Files in zhenkewu/baker
Nested Partially Latent Class Models

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

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CRAN-SUBMISSION

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/adhoc-imports.R R/baker.R R/clean-perch-data.R R/compute_functionals_of_model.R R/eda.R R/example_data.R R/nplcm-read-folder.R R/nplcm.R R/plot-etiology-regression.R R/plot-model-check.R R/plot-panels.R R/set-prior.R R/simulate-nplcm.R R/summarize_results.R R/utils.R R/write-model.R README.Rmd README.md

_pkgdown.yml

appveyor.yml

cran-comments.md

data/data_nplcm_noreg.rda

data/data_nplcm_reg_nest.rda

data/pathogen_category_perch.rda

data/pathogen_category_simulation.rda

docs/404.html

docs/LICENSE-text.html

docs/articles/baker_demo.html

docs/articles/baker_demo_files/figure-html/expl-1.png

docs/articles/index.html

docs/authors.html

docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js

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docs/deps/data-deps.txt

docs/deps/jquery-3.6.0/jquery-3.6.0.js

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docs/deps/jquery-3.6.0/jquery-3.6.0.min.map

docs/index.html

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docs/news/index.html

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/H.html

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docs/reference/Imat2cat.html

docs/reference/NA2dot.html

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docs/reference/add_meas_BrS_case_Nest_Slice.html

docs/reference/add_meas_BrS_case_Nest_Slice_jags.html

docs/reference/add_meas_BrS_case_NoNest_Slice.html

docs/reference/add_meas_BrS_case_NoNest_Slice_jags.html

docs/reference/add_meas_BrS_case_NoNest_reg_Slice_jags.html

docs/reference/add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags.html

docs/reference/add_meas_BrS_ctrl_Nest_Slice.html

docs/reference/add_meas_BrS_ctrl_NoNest_Slice.html

docs/reference/add_meas_BrS_ctrl_NoNest_reg_Slice_jags.html

docs/reference/add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags.html

docs/reference/add_meas_BrS_param_Nest_Slice.html

docs/reference/add_meas_BrS_param_Nest_Slice_jags.html

docs/reference/add_meas_BrS_param_Nest_reg_Slice_jags.html

docs/reference/add_meas_BrS_param_NoNest_Slice.html

docs/reference/add_meas_BrS_param_NoNest_Slice_jags.html

docs/reference/add_meas_BrS_param_NoNest_reg_Slice_jags.html

docs/reference/add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags.html

docs/reference/add_meas_BrS_subclass_Nest_Slice.html

docs/reference/add_meas_SS_case.html

docs/reference/add_meas_SS_param.html

docs/reference/as.matrix_or_vec.html

docs/reference/assign_model.html

docs/reference/baker.html

docs/reference/beta_parms_from_quantiles.html

docs/reference/beta_plot-1.png

docs/reference/beta_plot.html

docs/reference/bin2dec.html

docs/reference/check_dir_create.html

docs/reference/clean_combine_subsites.html

docs/reference/clean_perch_data.html

docs/reference/combine_data_nplcm.html

docs/reference/compute_logOR_single_cause-1.png

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docs/reference/compute_logOR_single_cause.html

docs/reference/compute_marg_PR_nested_reg.html

docs/reference/compute_marg_PR_nested_reg_array.html

docs/reference/create_bugs_regressor_Eti.html

docs/reference/create_bugs_regressor_FPR.html

docs/reference/data_nplcm_noreg.html

docs/reference/data_nplcm_reg_nest.html

docs/reference/delete_start_with.html

docs/reference/dm_Rdate_Eti.html

docs/reference/dm_Rdate_FPR.html

docs/reference/expit.html

docs/reference/extract_data_raw.html

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docs/reference/get_coverage.html

docs/reference/get_direct_bias.html

docs/reference/get_fitted_mean_nested.html

docs/reference/get_fitted_mean_no_nested.html

docs/reference/get_individual_data.html

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docs/reference/get_individual_prediction.html

docs/reference/get_latent_seq.html

docs/reference/get_marginal_rates_nested.html

docs/reference/get_marginal_rates_no_nested.html

docs/reference/get_metric.html

docs/reference/get_pEti_samp.html

docs/reference/get_plot_num.html

docs/reference/get_plot_pos.html

docs/reference/get_postsd.html

docs/reference/get_top_pattern.html

docs/reference/has_non_basis.html

docs/reference/index.html

docs/reference/init_latent_jags_multipleSS.html

docs/reference/insert_bugfile_chunk_noreg_etiology.html

docs/reference/insert_bugfile_chunk_noreg_meas.html

docs/reference/insert_bugfile_chunk_reg_discrete_predictor_etiology.html

docs/reference/insert_bugfile_chunk_reg_discrete_predictor_nonest_meas.html

docs/reference/insert_bugfile_chunk_reg_etiology.html

docs/reference/insert_bugfile_chunk_reg_nest_meas.html

docs/reference/insert_bugfile_chunk_reg_nonest_meas.html

docs/reference/is.error.html

docs/reference/is_discrete.html

docs/reference/is_intercept_only.html

docs/reference/is_jags_folder.html

docs/reference/is_length_all_one.html

docs/reference/jags2_baker.html

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docs/reference/line2user.html

