Man pages for franciscorichter/emphasis
Evolutionary Modeling on Phylogenetic Applications with Simulations and Importance Sampling
| AugmentMultiplePhyloPD | Augment Multiple Phylogenetic Trees with Parameter Diversity |
| augmentPD | Augment Phylogenetic Diversity using MCEM |
| check_convergence | Check Convergence in Parameters |
| dd_ML_est | Optimize GAM Model Parameters with Fixed betaP |
| e_cpp | function to perform one step of the E-M algorithm |
| em_cpp | function to perform one step of the E-M algorithm |
| emphasis | Emphasis main function |
| emphasis_de | perform emphasis analysis using DE method |
| emphasis_de_factorial | perform emphasis analysis using DE method |
| emphasis-package | A short title line describing what the package does |
| ExponentialRate | Compute the Rate of a Non-Homogeneous Exponential Process |
| generateNonHomogeneousExp | Generate Variates for a Non-Homogeneous Exponential Process |
| generatePhyloPD | Generate Phylogenetic trees under PD model |
| loglikelihood | function to calculate log likelihood of pars for a tree set, |
| mcGrid | Monte Carlo Grid Calculation |
| m_cpp | function to perform one step of the E-M algorithm |
| nhExpRand | Generate Non-Homogeneous Exponential Random Variables |
| pd_ML | Parameter Discovery using Monte Carlo EM Algorithm |
| rate_t | Compute the Rate at a Given Time for a Non-Homogeneous... |
| rescale_tree | function to rescale the branching times of a phylogenetic... |
| sim_tree_is_extinct_pd | simulation function to simulate a tree under the pd model,... |
| sim_tree_pd_cpp | simulation function to simulate a tree under the pd model |
| sim_tree_pd_grid | simulation function to simulate a tree under the pd model |
| sim_tree_pd_R | simulation function to simulate a tree under the pd model,... |
| simulate_evolution | Simulate Evolutionary Processes |
| simulate_single_pd_tree_cpp | Simulate a single phylogenetic diversity tree using C++... |
| train_GAM | Train a Generalized Additive Model on Simulation Data |
