GUILDS: Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure
Version 1.3

A collection of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).

Browse man pages Browse package API and functions Browse package files

AuthorThijs Janzen [aut, cre], Bart Haegeman [ctb], Franck Jabot [ctb], Jerome Chave [ctb]
Date of publication2016-09-26 21:21:03
MaintainerThijs Janzen <thijsjanzen@gmail.com>
LicenseGPL-2
Version1.3
URL https://github.com/thijsjanzen/GUILDS
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("GUILDS")

Man pages

expected.SAD: Calculate the expected species abundance distribution of the...
expected.SAD.Guilds: Estimate the expected species abundance distribution of both...
expected.SAD.Guilds.Conditional: Estimate the expected species abundance distribution of both...
generate.ESF: Generate community data under the standard neutral model of...
generate.Guilds: Generate Artificial data under the GUILDS model
generate.Guilds.Cond: Generate Artificial data under the GUILDS model, conditioned...
GUILDS-internal: Internal Guilds functions
GUILDS-package: Package implementing the Guilds sampling formula for the...
logLikelihood.ESF: Likelihood of the Etienne sampling formula
logLikelihood.Guilds: Likelihood of the Guilds sampling formula
logLikelihood.Guilds.Conditional: Likelihood of the Guilds sampling formula, conditional on...
maxLikelihood.ESF: Maximization of the loglikelihood given the standard Neutral...
maxLikelihood.Guilds: Maximization of the loglikelihood under the Guilds Model.
maxLikelihood.Guilds.Conditional: Maximization of the loglikelihood under the Guilds Model,...
preston_plot: Barplot in Preston style of an abundance dataset

Functions

GUILDS Man page
calcKDA Man page Source code
calc_conditional Man page Source code
calc_sum_kda Man page Source code
conditional.LogLik Man page Source code
draw_local Man page Source code
draw_local_cond Man page Source code
esf_local Man page Source code
evaluateLogLik Man page Source code
evaluate_cond_lik Man page Source code
expected.SAD Man page Source code
expected.SAD.Guilds Man page Source code
expected.SAD.Guilds.Conditional Man page Source code
generate.ESF Man page Source code
generate.Guilds Man page Source code
generate.Guilds.Cond Man page Source code
generate.ZSM Man page Source code
getpx Man page Source code
localComm Man page Source code
logLikelihood.ESF Man page Source code
logLikelihood.Guilds Man page Source code
logLikelihood.Guilds.Conditional Man page Source code
logLikguilds Man page Source code
maxLikelihood.ESF Man page Source code
maxLikelihood.Guilds Man page Source code
maxLikelihood.Guilds.Conditional Man page Source code
octave_index Man page Source code
pm_sad Man page Source code
pm_sadaux Man page Source code
polyaeggenberger Man page Source code
preston_plot Man page Source code
preston_sort Man page Source code
rho Man page Source code
simplex Man page Source code
sort_aux Man page Source code

Files

inst
inst/doc
inst/doc/GUILDS.Rmd
inst/doc/GUILDS.R
inst/doc/GUILDS.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test-logLikelihood.Guilds.Conditional.R
tests/testthat/test-maxLikelihood.ESF.R
tests/testthat/test-expected.SAD.Guilds.R
tests/testthat/test-simplex.R
tests/testthat/test-logLikelihood.Guilds.R
tests/testthat/test-maxLikelihood.Guilds.Conditional.R
tests/testthat/test-expected.SAD.Guilds.Conditional.R
tests/testthat/test-generate.Guilds.R
tests/testthat/test-logLikelihood.ESF.R
tests/testthat/test-expected.SAD.R
tests/testthat/test-calcKDA.R
tests/testthat/test-maxLikelihood.Guilds.R
tests/testthat/test-preston_plot.R
src
src/KDA_R.cpp
src/RcppExports.cpp
NAMESPACE
R
R/ESF_function.R
R/drawLocal.R
R/generateData.R
R/Condition.R
R/RcppExports.R
R/LogLikFunctions.R
R/simplex.R
R/evaluateLogLik2.R
R/visualisation.R
R/calcSumKDA2.R
R/expected.R
vignettes
vignettes/GUILDS.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/maxLikelihood.ESF.Rd
man/generate.Guilds.Rd
man/generate.ESF.Rd
man/expected.SAD.Guilds.Conditional.Rd
man/maxLikelihood.Guilds.Conditional.Rd
man/logLikelihood.ESF.Rd
man/logLikelihood.Guilds.Rd
man/expected.SAD.Rd
man/GUILDS-package.Rd
man/expected.SAD.Guilds.Rd
man/maxLikelihood.Guilds.Rd
man/logLikelihood.Guilds.Conditional.Rd
man/preston_plot.Rd
man/generate.Guilds.Cond.Rd
man/GUILDS-internal.Rd
GUILDS documentation built on May 19, 2017, 8:47 p.m.