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baker
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]
[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 18 Sep. 2026.
Previous versions and publish date:
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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