Files in psborrow2

Bayesian Dynamic Borrowing Analysis and Simulation

NEWS.md R/borrowing_class.R R/prepare_stan_data_inputs.R R/simulate_data.R R/prior_exponential.R R/treatment_class.R R/borrowing_none.R R/sim_is_null_effect_covered.R R/prior_gamma.R R/mcmc_sample.R R/outcome_cont_normal.R R/prior_poisson.R R/analysis_class.R R/sim_borrowing_list.R R/check_data_matrix_has_columns.R R/prior_beta.R R/sim_covariate_list.R R/sim_is_true_effect_covered.R R/data.R R/prior_bernoulli.R R/add_covariates.R R/borrowing_hierarchical_commensurate.R R/prior_half_normal.R R/create_data_matrix.R R/outcome_surv_exponential.R R/sim_data_list.R R/uniform_prior.R R/cmdstan.R R/sim_estimate_bias.R R/create_simulation_obj.R R/prior_half_cauchy.R R/sim_estimate_mse.R R/simvar_class.R R/mcmc_simulation_result.R R/outcome_surv_weibull_ph.R R/sim_treatment_list.R R/generics.R R/package.R R/sim_covariates.R R/treatment_details.R R/borrowing_details.R R/sim_samplesize.R R/load_stan_file.R R/simulation_class.R R/sim_outcome_list.R R/outcome_surv_pem.R R/zzz.R R/get_prior_string_covariates.R R/prior_class.R R/trim_data_matrix.R R/load_and_interpolate_stan_model.R R/prior_cauchy.R R/simulate_data_baseline.R R/borrowing_full.R R/create_analysis_obj.R R/helpers.R R/prior_normal.R R/make_analysis_object_list.R R/outcome_bin_logistic.R R/covariate_class.R R/outcome_class.R R/sim_estimate_effect_variance.R R/cast_mat_to_long_pem.R inst/doc/simulation_study.Rmd inst/doc/weighting.Rmd inst/doc/propensity_scores.Rmd inst/doc/psborrow2.Rmd inst/doc/match_weight_02_application.Rmd inst/doc/simple_overview.Rmd inst/doc/match_weight_01_methods.Rmd inst/doc/dataset.Rmd inst/doc/prior_distributions.Rmd inst/doc/data_simulation.Rmd tests/testthat.R tests/testthat/test-prior_beta.R tests/testthat/test-check_data_matrix_has_columns.R tests/testthat/test-analysis_class.R tests/testthat/test-simvar_class.R tests/testthat/test-prior_poisson.R tests/testthat/test-cmdstan.R tests/testthat/test-create_analysis_obj.R tests/testthat/test-sim_treatment_list.R tests/testthat/test-prior_half_cauchy.R tests/testthat/test-sim_estimate_effect_variance.R tests/testthat/test-prior_exponential.R tests/testthat/test-borrowing_full.R tests/testthat/test-simulate_data_baseline.R tests/testthat/test-cast_mat_to_long_pem.R tests/testthat/test-prepare_stan_data_inputs.R tests/testthat/test-prior_cauchy.R tests/testthat/test-prior_gamma.R tests/testthat/test-borrowing_hierarchical_commensurate.R tests/testthat/test-outcome_bin_logistic.R tests/testthat/test-sim_covariate_list.R tests/testthat/test-uniform_prior.R tests/testthat/test-treatment_details.R tests/testthat/test-sim_data_list.R tests/testthat/test-add_covariates.R tests/testthat/test-sim_outcome_list.R tests/testthat/test-outcome_surv_weibull_ph.R tests/testthat/test-borrowing_none.R tests/testthat/test-helpers.R tests/testthat/test-outcome_surv_exponential.R tests/testthat/test-prior_normal.R tests/testthat/test-sim_samplesize.R tests/testthat/test-sim_covariates.R tests/testthat/test-create_simulation_obj.R tests/testthat/test-create_data_matrix.R tests/testthat/test-mcmc_sample-simulation.R tests/testthat/test-mcmc_sample-analysis.R tests/testthat/test-trim_data_matrix.R tests/testthat/test-outcome_cont_normal.R tests/testthat/test-simulate_data.R tests/testthat/test-outcome_surv_pem.R tests/testthat/test-prior_half_normal.R tests/testthat/test-sim_borrowing_list.R tests/testthat/test-prior_bernoulli.R tests/testthat/_snaps/prior_normal.md tests/testthat/_snaps/simulate_data.md tests/testthat/_snaps/prior_poisson.md tests/testthat/_snaps/prior_bernoulli.md tests/testthat/_snaps/prior_exponential.md tests/testthat/_snaps/uniform_prior.md tests/testthat/_snaps/simulate_data_baseline.md tests/testthat/_snaps/prior_beta.md tests/testthat/_snaps/prior_gamma.md tests/testthat/_snaps/prior_half_cauchy.md tests/testthat/_snaps/prior_cauchy.md tests/testthat/_snaps/analysis_class.md