Files in statdivlab/tinyvamp

Modeling complex measurement error in microbiome experiments

R/bootstrap_ci.R R/bootstrap_lrt.R R/calculate_U.R R/calculate_criterion_lr.R R/calculate_log_penalty.R R/construct_Z_tilde.R R/crossfit_U.R R/d_mu_d_P_original.R R/d_mu_d_gamma_original.R R/data.R R/dataframes_to_parameters.R R/deriv_criterion_lr.R R/dfs_to_derivs.R R/dfs_to_mean.R R/do_one_boot.R R/do_one_lrt.R R/do_one_simulation.R R/estimate_parameters.R R/evaluate_criterion_lr.R R/fit_simple_model.R R/fit_simulation_model.R R/get_A_tilde_k_list.R R/get_Ak_list.R R/get_gmm_inv_weights.R R/gmm_criterion.R R/log_penalty.R R/log_penalty_gradient.R R/log_penalty_hessian.R R/logpois.R R/lr_to_ra.R R/make_model_bundle.R R/mean_jac.R R/mean_jac_lr_faster.R R/meaninate.R R/mu_d_alpha_tilde.R R/mu_d_beta.R R/mu_d_beta_faster.R R/mu_d_gamma_faster.R R/mu_d_gamma_tilde.R R/mu_d_rho_faster.R R/mu_d_rho_tilde_faster.R R/nullify.R R/numerical_jacobian.R R/par_to_jacobian_row.R R/parameters_to_dataframes.R R/pb_update_one_constrained.R R/pb_update_unconstrained.R R/poisson_criterion.R R/proximal_bootstrap.R R/push_row.R R/ra_to_lr.R R/refit_model.R R/safe_divide.R R/safe_multiply.R R/simpl_auglag_fnnls.R R/simpl_opt_linesearch_fnnls.R R/simple_poisson.R R/simulate_paper_data.R R/simulate_simple_data.R R/universal_test.R README.Rmd README.md man/bootstrap_ci.Rd man/calculate_log_penalty.Rd man/costea2017_mock_composition.Rd man/dataframes_to_parameters.Rd man/estimate_parameters.Rd man/mu_d_P.Rd man/mu_d_beta.Rd man/mu_d_gamma.Rd man/mu_d_gamma_tilde.Rd man/mu_d_rho_faster.Rd man/mu_d_rho_tilde_faster.Rd tests/testthat.R tests/testthat/test-bootstrap_ci.R tests/testthat/test-bootstrap_lrt.R tests/testthat/test-calculate_log_penalty.R tests/testthat/test-d_mu_d_beta_original.R tests/testthat/test-d_mu_d_gamma_original.R tests/testthat/test-deriv_criterion_lr.R tests/testthat/test-dfs_to_derivs.R tests/testthat/test-do_one_simulation.R tests/testthat/test-estimate_parameters.R tests/testthat/test-fit_simulation_model.R tests/testthat/test-get_A_tilde_k_list.R tests/testthat/test-gmm_criterion.R tests/testthat/test-lr_to_ra.R tests/testthat/test-mean_jac_lr_faster.R tests/testthat/test-mu_d_P.R tests/testthat/test-mu_d_beta.R tests/testthat/test-mu_d_gamma_faster.R tests/testthat/test-mu_d_gamma_tilde.R tests/testthat/test-mu_d_rho.R tests/testthat/test-mu_d_rho_tilde.R tests/testthat/test-optimization.R tests/testthat/test-par_to_jacobian_row.R tests/testthat/test-safe_divide.R tests/testthat/test-simulate_paper_data.R tests/testthat/test-test_meanination.R tests/testthat/test-universal_test.R vignettes/compare-experiments.Rmd vignettes/dilution-series.Rmd