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baker  

"Nested Partially Latent Class Models"
View on CRAN: Click here


Download and install baker package within the R console
Install from CRAN:
install.packages("baker")

Install from Github:
library("remotes")
install_github("cran/baker")

Install by package version:
library("remotes")
install_version("baker", "1.0.4")



Attach the package and use:
library("baker")
Maintained by
Zhenke Wu
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-02-02
Latest Update: 2024-01-30
Description:
Provides functions to specify, fit and visualize nested partially-latent class models ( Wu, Deloria-Knoll, Hammitt, and Zeger (2016) ; Wu, Deloria-Knoll, and Zeger (2017) ; Wu and Chen (2021) ) for inference of population disease etiology and individual diagnosis. In the motivating Pneumonia Etiology Research for Child Health (PERCH) study, because both quantities of interest sum to one hundred percent, the PERCH scientists frequently refer to them as population etiology pie and individual etiology pie, hence the name of the package.
How to cite:
Zhenke Wu (2022). baker: "Nested Partially Latent Class Models". R package version 1.0.4, https://cran.r-project.org/web/packages/baker. Accessed 31 Oct. 2026.
Previous versions and publish date:
(2026-07-09 07:20), 1.0.0 (2022-02-02 09:40), 1.0.2 (2023-12-21 12:40), 1.0.3 (2024-01-30 09:40)
Other packages that cited baker R package
View baker citation profile
Other R packages that baker depends, imports, suggests or enhances
Complete documentation for baker
Functions, R codes and Examples using the baker R package
Some associated functions: H . I2symb . Imat2cat . NA2dot . add_meas_BrS_case_Nest_Slice . add_meas_BrS_case_Nest_Slice_jags . add_meas_BrS_case_NoNest_Slice . add_meas_BrS_case_NoNest_Slice_jags . add_meas_BrS_case_NoNest_reg_Slice_jags . add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags . add_meas_BrS_ctrl_Nest_Slice . add_meas_BrS_ctrl_NoNest_Slice . add_meas_BrS_ctrl_NoNest_reg_Slice_jags . add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags . add_meas_BrS_param_Nest_Slice . add_meas_BrS_param_Nest_Slice_jags . add_meas_BrS_param_Nest_reg_Slice_jags . add_meas_BrS_param_NoNest_Slice . add_meas_BrS_param_NoNest_Slice_jags . add_meas_BrS_param_NoNest_reg_Slice_jags . add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags . add_meas_BrS_subclass_Nest_Slice . add_meas_SS_case . add_meas_SS_param . as.matrix_or_vec . assign_model . baker . beta_parms_from_quantiles . beta_plot . bin2dec . check_dir_create . clean_combine_subsites . clean_perch_data . combine_data_nplcm . compute_logOR_single_cause . compute_marg_PR_nested_reg . compute_marg_PR_nested_reg_array . create_bugs_regressor_Eti . create_bugs_regressor_FPR . data_nplcm_noreg . data_nplcm_reg_nest . delete_start_with . dm_Rdate_Eti . dm_Rdate_FPR . expit . extract_data_raw . get_coverage . get_direct_bias . get_fitted_mean_nested . get_fitted_mean_no_nested . get_individual_data . get_individual_prediction . get_latent_seq . get_marginal_rates_nested . get_marginal_rates_no_nested . get_metric . get_pEti_samp . get_plot_num . get_plot_pos . get_postsd . get_top_pattern . has_non_basis . init_latent_jags_multipleSS . insert_bugfile_chunk_noreg_etiology . insert_bugfile_chunk_noreg_meas . insert_bugfile_chunk_reg_discrete_predictor_etiology . insert_bugfile_chunk_reg_discrete_predictor_nonest_meas . insert_bugfile_chunk_reg_etiology . insert_bugfile_chunk_reg_nest_meas . insert_bugfile_chunk_reg_nonest_meas . is.error . is_discrete . is_intercept_only . is_jags_folder . is_length_all_one . jags2_baker . line2user . loadOneName . logOR . logit . logsumexp . lookup_quality . make_filename . make_foldername . make_list . make_meas_object . make_numbered_list . make_template . marg_H . match_cause . merge_lists . my_reorder . nplcm . nplcm_fit_NoReg . nplcm_fit_Reg_Nest . nplcm_fit_Reg_NoNest . nplcm_fit_Reg_discrete_predictor_NoNest . nplcm_read_folder . null_as_zero . order_post_eti . overall_uniform . parse_nplcm_reg . pathogen_category_perch . pathogen_category_simulation . plot.nplcm . plot_BrS_panel . plot_SS_panel . plot_case_study . plot_check_common_pattern . plot_check_pairwise_SLORD . plot_etiology_regression . plot_etiology_strat . plot_leftmost . plot_logORmat . plot_panels . plot_pie_panel . plot_subwt_regression . print.nplcm . print.summary.nplcm.no_reg . print.summary.nplcm.reg_nest . print.summary.nplcm.reg_nest_strat . print.summary.nplcm.reg_nonest . print.summary.nplcm.reg_nonest_strat . read_meas_object . rvbern . s_date_Eti . s_date_FPR . set_prior_tpr_BrS_NoNest . set_prior_tpr_SS . set_strat . show_dep . show_individual . simulate_brs . simulate_latent . simulate_nplcm . simulate_ss . softmax . subset_data_nplcm_by_index . summarize_BrS . summarize_SS . summary.nplcm . sym_diff_month . symb2I . tsb . unfactor . unique_cause . unique_month . visualize_case_control_matrix . visualize_season . write.model . write_model_NoReg . write_model_Reg_Nest . write_model_Reg_NoNest . write_model_Reg_discrete_predictor_NoNest . 
Some associated R codes: adhoc-imports.R . baker.R . clean-perch-data.R . compute_functionals_of_model.R . eda.R . example_data.R . nplcm-read-folder.R . nplcm.R . plot-etiology-regression.R . plot-model-check.R . plot-panels.R . set-prior.R . simulate-nplcm.R . summarize_results.R . utils.R . write-model.R .  Full baker package functions and examples
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