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

View on CRAN

Functions

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

Files

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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