%nin%                   Not in
align_comm_V            Create phylogenetic var-cov matrix based on
                        phylogeny and community data
boot_ci                 Generic method to output bootstrap confidence
                        intervals from an object.
comm_a                  Example community data
comm_b                  Example community data
cor_phylo               Correlations among multiple variates with
                        phylogenetic signal
envi                    Example environmental data
family.communityPGLMM   Family Objects for communityPGLMM objects
fitted.communityPGLMM   Fitted values for communityPGLMM
fixef                   Extract fixed-effects estimates
get_design_matrix       'get_design_matrix' gets design matrix for
                        gaussian, binomial, and poisson models
match_comm_tree         Match phylogeny with community data
model.frame.communityPGLMM
                        Extracting the Model Frame from a
                        communityPGLMM Model object
nobs.communityPGLMM     Number of Observation in a communityPGLMM Model
oldfield                Phylogeny and community data from an Oldfield
                        ecosystem in Southern Ontario, Canada
pcd                     pairwise site phylogenetic community
                        dissimilarity (PCD) within a community
pcd_pred                Predicted PCD with species pool
pglmm                   Phylogenetic Generalized Linear Mixed Model for
                        Community Data
pglmm_compare           Phylogenetic Generalized Linear Mixed Model for
                        Comparative Data
pglmm_matrix_structure
                        'pglmm_matrix_structure' produces the entire
                        covariance matrix structure (V) when you
                        specify random effects.
pglmm_plot_ranef        Visualize random terms of communityPGLMMs
pglmm_predicted_values
                        Predicted values of PGLMM
pglmm_profile_LRT       Testing statistical significance of random
                        effect
phylotree               Example phylogeny
plot_bayes              plot_bayes generic
plot_data               Plot the original dataset and predicted values
                        (optional)
predict.communityPGLMM
                        Predict Function for communityPGLMM Model
                        Objects
prep_dat_pglmm          Prepare data for 'pglmm'
print.communityPGLMM    Print summary information of fitted model
print.pglmm_compare     Print summary information of fitted model
psv                     Phylogenetic Species Diversity Metrics
ranef                   Extract random-effects estimates
refit_boots             Refit bootstrap replicates that failed to
                        converge in a call to 'cor_phylo'
residuals.communityPGLMM
                        Residuals of communityPGLMM objects
rm_site_noobs           Remove site that has no observations of any
                        species
rm_sp_noobs             Remove species that not observed in any site
simulate.communityPGLMM
                        Simulate from a communityPGLMM object
summary.communityPGLMM
                        Summary information of fitted model
summary.pglmm_compare   Summary information of fitted pglmm_compare
                        model
traits                  Example species traits data
vcv2                    Create phylogenetic var-cov matrix