tests/testthat/_snaps/prior_half_normal.md vignettes/simulation_study.Rmd vignettes/weighting.Rmd vignettes/propensity_scores.Rmd vignettes/psborrow2.Rmd vignettes/match_weight_02_application.Rmd vignettes/simple_overview.Rmd vignettes/match_weight_01_methods.Rmd vignettes/dataset.Rmd vignettes/prior_distributions.Rmd vignettes/data_simulation.Rmd man/SimVar-class.Rd man/PriorGamma-class.Rd man/set_transformations.Rd man/SimVarCont-class.Rd man/set_transformations-BaselineObject-method.Rd man/BaselineDataList-class.Rd man/eval_constraints.Rd man/sim_covariates_summ.Rd man/borrowing_none.Rd man/possible_data_sim_vars.Rd man/normal_prior.Rd man/PriorExponential-class.Rd man/uniform_prior.Rd man/PriorHalfNormal-class.Rd man/Outcome-class.Rd man/BaselineObject-class.Rd man/prior_half_normal.Rd man/set_cut_off.Rd man/PriorCauchy-class.Rd man/load_and_interpolate_stan_model.Rd man/outcome_surv_exponential.Rd man/outcome_cont_normal.Rd man/Treatment-class.Rd man/generate.Rd man/plot_pdf.Rd man/SimSampleSize-class.Rd man/prior_gamma.Rd man/SimDataList-class.Rd man/SimBorrowingList-class.Rd man/SimOutcomeList-class.Rd man/generate-BaselineObject-method.Rd man/cut_off_funs.Rd man/DataSimEnrollment-class.Rd man/add_covariates.Rd man/check_data_matrix_has_columns.Rd man/outcome_surv_pem.Rd man/Covariates-class.Rd man/check_fixed_external_data.Rd man/exponential_prior.Rd man/baseline_covariates.Rd man/example_matrix.Rd man/PriorHalfCauchy-class.Rd man/PriorBeta-class.Rd man/BinaryOutcome-class.Rd man/variable_dictionary.Rd man/create_baseline_object.Rd man/OutcomeSurvExponential-class.Rd man/create_alpha_string.Rd man/get_data.Rd man/Borrowing-class.Rd man/prior_bernoulli.Rd man/load_stan_file.Rd man/set_dropout.Rd man/half_normal_prior.Rd man/cont_var.Rd man/poisson_prior.Rd man/bin_var.Rd man/outcome_surv_weibull_ph.Rd man/trim_rows.Rd man/prior_beta.Rd man/TimeToEvent-class.Rd man/get_vars.Rd man/trim_cols.Rd man/PriorNormal-class.Rd man/PriorBernoulli-class.Rd man/outcome_bin_logistic.Rd man/DataSimEvent-class.Rd man/half_cauchy_prior.Rd man/sim_covariates.Rd man/ContinuousOutcome-class.Rd man/DataSimFixedExternalData-class.Rd man/sim_data_list.Rd man/exp_surv_dist.Rd man/SimVarBin-class.Rd man/logistic_bin_outcome.Rd man/enrollment_constant.Rd man/borrowing_hierarchical_commensurate.Rd man/BaselineDataFrame-class.Rd man/borrowing_full.Rd man/psborrow2-package.Rd man/OutcomeContinuousNormal-class.Rd man/covariance_matrix.Rd man/sim_covariate_list.Rd man/get_results.Rd man/binary_cutoff.Rd man/weib_ph_surv_dist.Rd man/get_stan_code.Rd man/sim_outcome_list.Rd man/Simulation-class.Rd man/create_tau_string.Rd man/create_data_matrix.Rd man/gamma_prior.Rd man/prior_poisson.Rd man/prior_cauchy.Rd man/create_analysis_obj.Rd man/OutcomeSurvPEM-class.Rd man/borrowing_details.Rd man/PriorPoisson-class.Rd man/set_enrollment.Rd man/plot.Rd man/BorrowingFull-class.Rd man/prior_normal.Rd man/DataSimObject-class.Rd man/get_prior_string_covariates.Rd man/build_model_string.Rd man/create_event_dist.Rd man/SimTreatmentList-class.Rd man/get_quantiles.Rd man/beta_prior.Rd man/prior_half_cauchy.Rd man/create_simulation_obj.Rd man/UniformPrior-class.Rd man/cauchy_prior.Rd man/generate-DataSimObject-method.Rd man/Prior-class.Rd man/prior_exponential.Rd man/example_surv.Rd man/show_guide.Rd man/bernoulli_prior.Rd man/OutcomeSurvWeibullPH-class.Rd man/SimCovariates-class.Rd man/DataSimCutOff-class.Rd man/as_data_frame.Rd man/Analysis-class.Rd man/sim_borrowing_list.Rd man/mcmc_sample.Rd man/BorrowingNone-class.Rd man/check_cmdstanr.Rd man/treatment_details.Rd man/custom_enrollment.Rd man/SimCovariateList-class.Rd man/OutcomeBinaryLogistic-class.Rd man/MCMCSimulationResult-class.Rd man/sim_treatment_list.Rd man/get_cmd_stan_models.Rd man/create_data_simulation.Rd man/plot_pmf.Rd man/c.Rd man/sim_samplesize.Rd man/rename_draws_covariates.Rd man/BorrowingHierarchicalCommensurate-class.Rd