Model Based Phylogenetic Analysis
Family Objects for communityPGLMM objects
Fitted values for communityPGLMM
Extract fixed-effects estimates
Print summary information of fitted model
Print summary information of fitted model
Phylogenetic Species Diversity Metrics
Extract random-effects estimates
Create phylogenetic var-cov matrix based on phylogeny and community da...
Generic method to output bootstrap confidence intervals from an object...
Correlations among multiple variates with phylogenetic signal
get_design_matrix gets design matrix for gaussian, binomial, and poi...
Match phylogeny with community data
Extracting the Model Frame from a communityPGLMM Model object
Not in
Number of Observation in a communityPGLMM Model
pairwise site phylogenetic community dissimilarity (PCD) within a comm...
Predicted PCD with species pool
pglmm_matrix_structure produces the entire covariance matrix structu...
Plot the original dataset and predicted values (optional)
Visualize random terms of communityPGLMMs
Predicted values of PGLMM
pglmm_profile_LRT tests statistical significance of the phylogenetic...
Phylogenetic Generalized Linear Mixed Model for Community Data
Phylogenetic Generalized Linear Mixed Model for Comparative Data
plot_bayes generic
Predict Function for communityPGLMM Model Objects
Prepare data for pglmm
Refit bootstrap replicates that failed to converge in a call to `cor_p...
Residuals of communityPGLMM objects
Remove site that has no observations of any species
Remove species that not observed in any site
Simulate from a communityPGLMM object
Summary information of fitted model
Summary information of fitted pglmm_compare model
Create phylogenetic var-cov matrix
A collection of functions to do model-based phylogenetic analysis. It includes functions to calculate community phylogenetic diversity, to estimate correlations among functional traits while accounting for phylogenetic relationships, and to fit phylogenetic generalized linear mixed models. The Bayesian phylogenetic generalized linear mixed models are fitted with the 'INLA' package (<https://www.r-inla.org>).
Useful links