Package: GUILDS 1.4.3

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).

Authors:Thijs Janzen [aut, cre], Bart Haegeman [ctb], Franck Jabot [ctb], Jerome Chave [ctb]

GUILDS_1.4.3.tar.gz
GUILDS_1.4.3.zip(r-4.5)GUILDS_1.4.3.zip(r-4.4)GUILDS_1.4.3.zip(r-4.3)
GUILDS_1.4.3.tgz(r-4.4-x86_64)
GUILDS_1.4.3.tar.gz(r-4.5-noble)GUILDS_1.4.3.tar.gz(r-4.4-noble)
GUILDS_1.4.3.tgz(r-4.4-emscripten)GUILDS_1.4.3.tgz(r-4.3-emscripten)
GUILDS.pdf |GUILDS.html✨
GUILDS/json (API)

# Install 'GUILDS' in R:
install.packages('GUILDS', repos = c('https://thijsjanzen.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/thijsjanzen/guilds/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

5.03 score 2 stars 2 packages 18 scripts 488 downloads 14 exports 3 dependencies

Last updated 1 years agofrom:c490dcd54f. Checks:OK: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-win-x86_64OKOct 10 2024
R-4.5-linux-x86_64OKOct 10 2024
R-4.4-win-x86_64OKOct 10 2024
R-4.4-mac-x86_64OKOct 10 2024
R-4.3-win-x86_64OKOct 10 2024

Exports:calcKDAexpected.SADexpected.SAD.Guildsexpected.SAD.Guilds.Conditionalgenerate.ESFgenerate.Guildsgenerate.Guilds.CondlogLikelihood.ESFlogLikelihood.GuildslogLikelihood.Guilds.ConditionalmaxLikelihood.ESFmaxLikelihood.GuildsmaxLikelihood.Guilds.Conditionalpreston_plot

Dependencies:nloptrpracmaRcpp

GUILDS Vignette

Thijs Janzen

Rendered fromGUILDS.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2022-03-10
Started: 2016-09-22

Readme and manuals

Help Manual

Help pageTopics
Package implementing the Guilds sampling formula for the Neutral Theory of BiodiversityGUILDS-package GUILDS
Calculate the expected species abundance distribution of the standard neutral model, given theta, m and Jexpected.SAD
Estimate the expected species abundance distribution of both guilds using the guilds model, provided theta, alpha_x, alpha_y and J.expected.SAD.Guilds
Estimate the expected species abundance distribution of both guilds using the guilds model, provided theta, alpha_x, alpha_y, conditional on the size of guild X, Jx and the size of guild Y, Jy.expected.SAD.Guilds.Conditional
Generate community data under the standard neutral model of biodiversity, using the urn scheme as described in Etienne 2005generate.ESF
Generate Artificial data under the GUILDS modelgenerate.Guilds
Generate Artificial data under the GUILDS model, conditioned on Guild sizegenerate.Guilds.Cond
Likelihood of the Etienne sampling formulalogLikelihood.ESF
Likelihood of the Guilds sampling formulalogLikelihood.Guilds
Likelihood of the Guilds sampling formula, conditional on guild sizelogLikelihood.Guilds.Conditional
Maximization of the loglikelihood given the standard Neutral Model, using the Etienne Sampling FormulamaxLikelihood.ESF
Maximization of the loglikelihood under the Guilds Model.maxLikelihood.Guilds
Maximization of the loglikelihood under the Guilds Model, conditioned on guild size.maxLikelihood.Guilds.Conditional
Barplot in Preston style of an abundance datasetpreston_plot