# Model Based Phylogenetic Analysis

## Documentation for package ‘phyr’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

%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.
boot_ci.cor_phylo | Correlations among multiple variates with phylogenetic signal
communityPGLMM | Phylogenetic Generalized Linear Mixed Model for Community Data
communityPGLMM.matrix.structure | 'pglmm_matrix_structure' produces the entire covariance matrix structure (V) when you specify random effects.
communityPGLMM.plot.re | Visualize random terms of communityPGLMMs
communityPGLMM.predicted.values | Predicted values of PGLMM
communityPGLMM.profile.LRT | 'pglmm_profile_LRT' tests statistical significance of the phylogenetic random effect of binomial models on species slopes using a likelihood ratio test.
communityPGLMM.show.re | Visualize random terms of communityPGLMMs
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
fixed.effects | Extract fixed-effects estimates
fixef | Extract fixed-effects estimates
fixef.communityPGLMM | 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_plot_re | Visualize random terms of communityPGLMMs
pglmm_predicted_values | Predicted values of PGLMM
pglmm_profile_LRT | 'pglmm_profile_LRT' tests statistical significance of the phylogenetic random effect of binomial models on species slopes using a likelihood ratio test.
phylotree | Example phylogeny
plot_bayes | plot_bayes generic
plot_bayes.communityPGLMM | Plot the original dataset and predicted values (optional)
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.cor_phylo | Correlations among multiple variates with phylogenetic signal
print.cp_refits | Refit bootstrap replicates that failed to converge in a call to 'cor_phylo'
print.pglmm_compare | Print summary information of fitted model
psc | Phylogenetic Species Diversity Metrics
psd | Phylogenetic Species Diversity Metrics
pse | Phylogenetic Species Diversity Metrics
psr | Phylogenetic Species Diversity Metrics
psv | Phylogenetic Species Diversity Metrics
psv.spp | Phylogenetic Species Diversity Metrics
random.effects | Extract random-effects estimates
ranef | Extract random-effects estimates
ranef.communityPGLMM | 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