Man pages for daijiang/phyr
Phylogenetic Analysis with R

align_comm_VCreate phylogenetic var-cov matrix based on phylogeny and...
binaryPGLMM_apePhylogenetic Generalized Linear Mixed Model for Binary Data
boot_ciGeneric method to output bootstrap confidence intervals from...
comm_aExample community data
comm_bExample community data
communityPGLMM.predicted.valuesPredicted values of PGLMM
cor_phyloCorrelations among multiple traits with phylogenetic signal
enviExample environmental data
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
ninNot in
pcdpairwise site phylogenetic community dissimilarity (PCD)...
pcd_predPredicted PCD with species pool
pglmmPhylogenetic Generalised Linear Mixed Model for Community...
pglmm-plot-dataPlot the original dataset and predicted values (optional)
pglmm-plot-reVisualize random terms of communityPGLMMs
pglmm-utils'communityPGLMM.profile.LRT' tests statistical significance...
phylotreeExample phylogeny
prep_dat_pglmmPrepare data for 'communityPGLMM'
psdPhylogenetic Species Diversity Metrics
refit_bootsRefit bootstrap replicates that failed to converge in a call...
residuals.pglmmResiduals of communityPGLMM objects
rm_site_noobsRemove site that has no obsrevations of any species.
rm_sp_noobsRemove species that not observed in any site.
traitsExample species traits data
vcv2Create phylogenetic var-cov matrix
daijiang/phyr documentation built on Nov. 16, 2018, 7:05 a.m.