docs/reference/loadOneName.html

docs/reference/logOR.html

docs/reference/logit.html

docs/reference/logsumexp.html

docs/reference/lookup_quality.html

docs/reference/make_filename.html

docs/reference/make_foldername.html

docs/reference/make_list.html

docs/reference/make_meas_object.html

docs/reference/make_numbered_list.html

docs/reference/make_template.html

docs/reference/marg_H.html

docs/reference/match_cause.html

docs/reference/merge_lists.html

docs/reference/my_reorder.html

docs/reference/nplcm.html

docs/reference/nplcm_fit_NoReg.html

docs/reference/nplcm_fit_Reg_Nest.html

docs/reference/nplcm_fit_Reg_NoNest.html

docs/reference/nplcm_fit_Reg_discrete_predictor_NoNest.html

docs/reference/nplcm_read_folder.html

docs/reference/null_as_zero.html

docs/reference/order_post_eti.html

docs/reference/overall_uniform.html

docs/reference/parse_nplcm_reg.html

docs/reference/pathogen_category_perch.html

docs/reference/pathogen_category_simulation.html

docs/reference/plot.nplcm.html

docs/reference/plot_BrS_panel.html

docs/reference/plot_SS_panel.html

docs/reference/plot_case_study.html

docs/reference/plot_check_common_pattern-1.png

docs/reference/plot_check_common_pattern.html

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docs/reference/plot_check_pairwise_SLORD.html

docs/reference/plot_etiology_regression.html

docs/reference/plot_etiology_strat.html

docs/reference/plot_leftmost.html

docs/reference/plot_logORmat-1.png

docs/reference/plot_logORmat.html

docs/reference/plot_panels.html

docs/reference/plot_pie_panel.html

docs/reference/plot_subwt_regression.html

docs/reference/print.nplcm.html

docs/reference/print.summary.nplcm.no_reg.html

docs/reference/print.summary.nplcm.reg_nest.html

docs/reference/print.summary.nplcm.reg_nest_strat.html

docs/reference/print.summary.nplcm.reg_nonest.html

docs/reference/print.summary.nplcm.reg_nonest_strat.html

docs/reference/read_meas_object.html

docs/reference/rvbern.html

docs/reference/s_date_Eti.html

docs/reference/s_date_FPR.html

docs/reference/set_prior_tpr_BrS_NoNest.html

docs/reference/set_prior_tpr_SS.html

docs/reference/set_strat.html

docs/reference/show_dep-1.png

docs/reference/show_dep-2.png

docs/reference/show_dep.html

docs/reference/show_individual.html

docs/reference/simulate_brs.html

docs/reference/simulate_latent.html

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docs/reference/simulate_nplcm.html

docs/reference/simulate_ss.html

docs/reference/softmax.html

docs/reference/subset_data_nplcm_by_index.html

docs/reference/summarize_BrS.html

docs/reference/summarize_SS.html

docs/reference/summary.nplcm.html

docs/reference/sym_diff_month.html

docs/reference/symb2I.html

docs/reference/tsb-1.png

docs/reference/tsb.html

docs/reference/unfactor.html

docs/reference/unique_cause.html

docs/reference/unique_month.html

docs/reference/visualize_case_control_matrix.html

docs/reference/visualize_season.html

docs/reference/write.model.html

docs/reference/write_model_NoReg.html

docs/reference/write_model_Reg_Nest.html

docs/reference/write_model_Reg_NoNest.html

docs/reference/write_model_Reg_discrete_predictor_NoNest.html

docs/search.json

docs/sitemap.xml

figure/common_pattern_check-1.png

figure/pairwise_SLORD-1.png

figure/plot_etiology_strat-1.png

figure/plot_etiology_strat-2.png

figure/plot_logORmat-1.png

figure/plot_panels_with_SS-1.png

figure/traceplots-1.png

figure/traceplots-2.png

figure/visualize_posterior_dist-1.png

inst/CITATION

inst/WORDLIST

inst/example/plot_associations.R inst/example/simulate_data_example_nplcm_noreg.R inst/example/simulate_data_example_nplcm_reg_nest.R

