Man pages for PhylogeneticEM
Automatic Shift Detection using a Phylogenetic EM

add_complementaryAdd several entries, when only one is not NA.
allocate_regimes_from_shiftsAllocation of regimes to nodes.
allocate_shifts_from_regimesAllocation of shifts to edges
allocate_subset_node.simulateIteration allocation
check_dataTest the format of data entry.
check_dimensionsCheck dimensions of the parameters
check_parsimonyCheck Parsimony, assuming no homoplasy
check_parsimony_clustersCheck whether an allocation of the shifts is parsimonious, in...
check.selection.strengthCheck selection strength
clusters_from_shiftsClustering associated to a shift allocation, assuming no...
compute_actualization_matrix_ultrametricCompute Matrix W of actualization (Ultrametric case)
compute_betas_from_shiftsComputation of the optimal values at nodes and tips.
compute_diff_exp.BMCompute differences of expectations between node and parent.
compute_dist_phyPhylogenetic Distances
compute_E.simpleE step
compute_expectations.BMCompute the expected states of a BM
compute_expectations.scOUCompute the expected states of a scOU
compute_fixed_momentsCompute fixed moments for E step.
compute_gauss_lassoDo a lm on top of a lasso regression.
compute_log_likelihood.simpleLog Likelihood
compute_mahalanobis_distance.simpleSquared Mahalanobis Distance
compute_mean_variance.simpleCompute moments of params_old
compute_residuals.simpleResiduals
compute_shifts_from_betasComputation of shifts from the vector of optimal values
compute_state_filterList of potential daughter states when parent is in state k.
compute_stationary_varianceCompute the stationary variance matrix
compute_sum_var_diffCompute weighted sum of var_diff
compute_times_caCommon Ancestors Times
compute_tree_correlations_matrix.BMMatrix of tree-induced correlations for the BM
compute_tree_correlations_matrix.scOUMatrix of tree-induced correlations for the scOU
compute_var_diff.BMCompute variances of differences between nodes and parents.
compute_variance_covariance.BMComplete variance covariance matrix for BM
compute_variance_covariance.OUComplete variance covariance matrix for OU
compute_variance_covariance.scOUComplete variance covariance matrix for scOU
compute_var_M.BMComputation of the variance.
correspondenceEdgesCorrespondence between edges numbers
enlightMake the result lighter
enumerate_parsimonyEnumerate all the possible regime allocations, given a...
enumerate_tips_under_edgesTips descendants of nodes.
equivalent_shiftsFind all equivalent shifts allocations and values.
equivalent_shifts_edgesFind all the equivalent shift edges allocations.
equivalent_shifts_valuesFind values given edges. OU stationary case. Ultrametric...
estimate.alphaFunction to estimate alpha
estimateEMPerform One EM
extractExtraction function
extract.enumerate_parsimonyExtract the result of 'enumerate_parsimony' at a node.
extract.equivalent_shiftsExtract the shifts values for one trait.
extract.parsimonyCostExtraction of the actual number of solutions.
extract.parsimonyNumberExtraction of the actual number of solutions.
extract.partitionsNumberExtract from object 'partitionsNumber'
extract.simul_processExtraction of simulated traits
extract.variance_covarianceExtract sub-matrices of variance.
find_grid_alphaFind a reasonable grid for alpha
find_independent_regression_vectors.glmnet_multivariateGiven a regularization path, find K selected independent...
find_shift_valuesFind values given edges. OU stationary case. Ultrametric...
format_outputRun the EM for several values of K
get_variance_nodeGet variance matrix of a node
go_back_to_original_processScale the parameters back to the original process
impute.data.RphyloparsInitial imputation of missing data for lasso
imputed_traitsAncestral State Reconstruction
incidence.matrixIncidence matrix of a tree.
incidence_matrix_actualization_factorsCompute the actualizations factors to apply to the incidence...
incidence.matrix.fullIncidence matrix of a tree.
init.allocate_regimes_from_shiftsInitialization for the allocation of shifts.
init.alpha.gamma.estimationInitialization the selection strength alpha using robust...
