Files in abichat/zazou
Z-Scores As Ornstein-Uhlenbeck
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check-dev.yaml
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/algebra.R
R/clusters.R
R/confint_colwiseinverse.R
R/confint_global.R
R/confint_scoresystem.R
R/confint_utils.R
R/correction.R
R/covariance_matrix.R
R/criteria.R
R/datasets.R
R/extract_leaves.R
R/extraction.R
R/generate_hyperparameters.R
R/incidence_matrix.R
R/method_colwiseinverse.R
R/method_scoresystem.R
R/open_doc.R
R/optim_functions.R
R/optim_global.R
R/optim_lbfgsb.R
R/optim_scaled.R
R/optim_shooting.R
R/plot_shifts.R
R/pull_pvalues.R
R/shiftconf.R
R/shiftpunct.R
R/simulations.R
R/smooth_pvalues.R
R/tree_helpers.R
R/vectorized_tests.R
R/zazou-package.R
R/zscores.R
README.Rmd
README.md
_pkgdown.yml
data-raw/age.R
data-raw/alcohol.R
data-raw/chlamydiae.R
data/age.rda
data/alcohol.rda
data/chlamydiae.rda
dev_history.R
inst/WORDLIST
inst/docs/404.html
inst/docs/LICENSE.html
inst/docs/articles/alcohol.html
inst/docs/articles/alcohol_files/figure-html/lbfgsb-1.png
inst/docs/articles/alcohol_files/figure-html/shooting-1.png
inst/docs/articles/alcohol_files/figure-html/shootingn-1.png
inst/docs/articles/alcohol_files/figure-html/shootingp-1.png
inst/docs/articles/alcohol_files/figure-html/tree-1.png
inst/docs/articles/alcohol_files/figure-html/unnamed-chunk-4-1.png
inst/docs/articles/alcohol_files/figure-html/unnamed-chunk-4-2.png
inst/docs/articles/alcohol_files/figure-html/unnamed-chunk-4-3.png
inst/docs/articles/alcohol_files/figure-html/unnamed-chunk-4-4.png
inst/docs/articles/chlamydiae.html
inst/docs/articles/chlamydiae_files/figure-html/lbfgsb-1.png
inst/docs/articles/chlamydiae_files/figure-html/shooting-1.png
inst/docs/articles/chlamydiae_files/figure-html/tree-1.png
inst/docs/articles/chlamydiae_files/figure-html/unnamed-chunk-4-1.png
inst/docs/articles/chlamydiae_files/figure-html/unnamed-chunk-4-2.png
inst/docs/articles/chlamydiae_files/figure-html/unnamed-chunk-4-3.png
inst/docs/articles/comparisons.html
inst/docs/articles/comparisons_files/figure-html/lbfgsb-1.png
inst/docs/articles/comparisons_files/figure-html/shooting-1.png
inst/docs/articles/comparisons_files/figure-html/simulations-1.png
inst/docs/articles/constraints.html
inst/docs/articles/constraints_files/figure-html/tree-1.png
inst/docs/articles/constraints_files/figure-html/unnamed-chunk-2-1.png
inst/docs/articles/constraints_files/figure-html/unnamed-chunk-3-1.png
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inst/docs/articles/constraints_files/figure-html/unnamed-chunk-9-1.png
inst/docs/articles/index.html
inst/docs/articles/simulations.html
inst/docs/articles/simulations_files/figure-html/AUC-1.png
inst/docs/articles/simulations_files/figure-html/estimationwithselection-1.png
inst/docs/articles/simulations_files/figure-html/estimationwithselection-2.png
inst/docs/articles/simulations_files/figure-html/estimationwithselection-3.png
inst/docs/articles/simulations_files/figure-html/ggtree-1.png
inst/docs/articles/simulations_files/figure-html/ou_correlation_matrix-1.png
inst/docs/articles/simulations_files/figure-html/plotswithbh-1.png
