%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
communityPGLMM.predicted.values
                        Predicted values of PGLMM
communityPGLMM.profile.LRT
                        'communityPGLMM.profile.LRT' tests statistical
                        significance of the phylogenetic random effect
                        of binomial models on species slopes using a
                        likelihood ratio test.
cor_phylo               Correlations among multiple variates with
                        phylogenetic signal
envi                    Example environmental data
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
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
phylotree               Example phylogeny
plot.communityPGLMM     Plot the original dataset and predicted values
                        (optional)
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.
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
