Files in boennecd/dynamichazard
Dynamic Hazard Models using State Space Models

.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
.sandbox/Generalizing.Rmd
.sandbox/Generalizing.html
.sandbox/Sim_study_with_logit/Sim_study_with_logit.Rmd .sandbox/Sim_study_with_logit/Sim_study_with_logit.pdf
.sandbox/Sim_study_with_logit/Sim_study_with_logit.pdf.asis
.sandbox/Sim_study_with_logit/logit_sim_all_varying_200.RDS
.sandbox/Sim_study_with_logit/logit_sim_all_varying_2000.RDS
.sandbox/Sim_study_with_logit/logit_sim_diff_binning_200.RDS
.sandbox/Sim_study_with_logit/logit_sim_diff_binning_2000.RDS
.sandbox/Sim_study_with_logit/logit_sim_one_variying_200.RDS
.sandbox/Sim_study_with_logit/logit_sim_one_variying_2000.RDS
.sandbox/benchmark_parallelglm.R .sandbox/benchmarking.R
.sandbox/bibliography.bib
.sandbox/french_three.Rmd
.sandbox/french_three/frtcs.dat
.sandbox/pbc_data.Rmd .sandbox/profile.R
DESCRIPTION
NAMESPACE
NEWS.md R/HDs.R R/PF.R R/RcppExports.R R/boot_est.R R/ddhazard.R R/get_design_matrix.R R/hatvalues.R R/loglike.R R/options.R R/plot.R R/predict.R R/print.R R/release_questions.R R/residuals.R R/risk_obj.R R/roxygen_tags.R R/shiny_app.R R/sims.R R/static_glm.R R/summary.R R/utils.R
README-ddhazard_fit-1.png
README-ddhazard_fit-2.png
README-pf_fit-1.png
README-pf_plots-1.png
README-pf_plots-2.png
README-pf_plots-3.png
README.Rmd
README.bib
README.md
TODO
cran-comments.md
data-raw/hds
data/hds.rda
dynamichazard.Rproj
examples/.gitignore
examples/README.md examples/RW.Rmd
examples/RW.html
examples/bibliography.bib
examples/fig/RW-fig/ekf_est_plot-1.png
examples/fig/RW-fig/ekf_est_plot-2.png
examples/fig/RW-fig/fearnhead_w_a_0_logLik-1.png
examples/fig/RW-fig/fearnhead_w_a_0_plot-1.png
examples/fig/RW-fig/fearnhead_wo_a_0_ess-1.png
examples/fig/RW-fig/fearnhead_wo_a_0_logLik-1.png
examples/fig/RW-fig/fearnhead_wo_a_0_plot-1.png
examples/fig/RW-fig/sim_plot_latent-1.png
examples/fig/firstOrderVAR-fig/O_N_sq_show_sgd_res-1.png
examples/fig/firstOrderVAR-fig/brier_eff_far_F-1.png
examples/fig/firstOrderVAR-fig/brier_log_like_far_F-1.png
examples/fig/firstOrderVAR-fig/brier_plot_far_F-1.png
examples/fig/firstOrderVAR-fig/fear_eff_far_F-1.png
examples/fig/firstOrderVAR-fig/fear_log_like_far_F-1.png
examples/fig/firstOrderVAR-fig/fear_log_like_far_F_tail-1.png
examples/fig/firstOrderVAR-fig/fear_plot_far_F-1.png
examples/fig/firstOrderVAR-fig/fear_true_log_like-1.png
examples/fig/firstOrderVAR-fig/more_parts_pf_Fear_log_like-1.png
examples/fig/firstOrderVAR-fig/show_averaging_res-1.png
examples/fig/firstOrderVAR-fig/show_obs_info_sgd-1.png
examples/fig/firstOrderVAR-fig/show_obs_info_sgd-2.png
examples/fig/firstOrderVAR-fig/show_sgd_res-1.png
examples/fig/firstOrderVAR-fig/sim_plot_latent-1.png
examples/fig/iid-fig/fearn_ests-1.png
examples/fig/iid-fig/glmer_get_dat-1.png
examples/fig/iid-fig/log_like_ohter-1.png
examples/fig/iid-fig/plot_ess-1.png
examples/fig/iid-fig/plot_log_like-1.png
examples/fig/iid-fig/plot_smooth_est-1.png
examples/fig/iid-fig/plot_smooth_est_other-1.png
examples/fig/iid-fig/sim_obs-1.png
examples/fig/iid-fig/sim_obs-2.png
examples/fig/iid-fig/sim_plot_latent-1.png
examples/fig/iid-fig/unnamed-chunk-1-1.png
examples/fig/iid-fig/unnamed-chunk-2-1.png
examples/fig/overhead-fig/ass_res_func-1.png
examples/fig/overhead-fig/show_res_many_obs-1.png
