Package: eicm 1.0.3

eicm: Explicit Interaction Community Models

Model fitting and species biotic interaction network topology selection for explicit interaction community models. Explicit interaction community models are an extension of binomial linear models for joint modelling of species communities, that incorporate both the effects of species biotic interactions and the effects of missing covariates. Species interactions are modelled as direct effects of each species on each of the others, and are estimated alongside the effects of missing covariates, modelled as latent factors. The package includes a penalized maximum likelihood fitting function, and a genetic algorithm for selecting the most parsimonious species interaction network topology.

Authors:Miguel Porto [aut, cre], Pedro Beja [aut]

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eicm.pdf |eicm.html✨
eicm/json (API)

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

Bug tracker:https://github.com/miguel-porto/eicm/issues

Datasets:
  • truemodel - A parameterized EICM model for simulation

On CRAN:

Conda:

community-modelingecological-modellinginteraction-networkjoint-modelsjsdmmissing-covariatesspecies-distribution-modellingspecies-interactions

4.48 score 6 stars 2 scripts 260 downloads 11 exports 13 dependencies

Last updated 2 years agofrom:f6955860cc. Checks:1 OK, 10 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 19 2025
R-4.5-win-x86_64NOTEFeb 19 2025
R-4.5-mac-x86_64NOTEFeb 19 2025
R-4.5-mac-aarch64NOTEFeb 19 2025
R-4.5-linux-x86_64NOTEFeb 19 2025
R-4.4-win-x86_64NOTEFeb 19 2025
R-4.4-mac-x86_64NOTEFeb 19 2025
R-4.4-mac-aarch64NOTEFeb 19 2025
R-4.3-win-x86_64NOTEFeb 19 2025
R-4.3-mac-x86_64NOTEFeb 19 2025
R-4.3-mac-aarch64NOTEFeb 19 2025

Exports:as.eicmcoefficientComparisonPloteicmeicm.dataeicm.fiteicm.matrixeicm.optionsgenerateEICMinteractionPlotisCyclicplotNetworkFromMatrix

Dependencies:clicodetoolscrayondoSNOWforeachGAiteratorsoptimParallelpsoRcppRcppArmadillosnowucminf

Explicit Interaction Community Models

Miguel Porto, Pedro Beja^[CIBIO/InBio – Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal; Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal]

Rendered fromeicm.Rmdusingknitr::rmarkdownon Feb 19 2025.

Last update: 2020-03-27
Started: 2020-03-27