inst/example_data/pathogen_category_simulation.csv

inst/figs/legends_visualize_etiology_regression.png

man/figures/nplcm_functional_dependence.png

man/get_coverage.Rd man/get_direct_bias.Rd man/get_fitted_mean_nested.Rd man/get_fitted_mean_no_nested.Rd man/get_individual_data.Rd man/get_individual_prediction.Rd man/get_latent_seq.Rd man/get_marginal_rates_nested.Rd man/get_marginal_rates_no_nested.Rd man/get_metric.Rd man/get_pEti_samp.Rd man/get_plot_num.Rd man/get_plot_pos.Rd man/get_postsd.Rd man/get_top_pattern.Rd man/has_non_basis.Rd man/init_latent_jags_multipleSS.Rd man/insert_bugfile_chunk_noreg_etiology.Rd man/insert_bugfile_chunk_noreg_meas.Rd man/insert_bugfile_chunk_reg_discrete_predictor_etiology.Rd man/insert_bugfile_chunk_reg_discrete_predictor_nonest_meas.Rd man/insert_bugfile_chunk_reg_etiology.Rd man/insert_bugfile_chunk_reg_nest_meas.Rd man/insert_bugfile_chunk_reg_nonest_meas.Rd man/is.error.Rd man/is_discrete.Rd man/is_intercept_only.Rd man/is_jags_folder.Rd man/is_length_all_one.Rd man/jags2_baker.Rd man/line2user.Rd man/loadOneName.Rd man/logOR.Rd man/logit.Rd man/logsumexp.Rd man/lookup_quality.Rd man/make_filename.Rd man/make_foldername.Rd man/make_list.Rd man/make_meas_object.Rd man/make_numbered_list.Rd man/make_template.Rd man/marg_H.Rd man/match_cause.Rd man/merge_lists.Rd man/my_reorder.Rd man/nplcm.Rd man/nplcm_fit_NoReg.Rd man/nplcm_fit_Reg_Nest.Rd man/nplcm_fit_Reg_NoNest.Rd man/nplcm_fit_Reg_discrete_predictor_NoNest.Rd man/nplcm_read_folder.Rd man/null_as_zero.Rd man/order_post_eti.Rd man/overall_uniform.Rd man/parse_nplcm_reg.Rd man/pathogen_category_perch.Rd man/pathogen_category_simulation.Rd man/plot.nplcm.Rd man/plot_BrS_panel.Rd man/plot_SS_panel.Rd man/plot_case_study.Rd man/plot_check_common_pattern.Rd man/plot_check_pairwise_SLORD.Rd man/plot_etiology_regression.Rd man/plot_etiology_strat.Rd man/plot_leftmost.Rd man/plot_logORmat.Rd man/plot_panels.Rd man/plot_pie_panel.Rd man/plot_subwt_regression.Rd man/print.nplcm.Rd man/print.summary.nplcm.no_reg.Rd man/print.summary.nplcm.reg_nest.Rd man/print.summary.nplcm.reg_nest_strat.Rd man/print.summary.nplcm.reg_nonest.Rd man/print.summary.nplcm.reg_nonest_strat.Rd man/read_meas_object.Rd man/rvbern.Rd man/s_date_Eti.Rd man/s_date_FPR.Rd man/set_prior_tpr_BrS_NoNest.Rd man/set_prior_tpr_SS.Rd man/set_strat.Rd man/show_dep.Rd man/show_individual.Rd man/simulate_brs.Rd man/simulate_latent.Rd man/simulate_nplcm.Rd man/simulate_ss.Rd man/softmax.Rd man/subset_data_nplcm_by_index.Rd man/summarize_BrS.Rd man/summarize_SS.Rd man/summary.nplcm.Rd man/sym_diff_month.Rd man/symb2I.Rd man/tsb.Rd man/unfactor.Rd man/unique_cause.Rd man/unique_month.Rd man/visualize_case_control_matrix.Rd man/visualize_season.Rd man/write.model.Rd man/write_model_NoReg.Rd man/write_model_Reg_Nest.Rd man/write_model_Reg_NoNest.Rd man/write_model_Reg_discrete_predictor_NoNest.Rd tests/spelling.R tests/testthat.R tests/testthat/test-helpers.R tests/testthat/test-symbol-conversion.r vignettes/baker_demo.R vignettes/baker_demo.Rmd

vignettes/baker_demo.html

zhenkewu/baker documentation built on March 17, 2022, 9:54 p.m.

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zhenkewu/baker
Nested Partially Latent Class Models

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Nested Partially Latent Class Models

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zhenkewu/baker
Nested Partially Latent Class Models

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Nested Partially Latent Class Models