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

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).

Author
Thijs Janzen [aut, cre], Bart Haegeman [ctb], Franck Jabot [ctb], Jerome Chave [ctb]
Date of publication
2016-09-26 21:21:03
Maintainer
Thijs Janzen <thijsjanzen@gmail.com>
License
GPL-2
Version
1.3
URLs

View on CRAN

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

Files in this package

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