%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 |