inst/docs/articles/simulations_files/figure-html/pvalueswofoldchange-1.png
inst/docs/articles/simulations_files/figure-html/unnamed-chunk-2-1.png
inst/docs/articles/simulations_files/figure-html/unnamed-chunk-3-1.png
inst/docs/articles/simulations_files/figure-html/unnamed-chunk-4-1.png
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inst/docs/articles/simulations_files/figure-html/unnamed-chunk-9-1.png
inst/docs/articles/simulations_files/figure-html/unnamed-chunk-9-2.png
inst/docs/articles/simulations_files/figure-html/zscoressimudataset-1.png
inst/docs/authors.html
inst/docs/bootstrap-toc.css
inst/docs/bootstrap-toc.js
inst/docs/docsearch.css
inst/docs/docsearch.js
inst/docs/index.html
inst/docs/link.svg
inst/docs/pkgdown.css
inst/docs/pkgdown.js
inst/docs/pkgdown.yml
inst/docs/reference/Rplot001.png
inst/docs/reference/Rplot002.png
inst/docs/reference/alcohol.html
inst/docs/reference/as_shiftconf.html
inst/docs/reference/as_shiftpunct.html
inst/docs/reference/bic.html
inst/docs/reference/calculate_Z.html
inst/docs/reference/calculate_Z_column_with_best_lambda.html
inst/docs/reference/calculate_Z_with_best_lambda.html
inst/docs/reference/check_selection.html
inst/docs/reference/choose_best_lambda.html
inst/docs/reference/compute_gradient_function.html
inst/docs/reference/compute_objective_function.html
inst/docs/reference/confint_colwiseinverse.html
inst/docs/reference/confint_scoresystem.html
inst/docs/reference/correct_pvalues.html
inst/docs/reference/covarianceOU_matrix.html
inst/docs/reference/covariance_noise_matrix_scoresystem.html
inst/docs/reference/create_clusters-1.png
inst/docs/reference/create_clusters.html
inst/docs/reference/create_listopt_pms.html
inst/docs/reference/df_confint_pvalue.html
inst/docs/reference/estimate_confint.html
inst/docs/reference/estimate_shifts.html
inst/docs/reference/estimate_tstar.html
inst/docs/reference/extract_models.html
inst/docs/reference/extract_significant_leaves.html
inst/docs/reference/extract_significant_leaves.shiftconf.html
inst/docs/reference/extract_significant_leaves.shiftpunct.html
inst/docs/reference/fast_solve_colwiseinverse_col.html
inst/docs/reference/find_feasible.html
inst/docs/reference/fitch.html
inst/docs/reference/force_ultrametric.html
inst/docs/reference/generate_gamma.html
inst/docs/reference/get_lambda_sequence.html
inst/docs/reference/incidence_matrix.html
inst/docs/reference/index.html
inst/docs/reference/inverse_sqrt.html
inst/docs/reference/lambda_grid.html
inst/docs/reference/noise_factor_scoresystem.html
inst/docs/reference/norm0.html
inst/docs/reference/open_doc.html
inst/docs/reference/p2z.html
inst/docs/reference/plot_shifts-1.png
inst/docs/reference/plot_shifts.html
inst/docs/reference/pull_pvalues.html
inst/docs/reference/pull_pvalues.shiftconf.html
inst/docs/reference/pull_pvalues.shiftpunct.html
inst/docs/reference/rescale_score_system.html
inst/docs/reference/rmse_glmnet.html
inst/docs/reference/simu_zscores-1.png
inst/docs/reference/simu_zscores-2.png
inst/docs/reference/simu_zscores.html
inst/docs/reference/smooth_pvalues.html
inst/docs/reference/solve_colwiseinverse.html
inst/docs/reference/solve_scaled_lasso.html
inst/docs/reference/solve_univariate.html
