demoniche/

IPMpack

Suite of demographic tools for running IPMs

Metcalf et al. (2013). See also the blog at 〈http://ipmpack.r-forge.r-project.org/〉 and R code in the appendix of Merow et al. (2014).

popbio

Basic analyses of demographic models, including matrix models and PVA

Stubben and Milligan (2007)

popdemo

Novel methods for analysis of population projection models

Stott et al. (2012)

PVAClone

PVA with data cloning

Nadeem and Lele (2012)

survival

Survival analyses and tests

Additional R packages are listed at 〈http://cran.r-project.org/web/views/survival.html

Spatial patterns

ade4

Multivariate methods including ordinations and spatial pattern analysis

Thioulouse et al. (1997), 〈http://pbil.univ-lyon1.fr/ADE-4/home.php?lang = eng〉

betapart

Spatial patterns of beta diversity

Baselga and Orme (2012)

circular

Circular statistics

Pewsey et al. (2013)

deldir

Delaunay triangulation and Dirichlet or Voronoi tessellations

Spatstat

Analysis of spatial point patterns

Baddeley and Turner (2005)

spdep

Spatial regression analysis including spatial correlograms based on Moran’s I and Geary’s c

Phylogenetics

ape

Comparative phylogenetics, PICS

Paradis (2006), 〈http://ape.mpl.ird.fr/?

CRAN Task View: phylogenetics, especially comparative methods

Listing and description of R packages for comparative phylogenetic methods

http://cran.r-project.org/web/views/Phylogenetics.html

caper

Comparative analyses of phylogenetics and evolution in R

Orme et al (2012)

phytools

Methods for comparative phylogenetic biology, including tree inference, phylogeny input/output, plotting, and manipulation

Revell (2012)

picante

Package for analysing the phylogenetic and trait diversity of ecological communities

Kembel et al. (2010)

treebase

Provides access to phylogenetic data in the TreeBASE repository

Boettiger and Lang (2012)

Mixed models and related Statistics

abc

Approximate Bayesian computation for parameter inference and model selection under complex models

Csilléry et al. (2012)

coxme

Mixed effects Cox models containing Gaussian random effects (frailty models)

lme4

Linear mixed effects models, GLMMs

Bolker et al. (2009)

MCMCglmm

Markov chain Monte Carlo GLMMs

NCF

Spatial non-parametric covariance functions

nlme

Non-linear mixed effects models

odprism

Optimal design and performance of random intercept and slope models. Investigates accuracy, precision, and power of regression models used for quantifying reaction norms

van de Pol (2012)

pamm

Power analysis with mixed models. Measuring individual differences in reaction norms

Martin et al. (2011) (and corrections in Erratum)

Miscellaneous

bipartite

Analysis of patterns in ecological webs, e.g. pollinator networks or seed disperser networks

Dormann et al. (2008)

OpenMx

Advanced structural equation modelling

Boker et al. (2011), 〈http://openmx.psyc.virginia.edu/

pwr

Basic functions for power analysis

Champely (2009)

qtl

QTL mapping and LOD plots

Broman et al. (2003)

sem

Structural equation modelling

Fox (2006)

taxize

Taxonomic information and tasks including verification, hierarchies, and names

VEGAN

Multivariate methods including ordinations

Dixon (2009), 〈http://vegan.r-forge.r-project.org/

IPM, integral projection model; PVA, population viability analysis; PICS, phylogenetically independent contrasts; GLMMs, generalized linear mixed models; QTL, quantitative trait locus; LOD, log of the odds ratio.