examples/fig/overhead-fig/show_res_second-1.png
examples/fig/overhead-fig/sim_plot_latent-1.png
examples/fig/restrictedVAR-fig/pf_Fear_restric_plot_smooth-1.png
examples/fig/restrictedVAR-fig/pf_Fear_restric_show_log_like-1.png
examples/fig/restrictedVAR-fig/pf_Fear_restric_show_log_like-2.png
examples/fig/restrictedVAR-fig/plot_smooth-1.png
examples/fig/restrictedVAR-fig/plot_smooth-2.png
examples/fig/restrictedVAR-fig/plot_smooth-3.png
examples/fig/restrictedVAR-fig/plot_smooth-4.png
examples/fig/restrictedVAR-fig/show_log_like-1.png
examples/fig/restrictedVAR-fig/show_log_like-2.png
examples/fig/restrictedVAR-fig/show_sims-1.png
examples/fig/restrictedVAR-fig/sim_plot_latent-1.png
examples/firstOrderVAR.Rmd
examples/firstOrderVAR.html
examples/iid.Rmd
examples/iid.html
examples/overhead.Rmd
examples/overhead.html
examples/restrictedVAR.Rmd
examples/restrictedVAR.html
inst/CITATION
inst/shiny/app.R man/PF_EM.Rd man/PF_control.Rd man/PF_forward_filter.Rd man/PF_get_score_n_hess.Rd man/ddFixed.Rd man/ddhazard.Rd man/ddhazard_app.Rd man/ddhazard_boot.Rd man/ddhazard_control.Rd man/ddsurvcurve.Rd man/get_Q_0.Rd man/get_cloud_means.Rd man/get_cloud_quantiles.Rd man/get_risk_obj.Rd man/get_survival_case_weights_and_data.Rd man/hatvalues.ddhazard.Rd man/hds.Rd man/logLik.PF_EM.Rd man/logLik.ddhazard.Rd man/plot.PF_EM.Rd man/plot.PF_clouds.Rd man/plot.ddhazard.Rd man/plot.ddhazard_space_errors.Rd man/predict.ddhazard.Rd man/print.ddhazard_boot.Rd man/residuals.ddhazard.Rd man/static_glm.Rd man/summary.ddhazard.Rd speedtest/speedtest.Rmd speedtest/speedtest.pdf
src/BLAS_LAPACK/R_BLAS_LAPACK.cpp
src/BLAS_LAPACK/arma_BLAS_LAPACK.cpp
src/BLAS_LAPACK/dchur.f
src/Makevars
src/Makevars.win
src/PF.cpp
src/PF/PF_data.h
src/PF/PF_logger.cpp
src/PF/PF_score_n_Hess.cpp
src/PF/PF_utils.cpp
src/PF/PF_utils.h
src/PF/PFs.cpp
src/PF/PFs.h
src/PF/cond_approx.cpp
src/PF/cond_approx.h
src/PF/covarmat.cpp
src/PF/covarmat.h
src/PF/densities.cpp
src/PF/densities.h
src/PF/dists.cpp
src/PF/dists.h
src/PF/dmvnrm.cpp
src/PF/dmvnrm.h
src/PF/est_params.h
src/PF/est_params_RW.cpp
src/PF/est_params_dens.cpp
src/PF/get_work_blocks.h
src/PF/importance_samplers.cpp
src/PF/importance_samplers.h
src/PF/particles.cpp
src/PF/particles.h
src/PF/r_to_cpp_clouds_n_reverse.cpp
src/PF/resamplers.cpp
src/PF/resamplers.h
src/PF/smoother_output.cpp
src/PF_fixed_effects.cpp
src/R_BLAS_LAPACK.h
src/Rconfig-wrap.h
src/RcppExports.cpp
src/arma_BLAS_LAPACK.h
src/arma_n_rcpp.h
src/bigglm_wrapper.cpp
src/bigglm_wrapper.h
src/biglm/boundedQRf.f
src/ddhazard.h
src/ddhazard/EKF_solver.cpp
src/ddhazard/GMA_solver.cpp
src/ddhazard/SMA_solver.cpp
src/ddhazard/UKF_solver.cpp
src/ddhazard_fit.cpp
src/estimate_fixed_effects_M_step.cpp
src/estimate_fixed_effects_M_step.h
src/family.cpp
src/family.h
src/for_tests.cpp
src/lin_maps.cpp
src/lin_maps.h
src/loglike.cpp
src/parallel_glm.cpp
src/parallel_qr.cpp
src/parallel_qr.h
src/problem_data.h
src/risk_obj.cpp
src/sample_funcs.cpp
src/sample_funcs.h
src/thread_pool.cpp
src/thread_pool.h
src/utils.cpp
src/utils.h
tests/testthat.R
tests/testthat/Rossi.RData
tests/testthat/VAR_data.RDS
tests/testthat/VAR_restrict_vs_non_data.RDS
tests/testthat/binary.csv
tests/testthat/ddsurvcurve-fix-cont.RDS
tests/testthat/helper.R tests/testthat/pf-internals/approximation.R tests/testthat/pf-internals/dists.R tests/testthat/pf-internals/state-dists.R
