Man pages for baker
Nested Partially Latent Class Models
| add_meas_BrS_case_Nest_Slice | add likelihood for a BrS measurement slice among cases... |
| add_meas_BrS_case_Nest_Slice_jags | add likelihood for a BrS measurement slice among cases... |
| add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags | add likelihood component for a BrS measurement slice among... |
| add_meas_BrS_case_NoNest_reg_Slice_jags | add likelihood component for a BrS measurement slice among... |
| add_meas_BrS_case_NoNest_Slice | add a likelihood component for a BrS measurement slice among... |
| add_meas_BrS_case_NoNest_Slice_jags | add a likelihood component for a BrS measurement slice among... |
| add_meas_BrS_ctrl_Nest_Slice | add likelihood for a BrS measurement slice among controls... |
| add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags | add a likelihood component for a BrS measurement slice among... |
| add_meas_BrS_ctrl_NoNest_reg_Slice_jags | add a likelihood component for a BrS measurement slice among... |
| add_meas_BrS_ctrl_NoNest_Slice | add a likelihood component for a BrS measurement slice among... |
| add_meas_BrS_param_Nest_reg_Slice_jags | add parameters for a BrS measurement slice among cases and... |
| add_meas_BrS_param_Nest_Slice | add parameters for a BrS measurement slice among cases and... |
| add_meas_BrS_param_Nest_Slice_jags | add parameters for a BrS measurement slice among cases and... |
| add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags | add parameters for a BrS measurement slice among cases and... |
| add_meas_BrS_param_NoNest_reg_Slice_jags | add parameters for a BrS measurement slice among cases and... |
| add_meas_BrS_param_NoNest_Slice | add parameters for a BrS measurement slice among cases and... |
| add_meas_BrS_param_NoNest_Slice_jags | add parameters for a BrS measurement slice among cases and... |
| add_meas_BrS_subclass_Nest_Slice | add subclass indicators for a BrS measurement slice among... |
| add_meas_SS_case | add likelihood for a SS measurement slice among cases... |
| add_meas_SS_param | add parameters for a SS measurement slice among cases... |
| as.matrix_or_vec | convert one column data frame to a vector |
| assign_model | Interpret the specified model structure |
| baker | baker: *B*ayesian *A*nalytic *K*it for *E*tiology *R*esearch |
| beta_parms_from_quantiles | Pick parameters in the Beta distribution to match the... |
| beta_plot | Plot beta density |
| bin2dec | Convert a 0/1 binary-coded sequence into decimal digits |
| check_dir_create | check existence and create folder if non-existent |
| clean_combine_subsites | Combine subsites in raw PERCH data set |
| clean_perch_data | Clean PERCH data |
| combine_data_nplcm | combine multiple data_nplcm (useful when simulating data from... |
| compute_logOR_single_cause | Calculate marginal log odds ratios |
| compute_marg_PR_nested_reg | compute positive rates for nested model with subclass mixing... |
| compute_marg_PR_nested_reg_array | compute positive rates for nested model with subclass mixing... |
| create_bugs_regressor_Eti | create regressor summation equation used in regression for... |
| create_bugs_regressor_FPR | create regressor summation equation used in regression for... |
| data_nplcm_noreg | Simulated dataset that is structured in the format necessary... |
| data_nplcm_reg_nest | Simulated dataset that is structured in the format necessary... |
| delete_start_with | Deletes a pattern from the start of a string, or each of a... |
| dm_Rdate_Eti | Make etiology design matrix for dates with R format. |
| dm_Rdate_FPR | Make FPR design matrix for dates with R format. |
| expit | expit function |
| extract_data_raw | Import Raw PERCH Data 'extract_data_raw' imports and converts... |
| get_coverage | Obtain coverage status from a result folder |
| get_direct_bias | Obtain direct bias that measure the discrepancy of a... |
| get_fitted_mean_nested | get fitted mean for nested model with subclass mixing weights... |
| get_fitted_mean_no_nested | get model fitted mean for conditional independence model |
| get_individual_data | get individual data |
| get_individual_prediction | get individual prediction (Bayesian posterior) |
| get_latent_seq | get index of latent status |
| get_marginal_rates_nested | get marginal TPR and FPR for nested model |
| get_marginal_rates_no_nested | get marginal TPR and FPR for no nested model |
| get_metric | Obtain Integrated Squared Aitchison Distance, Squared Bias... |
| get_pEti_samp | get etiology samples by names (no regression) |
| get_plot_num | get the plotting positions (numeric) for the fitted means; 3... |
| get_plot_pos | get a list of measurement index where to look for data |
| get_postsd | Obtain posterior standard deviation from a result folder |
| get_top_pattern | get top patterns from a slice of bronze-standard measurement |
| H | Shannon entropy for multivariate discrete data |
| has_non_basis | test if a formula has terms not created by [s_date_Eti() or... |
| I2symb | Convert 0/1 coding to pathogen/combinations |
| Imat2cat | Convert a matrix of binary indicators to categorical... |
| init_latent_jags_multipleSS | Initialize individual latent status (for 'JAGS') |
| insert_bugfile_chunk_noreg_etiology | insert distribution for latent status code chunk into .bug... |
| insert_bugfile_chunk_noreg_meas | Insert measurement likelihood (without regression) code... |
| insert_bugfile_chunk_reg_discrete_predictor_etiology | insert etiology regression for latent status code chunk into... |
| insert_bugfile_chunk_reg_discrete_predictor_nonest_meas | Insert measurement likelihood (with regression; discrete)... |
| insert_bugfile_chunk_reg_etiology | insert etiology regression for latent status code chunk into... |
| insert_bugfile_chunk_reg_nest_meas | Insert measurement likelihood (nested model+regression) code... |
