├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── AllClasses.R ├── AllGenerics.R ├── calculate_distance.R ├── completion.R ├── generate_synthetic_data.R ├── methods.R ├── normalization.R ├── pd_lm.R ├── predict.R ├── proDA.R ├── simple_tests.R ├── stats_functions.R ├── test_diff.R └── util.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── docs ├── articles │ ├── Introduction.html │ ├── Introduction_files │ │ └── figure-html │ │ │ ├── protein_dist-1.png │ │ │ ├── qc-mis_barplot-1.png │ │ │ ├── qc-raw_boxplot-1.png │ │ │ └── sample_dist-1.png │ ├── data-import.html │ └── index.html ├── authors.html ├── docsearch.css ├── docsearch.js ├── index.html ├── index_files │ └── pagedtable-1.1 │ │ ├── css │ │ └── pagedtable.css │ │ └── js │ │ └── pagedtable.js ├── link.svg ├── man │ └── figures │ │ └── README-screenshot_fit_functions.png ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── abundances.html │ ├── accessor_methods.html │ ├── as_replicate.html │ ├── cash-proDAFit-method.html │ ├── coefficient_variance_matrices.html │ ├── coefficients.html │ ├── convergence.html │ ├── dist_approx-proDAFit-method.html │ ├── dist_approx.html │ ├── dist_approx_impl.html │ ├── distance_sq.html │ ├── feature_parameters.html │ ├── figures │ ├── README-protein_dist-1.png │ ├── README-qc-mis_barplot-1.png │ ├── README-qc-raw_boxplot-1.png │ ├── README-sample_dist-1.png │ └── README-screenshot_fit_functions.png │ ├── generate_synthetic_data.html │ ├── grapes-zero_dom_mat_mult-grapes.html │ ├── hyper_parameters.html │ ├── index.html │ ├── invprobit-1.png │ ├── invprobit.html │ ├── invprobit_fast.html │ ├── median_normalization.html │ ├── mply_dbl.html │ ├── pd_lm.fit.html │ ├── pd_lm.html │ ├── pd_row_t_test.html │ ├── predict-proDAFit-method.html │ ├── proDA.html │ ├── proDAFit-class.html │ ├── proDA_package.html │ ├── reference_level.html │ ├── result_names.html │ └── test_diff.html ├── inst ├── extdata │ └── proteinGroups.txt ├── script │ └── proteinGroups_information.txt └── site │ └── build-site.R ├── man ├── abundances.Rd ├── accessor_methods.Rd ├── as_replicate.Rd ├── cash-proDAFit-method.Rd ├── coefficient_variance_matrices.Rd ├── coefficients.Rd ├── convergence.Rd ├── dist_approx.Rd ├── dist_approx_impl.Rd ├── distance_sq.Rd ├── feature_parameters.Rd ├── generate_synthetic_data.Rd ├── grapes-zero_dom_mat_mult-grapes.Rd ├── hyper_parameters.Rd ├── invprobit.Rd ├── invprobit_fast.Rd ├── median_normalization.Rd ├── mply_dbl.Rd ├── pd_lm.Rd ├── pd_lm.fit.Rd ├── pd_row_t_test.Rd ├── predict-proDAFit-method.Rd ├── proDA.Rd ├── proDAFit-class.Rd ├── proDA_package.Rd ├── reference_level.Rd ├── result_names.Rd └── test_diff.Rd ├── tests ├── testthat.R └── testthat │ ├── test-calculate_distance.R │ ├── test-design_parsing.R │ ├── test-normalization.R │ ├── test-pd_lm.R │ ├── test-proDA.R │ ├── test-proDAFit_S4.R │ └── test-test_diff.R └── vignettes ├── .gitignore ├── Introduction.Rmd ├── data-import.Rmd └── figures 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