tests/testthat/previous_results/AUX_normal_approx_w_cloud_mean_cloud_means.RDS
tests/testthat/previous_results/AUX_normal_approx_w_particles_cloud_means.RDS
tests/testthat/previous_results/Brier_AUX_normal_w_particles_cloud_means.RDS
tests/testthat/previous_results/E_step_fixed_exp_head_neck.RDS
tests/testthat/previous_results/E_step_fixed_head_neck.RDS
tests/testthat/previous_results/E_step_fixed_pbc.RDS
tests/testthat/previous_results/E_step_sim_EKF_order_two.RDS
tests/testthat/previous_results/E_step_sim_UKF.RDS
tests/testthat/previous_results/E_step_sim_exp_UKF.RDS
tests/testthat/previous_results/E_step_sim_exp_UKF_order_two.RDS
tests/testthat/previous_results/GMA_head_neck_cancer_o1.RDS
tests/testthat/previous_results/GMA_pbc_fixed_E_step.RDS
tests/testthat/previous_results/GMA_pbc_fixed_M_step.RDS
tests/testthat/previous_results/GMA_pbc_o1_exp.RDS
tests/testthat/previous_results/GMA_pbc_o2_logit.RDS
tests/testthat/previous_results/GMA_pbc_o2_logit_lower_LR.RDS
tests/testthat/previous_results/PF_EM_print
tests/testthat/previous_results/PF_VARS.RDS
tests/testthat/previous_results/PF_VARS_non_zero_mean_inter.RDS
tests/testthat/previous_results/PF_VARS_non_zero_mean_slope.RDS
tests/testthat/previous_results/PF_clouds_print
tests/testthat/previous_results/PF_get_score_n_hess-help-res-O_N_sq-old.RDS
tests/testthat/previous_results/PF_get_score_n_hess-help-res-O_N_sq.RDS
tests/testthat/previous_results/PF_get_score_n_hess-help-res-old.RDS
tests/testthat/previous_results/PF_get_score_n_hess-help-res.RDS
tests/testthat/previous_results/PF_head_neck_cloud_means.RDS
tests/testthat/previous_results/PF_head_neck_w_Brier_method_cloud_means.RDS
tests/testthat/previous_results/PF_mean_2D.RDS
tests/testthat/previous_results/PF_normal_approx_w_cloud_mean_cloud_means.RDS
tests/testthat/previous_results/PF_normal_approx_w_particles_cloud_means.RDS
tests/testthat/previous_results/PF_quantile_2D.RDS
tests/testthat/previous_results/Rossi_pearson.RDS
tests/testthat/previous_results/Rossi_state.RDS
tests/testthat/previous_results/UKF1.RDS
tests/testthat/previous_results/UKF2.RDS
tests/testthat/previous_results/UKF4.RDS
tests/testthat/previous_results/UKF_exp_head_neck.RDS
tests/testthat/previous_results/boot1.RDS
tests/testthat/previous_results/boot2.RDS
tests/testthat/previous_results/boot3.RDS
tests/testthat/previous_results/boot4.RDS
tests/testthat/previous_results/boot_posterior_approx.RDS
tests/testthat/previous_results/boot_print
tests/testthat/previous_results/boot_print_w_o_fixed
tests/testthat/previous_results/bootstrap_filter_cloud_means.RDS
tests/testthat/previous_results/cloglog-preds.RDS
tests/testthat/previous_results/cloglog-sim-ekf-1-it.RDS
tests/testthat/previous_results/cloglog-sim-ekf-more-it.RDS
tests/testthat/previous_results/cloglog-sim-gma.RDS
tests/testthat/previous_results/ddhazard_boot_help_page.RDS
tests/testthat/previous_results/ddhazard_exp_clip.RDS
tests/testthat/previous_results/ddhazard_exp_clip_w_jump.RDS
tests/testthat/previous_results/ddhazard_exp_sim_data.RDS
tests/testthat/previous_results/ddhazard_head_neck.RDS
tests/testthat/previous_results/ddhazard_help_page_loglike.RDS
tests/testthat/previous_results/ddhazard_help_page_order_one.RDS
tests/testthat/previous_results/ddhazard_help_page_order_two.RDS
tests/testthat/previous_results/ddhazard_help_page_predict_response.RDS