| insert_bugfile_chunk_reg_nonest_meas | Insert measurement likelihood (with regression) code chunks... |
| is_discrete | Check if covariates are discrete |
| is.error | Test for 'try-error' class |
| is_intercept_only | check if the formula is intercept only |
| is_jags_folder | See if a result folder is obtained by JAGS |
| is_length_all_one | check if a list has elements all of length one |
| jags2_baker | Run 'JAGS' from R |
| line2user | convert line to user coordinates |
| loadOneName | load an object from .RDATA file |
| logit | logit function |
| logOR | calculate pairwise log odds ratios |
| logsumexp | log sum exp trick |
| lookup_quality | Get position to store in data_nplcm$Mobs: |
| make_filename | Create new file name |
| make_foldername | Create new folder name |
| make_list | Takes any number of R objects as arguments and returns a list... |
| make_meas_object | Make measurement slice |
| make_numbered_list | Make a list with numbered names |
| make_template | make a mapping template for model fitting |
| marg_H | Shannon entropy for binary data |
| match_cause | Match latent causes that might have the same combo but... |
| merge_lists | For a list of many sublists each of which has matrices as its... |
| my_reorder | Reorder the measurement dimensions to match the order for... |
| NA2dot | convert 'NA' to '.' |
| nplcm | Fit nested partially-latent class models (highest-level... |
| nplcm_fit_NoReg | Fit nested partially-latent class model (low-level) |
| nplcm_fit_Reg_discrete_predictor_NoNest | Fit nested partially-latent class model with regression... |
| nplcm_fit_Reg_Nest | Fit nested partially-latent class model with regression... |
| nplcm_fit_Reg_NoNest | Fit nested partially-latent class model with regression... |
| nplcm_read_folder | Read data and other model information from a folder that... |
| null_as_zero | Convert 'NULL' to zero. |
| order_post_eti | order latent status by posterior mean |
| overall_uniform | specify overall uniform (symmetric Dirichlet distribution)... |
| parse_nplcm_reg | parse regression components (either false positive rate or... |
| pathogen_category_perch | pathogens and their categories in PERCH study (virus or... |
| pathogen_category_simulation | Hypothetical pathogens and their categories (virus or... |
| plot_BrS_panel | Plot bronze-standard (BrS) panel |
| plot_case_study | visualize the PERCH etiology regression with a continuous... |
| plot_check_common_pattern | Posterior predictive checking for the nested partially class... |
| plot_check_pairwise_SLORD | Posterior predictive checking for nested partially latent... |
| plot_etiology_regression | visualize the etiology regression with a continuous covariate |
| plot_etiology_strat | visualize the etiology estimates for each discrete levels |
| plot_leftmost | plotting the labels on the left margin for panels plot |
| plot_logORmat | Visualize pairwise log odds ratios (LOR) for data that are... |
| plot.nplcm | 'plot.nplcm' plot the results from 'nplcm()'. |
| plot_panels | Plot three-panel figures for nested partially-latent model... |
| plot_pie_panel | Plot etiology (pie) panel |
| plot_SS_panel | Plot silver-standard (SS) panel |
| plot_subwt_regression | visualize the subclass weight regression with a continuous... |
| print.nplcm | 'print.nplcm' summarizes the results from 'nplcm()'. |
| print.summary.nplcm.no_reg | Compact printing of 'nplcm()' model fits |
| print.summary.nplcm.reg_nest | Compact printing of 'nplcm()' model fits |
| print.summary.nplcm.reg_nest_strat | Compact printing of 'nplcm()' model fits |
| print.summary.nplcm.reg_nonest | Compact printing of 'nplcm()' model fits |
| print.summary.nplcm.reg_nonest_strat | Compact printing of 'nplcm()' model fits |
| read_meas_object | Read measurement slices |
| rvbern | Sample a vector of Bernoulli variables. |
| s_date_Eti | Make Etiology design matrix for dates with R format. |
| s_date_FPR | Make false positive rate (FPR) design matrix for dates with R... |
| set_prior_tpr_BrS_NoNest | Set true positive rate (TPR) prior ranges for bronze-standard... |
| set_prior_tpr_SS | Set true positive rate (TPR) prior ranges for silver-standard... |
| set_strat | Stratification setup by covariates |
| show_dep | Show function dependencies |
| show_individual | get an individual's data from the output of... |
| simulate_brs | Simulate Bronze-Standard (BrS) Data |
| simulate_latent | Simulate Latent Status: |
| simulate_nplcm | Simulate data from nested partially-latent class model... |
| simulate_ss | Simulate Silver-Standard (SS) Data |
| softmax | softmax |
| subset_data_nplcm_by_index | subset data from the output of 'clean_perch_data()' |
| summarize_BrS | summarize bronze-standard data |
| summarize_SS | silver-standard data summary |
| summary.nplcm | 'summary.nplcm' summarizes the results from 'nplcm()'. |
| symb2I | Convert names of pathogen/combinations into 0/1 coding |
| sym_diff_month | get symmetric difference of months from two vector of... |
| tsb | generate stick-breaking prior (truncated) from a vector of... |
| unfactor | Convert factor to numeric without losing information on the... |
| unique_cause | get unique causes, regardless of the actual order in combo |
| unique_month | Get unique month from Date |
| visualize_case_control_matrix | Visualize matrix for a quantity measured on cases and... |
| visualize_season | visualize trend of pathogen observation rate for NPPCR data... |
| write.model | function to write bugs model (copied from R2WinBUGS) |
| write_model_NoReg | Write .bug model file for model without regression |
| write_model_Reg_discrete_predictor_NoNest | Write .bug model file for regression model without nested... |
| write_model_Reg_Nest | Write '.bug' model file for regression model WITH nested... |
| write_model_Reg_NoNest | Write .bug model file for regression model without nested... |
