Model Based Phylogenetic Analysis

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Documentation for package ‘phyr’ version 1.1.0

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

Help Pages

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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