tests/testthat/previous_results/ddhazard_help_page_predict_term.RDS
tests/testthat/previous_results/ddhazard_help_page_residuals.RDS
tests/testthat/previous_results/ddsurvcurve-fix-cont.RDS
tests/testthat/previous_results/ddsurvcurve-fix-disc-1.RDS
tests/testthat/previous_results/ddsurvcurve-fix-disc-2.RDS
tests/testthat/previous_results/fixed_terms1.RDS
tests/testthat/previous_results/fixed_terms_UKF.RDS
tests/testthat/previous_results/fixed_terms_UKF_exp.RDS
tests/testthat/previous_results/fixed_terms_UKF_exp_E_step.RDS
tests/testthat/previous_results/fixed_terms_pbc.RDS
tests/testthat/previous_results/get_risk_obj_help_page.RDS
tests/testthat/previous_results/get_survival_case_weights_and_data_help_page_1.RDS
tests/testthat/previous_results/get_survival_case_weights_and_data_help_page_2.RDS
tests/testthat/previous_results/hats_dym_Rossi.RDS
tests/testthat/previous_results/hats_dym_n_fixed_Rossi.RDS
tests/testthat/previous_results/hats_dym_n_fixed_whas500.RDS
tests/testthat/previous_results/hats_dym_whas500.RDS
tests/testthat/previous_results/hatvalues_help_page.RDS
tests/testthat/previous_results/head_neck_exp.RDS
tests/testthat/previous_results/local_tests/AUX_normal_approx_w_cloud_mean.RDS
tests/testthat/previous_results/local_tests/AUX_normal_approx_w_particles.RDS
tests/testthat/previous_results/local_tests/Brier_AUX_normal_w_particles.RDS
tests/testthat/previous_results/local_tests/PF_head_neck.RDS
tests/testthat/previous_results/local_tests/PF_head_neck_w_Brier_method.RDS
tests/testthat/previous_results/local_tests/PF_normal_approx_w_cloud_mean.RDS
tests/testthat/previous_results/local_tests/PF_normal_approx_w_particles.RDS
tests/testthat/previous_results/local_tests/bootstrap_filter.RDS
tests/testthat/previous_results/local_tests/cloglog-PF-RW.RDS
tests/testthat/previous_results/local_tests/cloud_example_no_transition_likelihoods.RDS
tests/testthat/previous_results/local_tests/cloud_example_with_transition_likelihoods.RDS
tests/testthat/previous_results/local_tests/compute_summary_stats.RDS
tests/testthat/previous_results/local_tests/compute_summary_stats_w_Brier_method.RDS
tests/testthat/previous_results/local_tests/pf-rw-w-no-obs-periods.RDS
tests/testthat/previous_results/local_tests/pf_logit_w_fixed.RDS
tests/testthat/previous_results/local_tests/pf_man_2nd_ddfit.RDS
tests/testthat/previous_results/local_tests/pf_man_2nd_ppfit.RDS
tests/testthat/previous_results/local_tests/pf_man_restrict_fit_ex.RDS
tests/testthat/previous_results/local_tests/pf_man_restrict_fit_ex_more.RDS
tests/testthat/previous_results/local_tests/survival_lung_example.RDS
tests/testthat/previous_results/n_smooth_final_RW.RDS
tests/testthat/previous_results/n_smooth_final_VAR.RDS
tests/testthat/previous_results/pearson.RDS
tests/testthat/previous_results/pf_t_dist_proposal.RDS
tests/testthat/previous_results/posterior_approx_exp_pbc.RDS
tests/testthat/previous_results/posterior_approx_logit_2_order.RDS
tests/testthat/previous_results/posterior_approx_logit_fixed_E.RDS
tests/testthat/previous_results/posterior_approx_logit_fixed_M.RDS
tests/testthat/previous_results/posterior_approx_logit_pbc.RDS
tests/testthat/previous_results/posterior_approx_logit_pbc_large_by.RDS
tests/testthat/previous_results/print-ddsurvcurve
tests/testthat/previous_results/print_ddhazard
