Package: GUILDS 1.4.7

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_1.4.7.tar.gz
GUILDS_1.4.7.zip(r-4.7)GUILDS_1.4.7.zip(r-4.6)GUILDS_1.4.7.zip(r-4.5)
GUILDS_1.4.7.tgz(r-4.6-x86_64)GUILDS_1.4.7.tgz(r-4.6-arm64)GUILDS_1.4.7.tgz(r-4.5-x86_64)GUILDS_1.4.7.tgz(r-4.5-arm64)
GUILDS_1.4.7.tar.gz(r-4.7-arm64)GUILDS_1.4.7.tar.gz(r-4.7-x86_64)GUILDS_1.4.7.tar.gz(r-4.6-arm64)GUILDS_1.4.7.tar.gz(r-4.6-x86_64)
GUILDS_1.4.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GUILDS/json (API)

# Install 'GUILDS' in R:

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

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

Pkgdown/docs site:https://thijsjanzen.github.io

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

5.97 score 3 stars 12 packages 16 scripts 1.1k downloads 14 exports 3 dependencies

Last updated from:927e1ca003. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	137
linux-devel-x86_64	OK	139
source / vignettes	OK	199
linux-release-arm64	OK	141
linux-release-x86_64	OK	123
macos-release-arm64	OK	106
macos-release-x86_64	OK	242
macos-oldrel-arm64	OK	82
macos-oldrel-x86_64	OK	202
windows-devel	OK	116
windows-release	OK	94
windows-oldrel	OK	106
wasm-release	OK	106

Exports:calcKDA expected.SAD expected.SAD.Guilds expected.SAD.Guilds.Conditional generate.ESF generate.Guilds generate.Guilds.Cond logLikelihood.ESF logLikelihood.Guilds logLikelihood.Guilds.Conditional maxLikelihood.ESF maxLikelihood.Guilds maxLikelihood.Guilds.Conditional preston_plot

Dependencies:nloptr pracma Rcpp

Walkthrough

Guilds Vignette | The standard neutral model | Dispersal Guilds | Conditioning on Guild size | Guilds model with differences in dispersal

Rendered fromWalkthrough.Rmdusingknitr::rmarkdown

Last update: 2025-03-11
Started: 2025-03-11

Help page	Topics
Package implementing the Guilds sampling formula for the Neutral Theory of Biodiversity	GUILDS-package GUILDS
Calculate the expected species abundance distribution of the standard neutral model, given theta, m and J	expected.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 2005	generate.ESF
Generate Artificial data under the GUILDS model	generate.Guilds
Generate Artificial data under the GUILDS model, conditioned on Guild size	generate.Guilds.Cond
Likelihood of the Etienne sampling formula	logLikelihood.ESF
Likelihood of the Guilds sampling formula	logLikelihood.Guilds
Likelihood of the Guilds sampling formula, conditional on guild size	logLikelihood.Guilds.Conditional
Maximization of the loglikelihood given the standard Neutral Model, using the Etienne Sampling Formula	maxLikelihood.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 dataset	preston_plot

Package: GUILDS 1.4.7

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

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