Man pages for wu-lab-uva/RasperGade
Reconstructing Ancestral State under Pulsed Evolution in R by Gaussian Decomposition
| analyzeResidualError | Analyze quality of uncertainty in ancestral or hidden state... |
| calculateBinomRSS | Calculate RSS |
| calculate_CI | Get confidence interval for ancestral or hidden states |
| calculate_error_mean_and_var | Calculate the mean and variance of an error distribution |
| calculateHeteroscedasticity | Calculate median Chi-square |
| calculate_R2CV | Calculating coefficient of determination |
| compoundNormalMoments | Calculate four central moments of a mixture of normal... |
| continuousAceByPIC | Predict global ancestral state under the BM model |
| discretizeResult | Discretize result |
| F_beta_score | Calculating recall, precision and F score |
| findBestNormalApproximation | Find approximation for a mixture of normal distributions... |
| findSisters | Find the sister nodes/tips of a node/tip |
| findTerminalPIC | Find only tip-pair contrasts in a tree |
| fitModel2Step | Wrapper function for optimization |
| fitPE | Fit pulsed evolution model |
| fullMarginalReconstructionWithPE | Reconstruct all marginal ancestral state in a phylogeny |
| getAncestor | Find the ancestor of a node or tip |
| getConnected | Find the edges/nodes connected to a node |
| getModel | Get a component of the fitted model |
| getNextDescendants | Find the descendants of a node |
| getRoot | Find the root of a phylogeny |
| globalReconstructionWithPE | Predict global ancestral state under the pulsed evolution... |
| initializeParams | Prepare model parameters for optimization |
| locate_query_sequences | Locate query sequences |
| logitSigmoid | Shift the center of deviations to a probability |
| LOO_CV_with_BM | Leave-one-out cross-validation under BM model |
| LOO_CV_with_PE | Leave-one-out cross-validation under pulsed evolution model |
| make_traceable_node_labels | Calculating traceable node labels |
| marginalReconstruction | Reconstruct marginal ancestral state from a node's immediate... |
| mix_errors_by_weight | Mix error distributions |
| MixNormal | Probability functions of mixture of normal distributions |
| partition_test_set_with_minimum_distance | Partition test set from reference data |
| PEpoisnorm | Probability functions of trait change under pulsed evolution... |
| predict_hidden_state_by_pic | Predict hidden state under the BM model |
| predictHiddenStateWithPE | Predict hidden state under the PE model |
| processVariance | Total evolution rate |
| productNormalDensity | Calculate the product of normal probability density functions |
| pseudoPIC | Calculate pseudo-PIC |
| pseudoZscore | Calculate pseudo-Z-score |
| reconstructAncestralStates | Reconstruct ancestral states under BM and time-independent... |
| reroot_tree_at_tip | Root the phylogeny at a tip |
| simulatePET | Simulate trait under pulsed evolution |
| sort_and_digest | Calculating the MD5 sum of an unordered character vector |
| summarizeModel | Summarize fitted model |
