API for USCbiostats/aphylo
Statistical Inference and Prediction of Annotations in Phylogenetic Trees
| Global functions | |
|---|---|
| .LogLike_pruner | Source code |
| .Nnode_aphylo_pruner | Source code |
| .onLoad | Source code |
| .posterior_prob | Source code |
| .sim_fun_on_tree | Source code |
| .sim_tree | Source code |
| APHYLO_DEFAULT_MCMC_CONTROL | Man page |
| APHYLO_PARAM_DEFAULT | Man page |
| LogLike | Man page Source code |
| LogLike.aphylo | Source code |
| LogLike.aphylo_pruner | Source code |
| LogLike.multiAphylo | Source code |
| MCMC | Man page |
| MLE | Man page |
| Nann | Man page Source code |
| Nann.aphylo | Source code |
| Nann.aphylo_estimates | Source code |
| Nann.aphylo_pruner | Source code |
| Nann.multiAphylo | Source code |
| Nannotated | Man page Source code |
| Nannotated.aphylo | Source code |
| Nannotated.aphylo_estimates | Source code |
| Nannotated.aphylo_pruner | Source code |
| Nannotated.multiAphylo | Source code |
| Nedge.aphylo | Source code |
| Nedge.aphylo_estimates | Source code |
| Nedge.multiAphylo | Source code |
| Nnode.aphylo | Source code |
| Nnode.aphylo_estimates | Source code |
| Nnode.aphylo_pruner | Source code |
| Nnode.multiAphylo | Source code |
| Ntip.aphylo | Source code |
| Ntip.aphylo_estimates | Source code |
| Ntip.aphylo_pruner | Source code |
| Ntip.multiAphylo | Source code |
| Ntip.multiAphylo_pruner | Source code |
| Ntrees | Man page Source code |
| Ntrees.aphylo | Source code |
| Ntrees.aphylo_estimates | Source code |
| Ntrees.multiAphylo | Source code |
| Ntrees.multiPhylo | Source code |
| Ntrees.phylo | Source code |
| PANTHER | Man page |
| PANTHERDB | Man page |
| Pi | Man page Source code |
| Tree_get_ann | Source code |
| Tree_get_offspring | Source code |
| Tree_get_parents | Source code |
| Tree_set_ann | Source code |
| [.aphylo | Man page |
| [<-.aphylo | Man page |
| `[.aphylo` | Source code |
| `[.multiAphylo` | Source code |
| `[<-.aphylo` | Source code |
| accuracy_sifter | Man page Source code |
| accuracy_sifter.aphylo_estimates | Man page Source code |
| accuracy_sifter.default | Man page Source code |
| ape-methods | Man page |
| aphylo | Man page |
| aphylo-class | Man page |
| aphylo-formula | Man page |
| aphylo-index | Man page |
| aphylo-info | Man page |
| aphylo-methods | Man page |
| aphylo-model | Man page |
| aphylo-package | Man page |
| aphylo_call | Source code |
| aphylo_cv | Man page Source code |
| aphylo_cv.formula | Man page Source code |
| aphylo_estimates | Man page |
| aphylo_formula | Man page Source code |
| aphylo_from_data_frame | Man page Source code |
| aphylo_hier | Source code |
| aphylo_mcmc | Man page Source code |
| aphylo_mle | Man page Source code |
| aphylo_pruner | Man page |
| as.phylo | Man page |
| as.phylo.aphylo | Man page Source code |
| as.phylo.matrix | Man page Source code |
| as_aphylo | Source code |
| auc | Man page Source code |
| balance_ann | Man page Source code |
| balance_ann.aphylo | Source code |
| balance_ann.default | Source code |
| balance_ann.multiAphylo | Source code |
| blue | Source code |
| bprior | Man page Source code |
| c.aphylo | Man page Source code |
| check_annotations | Source code |
| circle | Source code |
| coef.aphylo_estimates | Man page Source code |
| colorRamp2 | Source code |
| colorkey | Source code |
| comment_line_in_body | Source code |
| d_prediction_score | Source code |
| dist2root | Man page Source code |
| eta | Man page Source code |
| fakeexperiment | Man page |
| faketree | Man page |
| get_postorder | Man page Source code |
| imput_species | Source code |
| imputate_duplications | Man page Source code |
| is.aphylo | Source code |
| is.multiAphylo | Source code |
| list_offspring | Man page Source code |
| list_offspring.aphylo | Source code |
| list_offspring.phylo | Source code |
| list_parents | Man page Source code |
| list_parents.aphylo | Source code |
| list_parents.phylo | Source code |
| logLik.aphylo_estimates | Source code |
| mislabel | Man page Source code |
| mu_d | Man page Source code |
| mu_s | Man page Source code |
| multiAphylo | Man page |
| new_aphylo | Man page Source code |
| new_aphylo.phylo | Man page Source code |
| new_aphylo_estimates | Source code |
| new_aphylo_pruner | Man page Source code |
| new_aphylo_pruner.aphylo | Source code |
| new_aphylo_pruner.multiAphylo | Source code |
| new_aphylo_pruner_cpp | Source code |
| new_phylo | Source code |
| npolygon | Source code |
| p_prediction_score | Source code |
| panther-tree | Man page |
| piechart | Source code |
| pieslice | Source code |
| plot-prediction | Man page |
| plot.aphylo | Man page Source code |
| plot.aphylo_auc | Man page Source code |
| plot.aphylo_estimates | Man page Source code |
| plot.aphylo_prediction_score | Man page Source code |
| plot_logLik | Man page Source code |
| plot_logLik.aphylo | Man page Source code |
| plot_logLik.aphylo_estimates | Man page Source code |
| plot_logLik.formula | Man page |
| plot_multivariate | Man page Source code |
| posterior-probabilities | Man page |
| predict.aphylo_estimates | Man page Source code |
| predict_brute_force | Man page Source code |
| predict_pre_order | Man page Source code |
| predict_pre_order.aphylo | Man page Source code |
| predict_pre_order.aphylo_estimates | Man page Source code |
| predict_random | Source code |
| prediction_score | Man page Source code |
| prediction_score.aphylo_estimates | Man page Source code |
| prediction_score.default | Source code |
| prediction_score.list | Source code |
| prediction_score.matrix | Source code |
| prediction_score_backend | Source code |
| prediction_score_rand | Source code |
| print.aphylo | Source code |
| print.aphylo_auc | Man page Source code |
| print.aphylo_estimates | Man page Source code |
| print.aphylo_prediction_score | Man page Source code |
| print.multiAphylo | Man page Source code |
| prob_mat | Source code |
| psi | Man page Source code |
| raphylo | Man page Source code |
| rdrop_annotations | Man page Source code |
| read.panther | Man page |
| read_nhx | Man page Source code |
| read_panther | Man page Source code |
| read_pli | Man page Source code |
| reduce_pseq | Source code |
| release_questions | Source code |
| rescale_polygon | Source code |
| rmultiAphylo | Man page Source code |
| root_node_prob | Source code |
| rotate | Source code |
| segments_gradient | Source code |
| sim_fun_on_tree | Man page Source code |
| sim_tree | Man page Source code |
| sizeof_pruner | Source code |
| states | Man page Source code |
| stop_ifuninformative | Source code |
| summary.aphylo | Source code |
| try_solve | Source code |
| update_fun_in_body | Source code |
| uprior | Man page Source code |
| validate_aphylo_formula | Source code |
| validate_dots_in_term | Source code |
| validate_parameters | Source code |
| var_prediction_score | Source code |
| vcov.aphylo_estimates | Man page Source code |
| window.aphylo_estimates | Source code |
| write_pli | Man page Source code |
