Function reference • phyr

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

Reference

Phylogenetic Diversity

Phylogenetic Correlations

Phylogenetic Generalized Linear Mixed Models

Helper Functions

Data Sets