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).

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
https://github.com/thijsjanzen/GUILDS

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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

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