init.compute_betas_from_shiftsInitialization for the computation of the optimal values
init.EM.lassoInitialization of the shifts using Lasso.
init.enumerate_parsimonyInitialization for the enumeration of parsimonious solutions.
init.incidence.matrixInitialization for incidence matrix
init.incidence.matrix.fullInitialization for incidence matrix (full tree)
init.parsimonyCostInitialization for parsimonyCost.
init.parsimonyNumberInitialization for parsimonyNumber.
init.simulate.BMInitialize BM
init.simulate.OUInitialize state and expectation matrices
init.simulate.StateAndExpInitialize state and expectation matrices
is.in.rangesCheck whether parameters are in ranges.
lasso_regression_K_fixed.glmnet_multivariateDo a lasso regression with the number of non-zero variables...
log_likelihoodLog Likelihood of a fitted object
matrix_of_possiblesCompute parent matrix from possibles daughter matrices.
merge_complementary_vectorsMerge several complementary vectors into one.
merge_params_independentMerge a list of independent parameters into into one...
model_selectionModel Selection of a fitted object
monkeysNew World Monkeys dataset
params_BMCreate an object 'params_process' for a BM
params_OUCreate an object 'params_process' for an OU
params_processCreate an object params_process
params_process.characterCreate an object 'params_process'
params_process.PhyloEMParameter estimates
parsimonyCostMinimal number of shifts needed to get a clustering.
parsimonyNumberNumber of equivalent parsimonious allocations.
partitionsNumberNumber of different models
penalty_BaraudGiraudHuet_likelihoodPenalty function type Baraud Giraud Huet.
penalty_BirgeMassart_shape1Penalty function type Birg<c3><a9>-Massart 1
penalty_BirgeMassart_shape2Penalty function type Birg<c3><a9>-Massart 2
penalty_pBICPenalty function type pBIC
PhyloEMModel Estimation with Detection of Shifts
plot.enumerate_parsimonyPlot all the equivalent solutions.
plot.equivalent_shiftsPlot all the equivalent solutions.
plot.params_processPlot for class 'simul_process'
plot.PhyloEMPlot for class 'PhyloEM'
prod.indexProduct of elements of a matrix
qr.solve_exactexact qr.solve
recursionDownGeneric recursion down the tree.
residuals.PhyloEMResiduals of a fitted object
sample_edges_intervalsSample equally spaced edges.
sample_shifts_edgesSample shifts edges in a parsimonious way.
scale_paramsScale variance and selection strength from a linear transform
segmentation.BMSegmentation in the BM case
segmentation.OU.specialCase.lassoSegmentation in the OU special case, using lasso regression
segmentation.OU.specialCase.same_shiftsSegmentation in the OU special case, conserving the same...
shifts.list_to_matrixCompute the matrix of shifts.
shifts.list_to_vectorCompute the vector of shifts.
shifts.matrix_to_listCompute the list of shifts.
shifts_to_simmapSimmap format mapping from list of edges
shifts.vector_to_listCompute the list of shifts.
simulate_internalSimulate a Stochastic Process on a tree
simul_processSimulate a Stochastic Process on a tree
split_params_independentSplit independent parameters into a list of parameters
sum.partitionsSum on all subsets.
sum.partitions.cardFixedSum on subsets of a given cardinal.
sum.prod.combSum on a simplex
sum.simplexSum on a simplex
test.root.stateTest state of root.
transform_branch_lengthTransform branch length for a re-scaled BM
transform_shifts_valuesTransform the shift values
update.allocate_regimes_from_shiftsUpdate function for regime allocation.
update.compute_betas_from_shiftsUpdate function for optimal value computation
update.enumerate_parsimonyActualization of the enumeration.
update.incidence.matrixUpdate function for incidence matrix
update.incidence.matrix.fullUpdate function for incidence matrix
update.parsimonyCostActualization for parsimonyCost.
update.parsimonyNumberActualization for parsimonyNumber.
update.partitionsNumber.genUpdate formula in the general case
wrapper_E_stepWrapper for E step in EM
PhylogeneticEM documentation built on Sept. 9, 2017, 1:03 a.m.