tests/testthat/previous_results/print_ddhazard_UKF
tests/testthat/previous_results/print_ddhazard_exp
tests/testthat/previous_results/sim_exp.RDS
tests/testthat/previous_results/space_error_print
tests/testthat/previous_results/static1.RDS
tests/testthat/previous_results/static_glm_help_page.RDS
tests/testthat/previous_results/std_space_error_print
tests/testthat/previous_results/summary_ddhazard_UKF_object.RDS
tests/testthat/previous_results/summary_ddhazard_UKF_print
tests/testthat/previous_results/summary_ddhazard_all_coef_object.RDS
tests/testthat/previous_results/summary_ddhazard_all_coef_print
tests/testthat/previous_results/summary_ddhazard_exp_object.RDS
tests/testthat/previous_results/summary_ddhazard_exp_print
tests/testthat/previous_results/summary_ddhazard_fixed_object.RDS
tests/testthat/previous_results/summary_ddhazard_fixed_print
tests/testthat/previous_results/summary_ddhazard_object.RDS
tests/testthat/previous_results/summary_ddhazard_one_coef_object.RDS
tests/testthat/previous_results/summary_ddhazard_one_coef_print
tests/testthat/previous_results/summary_ddhazard_one_digit_object.RDS
tests/testthat/previous_results/summary_ddhazard_one_digit_print
tests/testthat/previous_results/summary_ddhazard_print
tests/testthat/previous_results/survival_lung_example_cloud_means.RDS
tests/testthat/previous_results/util_sim_exp.RDS
tests/testthat/previous_results/util_sim_logit.RDS
tests/testthat/previous_results/whas_pearson.RDS
tests/testthat/previous_results/whas_state.RDS
tests/testthat/test_GMA.R tests/testthat/test_LAPACK_BLAS.R tests/testthat/test_PF.R tests/testthat/test_SMA.R tests/testthat/test_UKF.R tests/testthat/test_bigglm_wrapper.R tests/testthat/test_boot_est.R tests/testthat/test_cloglog.R tests/testthat/test_cpp_sample_funcs.R tests/testthat/test_cpp_utils.R tests/testthat/test_ddhazard_n_EKF.R tests/testthat/test_design_mat_and_risk_obj.R tests/testthat/test_fixed_effects_in_E_step.R tests/testthat/test_fixed_effects_in_M_step.R tests/testthat/test_get_start_values.R tests/testthat/test_hatvalues.R tests/testthat/test_help_page_examples.R tests/testthat/test_loglike.R tests/testthat/test_options.R tests/testthat/test_parallelglm.R tests/testthat/test_plot.R tests/testthat/test_predict.R tests/testthat/test_print.R tests/testthat/test_residuals.R tests/testthat/test_shiny_app.R tests/testthat/test_static_glm.R tests/testthat/test_summary.R tests/testthat/test_test_utils.R tests/testthat/test_weights.R
tests/testthat/whas500.RData
vignettes/Bootstrap_illustration.pdf
vignettes/Bootstrap_illustration.pdf.asis
vignettes/Comparing_methods_for_logistic_models.Rmd vignettes/Diagnostics.Rmd
vignettes/Diagnostics/Rossi.RData
vignettes/Diagnostics/Rossi.txt
vignettes/Diagnostics/Rossi_ex.html
vignettes/Diagnostics/Rossi_source.url
vignettes/Diagnostics/data_prep.R
vignettes/Diagnostics/whas500.RData
vignettes/Particle_filtering.pdf
vignettes/Particle_filtering.pdf.asis
vignettes/Prebuild/Bootstrap_illustration.Rmd
vignettes/Prebuild/Bootstrap_illustration.bib
vignettes/Prebuild/Particle_filtering/PF.bib
vignettes/Prebuild/Particle_filtering/Particle_filtering.pdf
vignettes/Prebuild/Particle_filtering/Particle_filtering.tex
vignettes/bib_style.csl
vignettes/bibliography.bib
vignettes/ddbib.bib
vignettes/ddhazard.Rnw
boennecd/dynamichazard documentation built on Oct. 11, 2022, 2:41 p.m.