Files in pbastide/phylolimma

Phylogenetic Comparative Methods for limma

R/addReplicatesOnTree.R R/checkTreeMatrix.R R/ddfSatterthwaite.R R/importsFromLimma.R R/normalization.R R/phylogeneticCorrelations.R R/phylolimma-package.R R/phylolmFit.R R/utils.R README.md examples/ddf_satterthwaite.R examples/test_Satterthwaite.R examples/test_Satterthwaite_chen.R examples/test_Satterthwaite_lmer.R examples/test_gradient_hessian_exact.R examples/test_satterthwaite_lmer_startree.R examples/test_satterthwaite_star_tree.R examples/test_satterthwaite_utils.R examples/test_variances.R man/PhyloMArrayLM-class.Rd man/addReplicatesOnTree.Rd man/checkParamMatrix.Rd man/classifyTestsF.Rd man/compute_inv_hessian.Rd man/ddf_samples.Rd man/ddf_satterthwaite.Rd man/ddf_satterthwaite_BM_error.Rd man/ddf_satterthwaite_BM_error_approx.Rd man/ddf_species.Rd man/decideTests.Rd man/dots.Rd man/eBayes.Rd man/getBoundsSelectionStrength.Rd man/getMaxLambda.Rd man/getMinError.Rd man/getSpeciesNumber.Rd man/get_C_tree.Rd man/get_chol_tree.Rd man/get_consensus_tree.Rd man/get_consensus_tree_BM.Rd man/get_consensus_tree_OUfixedRoot.Rd man/get_consensus_tree_OUrandomRoot.Rd man/get_consensus_tree_delta.Rd man/get_consensus_tree_lambda.Rd man/get_ddf.Rd man/get_dots_args.Rd man/get_lambda_error.Rd man/get_lower_bounds.Rd man/get_starting_values.Rd man/get_upper_bounds.Rd man/hessianMinusLogLik.Rd man/lengthNormalizeRNASeq.Rd man/lmFitLimma.Rd man/normalize_RPKM.Rd man/normalize_TPM.Rd man/normalize_none.Rd man/parse_species.Rd man/phylogeneticCorrelations.Rd man/phylolimma-package.Rd man/phylolmFit.Rd man/pos_inv.Rd man/rescale_tree.Rd man/rho_prime.Rd man/rho_prime_inv.Rd man/transform_data_tree.Rd man/transform_design_tree.Rd man/transform_tree_model_BM.Rd man/transform_tree_model_OUfixedRoot.Rd man/transform_tree_model_OUrandomRoot.Rd man/transform_tree_model_delta.Rd man/transform_tree_model_lambda.Rd man/transform_tree_phylolm.Rd man/tree_height.Rd tests/testthat.R tests/testthat/test-addReplicates.R tests/testthat/test-ddf.R tests/testthat/test-equivalencies.R tests/testthat/test-errors.R tests/testthat/test-normalisation.R tests/testthat/test-phylogeneticCorrelations.R tests/testthat/test-phylolmFit.R tests/testthat/test-starTree.R tests/testthat/test-zero_branch_lengths.R