Man pages for phyr
Model Based Phylogenetic Analysis

align_comm_VCreate phylogenetic var-cov matrix based on phylogeny and...
boot_ciGeneric method to output bootstrap confidence intervals from...
comm_aExample community data
comm_bExample community data
cor_phyloCorrelations among multiple variates with phylogenetic signal
enviExample environmental data
family.communityPGLMMFamily Objects for communityPGLMM objects
fitted.communityPGLMMFitted values for communityPGLMM
fixefExtract fixed-effects estimates
get_design_matrix_pglmm'get_design_matrix' gets design matrix for gaussian,...
match_comm_treeMatch phylogeny with community data
model.frame.communityPGLMMExtracting the Model Frame from a communityPGLMM Model object
ninNot in
nobs.communityPGLMMNumber of Observation in a communityPGLMM Model
oldfieldPhylogeny and community data from an Oldfield ecosystem in...
pcdpairwise site phylogenetic community dissimilarity (PCD)...
pcd_predPredicted PCD with species pool
pglmmPhylogenetic Generalized Linear Mixed Model for Community...
pglmm_comparePhylogenetic Generalized Linear Mixed Model for Comparative...
pglmm-matrix-structure'pglmm_matrix_structure' produces the entire covariance...
pglmm-plot-dataPlot the original dataset and predicted values (optional)
pglmm-plot-reVisualize random terms of communityPGLMMs
pglmm-predicted-valuesPredicted values of PGLMM
pglmm-profile-LRT'pglmm_profile_LRT' tests statistical significance of the...
phylotreeExample phylogeny
plot_bayesplot_bayes generic
predict.communityPGLMMPredict Function for communityPGLMM Model Objects
prep_dat_pglmmPrepare data for 'pglmm'
print.communityPGLMMPrint summary information of fitted model
print.pglmm_comparePrint summary information of fitted model
psdPhylogenetic Species Diversity Metrics
ranefExtract random-effects estimates
refit_bootsRefit bootstrap replicates that failed to converge in a call...
residuals.communityPGLMMResiduals of communityPGLMM objects
rm_site_noobsRemove site that has no observations of any species
rm_sp_noobsRemove species that not observed in any site
simulate.communityPGLMMSimulate from a communityPGLMM object
summary.communityPGLMMSummary information of fitted model
summary.pglmm_compareSummary information of fitted pglmm_compare model
traitsExample species traits data
vcv2Create phylogenetic var-cov matrix
phyr documentation built on Jan. 13, 2021, 5:40 p.m.