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 |
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