netassoc: Inference of Species Associations from Co-Occurrence Data

Infers species associations from community matrices. Uses local and (optional) regional-scale co-occurrence data by comparing observed partial correlation coefficients between species to those estimated from regional species distributions. Extends Gaussian graphical models to a null modeling framework. Provides interface to a variety of inverse covariance matrix estimation methods.

Author
Benjamin Blonder, Naia Morueta-Holme
Date of publication
2015-11-24 07:46:52
Maintainer
Benjamin Blonder <bblonder@gmail.com>
License
GPL-3
Version
0.6.2

View on CRAN

Man pages

make_netassoc_network
Infer species-association network
netassoc-package
Inference of Species Associations from Co-Occurrence Data
pairwise_association
Pairwise associations
partial_correlation
Partial correlation coefficients
plot_netassoc_matrix
Plots matrix with colormap
plot_netassoc_network
Plots species association network

Files in this package

netassoc
netassoc/NAMESPACE
netassoc/R
netassoc/R/plot.R
netassoc/R/partial_correlation.R
netassoc/R/make_netassoc_network.R
netassoc/R/pairwise_association.R
netassoc/R/generate_nul_resample.R
netassoc/MD5
netassoc/DESCRIPTION
netassoc/man
netassoc/man/pairwise_association.Rd
netassoc/man/netassoc-package.Rd
netassoc/man/plot_netassoc_network.Rd
netassoc/man/plot_netassoc_matrix.Rd
netassoc/man/partial_correlation.Rd
netassoc/man/make_netassoc_network.Rd