API for franciscorichter/emphasis
Evolutionary Modeling on Phylogenetic Applications with Simulations and Importance Sampling
| Global functions | |
|---|---|
| AugmentMultiplePhyloPD | Man page Source code |
| ExponentialRate | Man page Source code |
| GPD | Source code |
| GPD_improved | Source code |
| PDTT_plot | Source code |
| augmentPD | Man page Source code |
| augmentPD_old | Source code |
| calc_D_stats | Source code |
| calc_p | Source code |
| calc_stats_for_perturbed_params | Source code |
| calculate_alpha | Source code |
| compile_results | Source code |
| computePhyloDistanceMatrix | Source code |
| diversity | Source code |
| e_cpp | Man page Source code Source code |
| em_cpp | Man page Source code Source code |
| emphasis | Man page Source code |
| emphasis-package | Man page |
| emphasis_de | Man page Source code |
| emphasis_de_factorial | Man page Source code |
| emphasis_de_mod | Source code |
| etree2phylo | Source code |
| explore_div_grid_cpp | Source code |
| explore_grid_cpp | Source code |
| extend_tree | Source code |
| generateNonHomogeneousExp | Man page Source code |
| generateNonHomogeneousExpCpp | Source code |
| generatePhyloDDD | Source code |
| generatePhyloDDD_minimal | Source code |
| generatePhyloPD | Man page Source code Source code |
| generatePhyloPD_old | Source code |
| generateStatistics | Source code |
| get.time | Source code |
| get_current_species | Source code |
| get_extant | Source code |
| get_random_grid | Source code |
| get_required_sampling_size | Source code |
| get_results | Source code |
| get_results_factorial | Source code |
| gradDescentEvolutionModel | Source code |
| handle_extinction | Source code |
| handle_speciation | Source code |
| initialize_input | Source code |
| initialize_results_storage | Source code |
| isStatsDiffIncreasing | Source code |
| iteration_step | Source code |
| learning.curves | Source code |
| lik_vis | Source code |
| loglikelihood | Man page Source code |
| m_cpp | Man page Source code Source code |
| mcEM_step | Source code |
| n_for_all_bt | Source code |
| n_from_time | Source code |
| newick | Source code |
| nhExpRand | Man page Source code |
| phylo2etree | Source code |
| phylodiversity | Source code |
| process_and_plot | Source code |
| rate_diversity | Source code |
| rate_t | Man page Source code |
| rcpp_mce_grid | Source code Source code |
| rcpp_mce_grid_factorial | Source code Source code |
| rescale_tree | Man page Source code |
| sample_and_update_event | Source code |
| sample_next_event_time | Source code |
| sim_tree_is_extinct_pd | Man page Source code |
| sim_tree_pd_R | Man page Source code |
| sim_tree_pd_cpp | Man page Source code |
| sim_tree_pd_grid | Man page Source code |
| simulate_div_tree_cpp | Source code |
| simulate_div_trees_cpp | Source code |
| simulate_evolution | Man page Source code |
| simulate_pd_trees_cpp | Source code Source code |
| simulate_single_pd_tree_cpp | Man page Source code Source code |
| train_GAM | Man page Source code |
| transf | Source code |
| updateE_extant | Source code Source code |
| update_pars | Source code |
| update_value | Source code |
| validate_inputs | Source code |
