Files in oslerinhealth/baker
Bayesian Analysis Kit for Etiology Research
.Rbuildignore
.github/workflows/autoci.yml
.github/workflows/autoci_pkgdown.yml
.gitignore
.travis.yml
CRAN-RELEASE
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/.Rapp.history
R/adhoc-imports.R
R/baker.R
R/bakerUI.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-etiology-side-by-side.R
R/plot-group-etiology.R
R/plot-model-check.R
R/plot-panels.R
R/set-prior.R
R/simulate-nplcm.R
R/utils.R
R/write-model.R
README.Rmd
README.md
appveyor.yml
codecov.yml
cran-comments.md
data/data_nplcm_reg.rda
data/pathogen_category_simulation.rda
inst/CITATION
inst/WORDLIST
inst/example/plot_associations.R
inst/example_data/pathogen_category_simulation.csv
inst/extdata/.Rapp.history
inst/figs/legends_visualize_etiology_regression.png
inst/figs/nplcm_functional_dependence.png
inst/figs/visualize_etiology_regression_SITE=1.pdf
inst/shiny/server.R
inst/shiny/ui.R
inst/shiny/www/PERCH_logo.jpg
inst/shiny/www/PERCH_logo.svg
inst/shiny/www/ajaxloaderq.gif
inst/shiny/www/busy.js
inst/shiny/www/gates_logo.jpg
inst/shiny/www/inhealth_logo.jpg
inst/shiny/www/pcori_logo.jpg
inst/shiny/www/style.css
man/.Rapp.history
man/H.Rd
man/I2symb.Rd
man/Imat2cat.Rd
man/NA2dot.Rd
man/add_meas_BrS_case_Nest_Slice.Rd
man/add_meas_BrS_case_Nest_Slice_jags.Rd
man/add_meas_BrS_case_NoNest_Slice.Rd
man/add_meas_BrS_case_NoNest_Slice_jags.Rd
man/add_meas_BrS_case_NoNest_reg_Slice_jags.Rd
man/add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags.Rd
man/add_meas_BrS_ctrl_Nest_Slice.Rd
man/add_meas_BrS_ctrl_NoNest_Slice.Rd
man/add_meas_BrS_ctrl_NoNest_reg_Slice_jags.Rd
man/add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags.Rd
man/add_meas_BrS_param_Nest_Slice.Rd
man/add_meas_BrS_param_Nest_Slice_jags.Rd
man/add_meas_BrS_param_Nest_reg_Slice_jags.Rd
man/add_meas_BrS_param_NoNest_Slice.Rd
man/add_meas_BrS_param_NoNest_Slice_jags.Rd
man/add_meas_BrS_param_NoNest_reg_Slice_jags.Rd
man/add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags.Rd
man/add_meas_BrS_subclass_Nest_Slice.Rd
man/add_meas_SS_case.Rd
man/add_meas_SS_param.Rd
man/as.matrix_or_vec.Rd
man/assign_model.Rd
man/assign_taxo_cause_list.Rd
man/baker.Rd
man/bakerUI.Rd
man/beta_parms_from_quantiles.Rd
man/beta_plot.Rd
man/bin2dec.Rd
man/check_dir_create.Rd
man/clean_combine_subsites.Rd
man/clean_perch_data.Rd
man/combine_data_nplcm.Rd
man/compute_logOR_single_cause.Rd
man/compute_marg_PR_nested_reg.Rd
man/compute_marg_PR_nested_reg_array.Rd
man/create_bugs_regressor_Eti.Rd
man/create_bugs_regressor_FPR.Rd
man/data_nplcm_reg.Rd
man/delete_start_with.Rd
man/dm_Rdate_Eti.Rd
man/dm_Rdate_FPR.Rd
man/expit.Rd
man/extract_data_raw.Rd
man/getPckg.Rd
man/get_cause_by_num.Rd
man/get_cause_by_taxo_group.Rd
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_pEti_samp_reg.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/load_or_install.Rd
man/logOR.Rd
man/logit.Rd
man/logsumexp.Rd
man/lookup_quality.Rd
man/lookup_side_by_side.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_simulation.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_side_by_side.Rd
man/plot_etiology_strat.Rd
man/plot_etiology_strat_nested.Rd
man/plot_group_etiology.Rd
man/plot_leftmost.Rd
man/plot_logORmat.Rd
man/plot_panels.Rd
man/plot_pie_panel.Rd
man/plot_selected_etiology.Rd
man/plot_subwt_regression.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/sort_data_frame.Rd
man/subset_data_nplcm_by_index.Rd
man/summarize_BrS.Rd
man/summarize_SS.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
tic.R
vignettes/baker_demo.Rmd