inst/docs/reference/test_wilcoxon.html
inst/docs/reference/tree_height.html
inst/docs/reference/update_beta_scoresystem.html
inst/docs/reference/update_confint.html
inst/docs/reference/update_sigma.html
inst/docs/reference/zazou-package.html
man/alcohol.Rd
man/as_shiftconf.Rd
man/as_shiftpunct.Rd
man/bic.Rd
man/calculate_Z.Rd
man/calculate_Z_column_with_best_lambda.Rd
man/calculate_Z_with_best_lambda.Rd
man/check_selection.Rd
man/choose_best_lambda.Rd
man/compute_gradient_function.Rd
man/compute_objective_function.Rd
man/confint_colwiseinverse.Rd
man/confint_scoresystem.Rd
man/correct_pvalues.Rd
man/covarianceOU_matrix.Rd
man/covariance_noise_matrix_scoresystem.Rd
man/create_clusters.Rd
man/create_listopt_pms.Rd
man/df_confint_pvalue.Rd
man/estimate_confint.Rd
man/estimate_shifts.Rd
man/estimate_tstar.Rd
man/extract_models.Rd
man/extract_significant_leaves.Rd
man/extract_significant_leaves.shiftconf.Rd
man/extract_significant_leaves.shiftpunct.Rd
man/fast_solve_colwiseinverse_col.Rd
man/find_feasible.Rd
man/fitch.Rd
man/force_ultrametric.Rd
man/generate_gamma.Rd
man/get_lambda_sequence.Rd
man/incidence_matrix.Rd
man/inverse_sqrt.Rd
man/lambda_grid.Rd
man/noise_factor_scoresystem.Rd
man/norm0.Rd
man/open_doc.Rd
man/p2z.Rd
man/plot_shifts.Rd
man/pull_pvalues.Rd
man/pull_pvalues.shiftconf.Rd
man/pull_pvalues.shiftpunct.Rd
man/rescale_score_system.Rd
man/rmse_glmnet.Rd
man/simu_zscores.Rd
man/smooth_pvalues.Rd
man/solve_colwiseinverse.Rd
man/solve_scaled_lasso.Rd
man/solve_univariate.Rd
man/test_wilcoxon.Rd
man/tree_height.Rd
man/update_beta_scoresystem.Rd
man/update_confint.Rd
man/update_sigma.Rd
man/zazou-package.Rd
tests/testthat.R
tests/testthat/previous_outputs/estCI_conoma
tests/testthat/previous_outputs/estCI_scoresystem
tests/testthat/previous_outputs/estCI_shift
tests/testthat/previous_outputs/estCI_zscore
tests/testthat/previous_outputs/estL_shift
tests/testthat/previous_outputs/estL_zscore
tests/testthat/previous_outputs/estSL_shift
tests/testthat/previous_outputs/estSL_sigma
tests/testthat/previous_outputs/estSL_zscore
tests/testthat/previous_outputs/estSS_conoma
tests/testthat/previous_outputs/estSS_scoresystem
tests/testthat/previous_outputs/estSS_shift
tests/testthat/previous_outputs/estSS_zscore
tests/testthat/previous_outputs/estS_bicselection
tests/testthat/previous_outputs/estS_shift
tests/testthat/previous_outputs/estS_zscore
tests/testthat/test-algebra.R
tests/testthat/test-clusters.R
tests/testthat/test-compute_functions.R
tests/testthat/test-correct_pvalues.R
tests/testthat/test-desparsified_internal.R
tests/testthat/test-desparsified_simulations.R
tests/testthat/test-lambda.R
tests/testthat/test-method_colwiseinverse.R
tests/testthat/test-model_selection.R
tests/testthat/test-previous_outputs.R
tests/testthat/test-score_system.R
tests/testthat/test-shiftpunct.R
tests/testthat/test-tree_helpers.R
tests/testthat/test-tree_matrices.R
tests/testthat/test-unidirectionnal.R
tests/testthat/test-vectorized_tests.R
tests/testthat/test-zscores.R
vignettes/.gitignore
vignettes/alcohol.Rmd
vignettes/chlamydiae.Rmd
vignettes/comparisons.Rmd
vignettes/constraints.Rmd
vignettes/simulations.Rmd
zazou.Rproj
