Man pages for phyr
Model Based Phylogenetic Analysis
| align_comm_V | Create phylogenetic var-cov matrix based on phylogeny and... |
| boot_ci | Generic method to output bootstrap confidence intervals from... |
| 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 |
| fixef | Extract fixed-effects estimates |
| get_design_matrix_pglmm | 'get_design_matrix' gets design matrix for gaussian,... |
| match_comm_tree | Match phylogeny with community data |
| model.frame.communityPGLMM | Extracting the Model Frame from a communityPGLMM Model object |
| nin | Not in |
| nobs.communityPGLMM | Number of Observation in a communityPGLMM Model |
| oldfield | Phylogeny and community data from an Oldfield ecosystem in... |
| pcd | pairwise site phylogenetic community dissimilarity (PCD)... |
| pcd_pred | Predicted PCD with species pool |
| pglmm | Phylogenetic Generalized Linear Mixed Model for Community... |
| pglmm_compare | Phylogenetic Generalized Linear Mixed Model for Comparative... |
| pglmm-matrix-structure | 'pglmm_matrix_structure' produces the entire covariance... |
| pglmm-plot-data | Plot the original dataset and predicted values (optional) |
| 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... |
| phylotree | Example phylogeny |
| plot_bayes | plot_bayes generic |
| predict.communityPGLMM | Predict Function for communityPGLMM Model Objects |
| prep_dat_pglmm | Prepare data for 'pglmm' |
| print.communityPGLMM | Print summary information of fitted model |
| print.pglmm_compare | Print summary information of fitted model |
| psd | Phylogenetic Species Diversity Metrics |
| ranef | Extract random-effects estimates |
| refit_boots | Refit bootstrap replicates that failed to converge in a call... |
| 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 |
