# "Nested Partially Latent Class Models"

## Documentation for package ‘baker’ version 1.0.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G H I J L M N O P R S T U V W

## -- A --

add_meas_BrS_case_Nest_Slice | add likelihood for a BrS measurement slice among cases (conditional dependence)
add_meas_BrS_case_Nest_Slice_jags | add likelihood for a BrS measurement slice among cases (conditional dependence)
add_meas_BrS_case_NoNest_reg_discrete_predictor_Slice_jags | add likelihood component for a BrS measurement slice among cases
add_meas_BrS_case_NoNest_reg_Slice_jags | add likelihood component for a BrS measurement slice among cases
add_meas_BrS_case_NoNest_Slice | add a likelihood component for a BrS measurement slice among cases (conditional independence)
add_meas_BrS_case_NoNest_Slice_jags | add a likelihood component for a BrS measurement slice among cases (conditional independence)
add_meas_BrS_ctrl_Nest_Slice | add likelihood for a BrS measurement slice among controls (conditional independence)
add_meas_BrS_ctrl_NoNest_reg_discrete_predictor_Slice_jags | add a likelihood component for a BrS measurement slice among controls
add_meas_BrS_ctrl_NoNest_reg_Slice_jags | add a likelihood component for a BrS measurement slice among controls
add_meas_BrS_ctrl_NoNest_Slice | add a likelihood component for a BrS measurement slice among controls (conditional independence)
add_meas_BrS_param_Nest_reg_Slice_jags | add parameters for a BrS measurement slice among cases and controls
add_meas_BrS_param_Nest_Slice | add parameters for a BrS measurement slice among cases and controls (conditional dependence)
add_meas_BrS_param_Nest_Slice_jags | add parameters for a BrS measurement slice among cases and controls (conditional dependence)
add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags | add parameters for a BrS measurement slice among cases and controls
add_meas_BrS_param_NoNest_reg_Slice_jags | add parameters for a BrS measurement slice among cases and controls
add_meas_BrS_param_NoNest_Slice | add parameters for a BrS measurement slice among cases and controls (conditional independence)
add_meas_BrS_param_NoNest_Slice_jags | add parameters for a BrS measurement slice among cases and controls (conditional independence)
add_meas_BrS_subclass_Nest_Slice | add subclass indicators for a BrS measurement slice among cases and controls (conditional independence)
add_meas_SS_case | add likelihood for a SS measurement slice among cases (conditional independence)
add_meas_SS_param | add parameters for a SS measurement slice among cases (conditional independence)
as.matrix_or_vec | convert one column data frame to a vector
assign_model | Interpret the specified model structure

## -- B --

beta_parms_from_quantiles | Pick parameters in the Beta distribution to match the specified range
beta_plot | Plot beta density
bin2dec | Convert a 0/1 binary-coded sequence into decimal digits

## -- C --

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 regression models)
compute_logOR_single_cause | Calculate marginal log odds ratios
compute_marg_PR_nested_reg | compute positive rates for nested model with subclass mixing weights that are the same across 'Jcause' classes for each person (people may have different weights.)
compute_marg_PR_nested_reg_array | compute positive rates for nested model with subclass mixing weights that are the same across 'Jcause' classes for each person (people may have different weights.)
create_bugs_regressor_Eti | create regressor summation equation used in regression for etiology
create_bugs_regressor_FPR | create regressor summation equation used in regression for FPR

## -- D --

data_nplcm_noreg | Simulated dataset that is structured in the format necessary for an 'nplcm()' without regression
data_nplcm_reg_nest | Simulated dataset that is structured in the format necessary for an 'nplcm()' with regression
delete_start_with | Deletes a pattern from the start of a string, or each of a vector of strings.
dm_Rdate_Eti | Make etiology design matrix for dates with R format.
dm_Rdate_FPR | Make FPR design matrix for dates with R format.

## -- E --

expit | expit function
extract_data_raw | Import Raw PERCH Data 'extract_data_raw' imports and converts the raw data to analyzable format

## -- G --

get_coverage | Obtain coverage status from a result folder
get_direct_bias | Obtain direct bias that measure the discrepancy of a posterior distribution of pie and a true pie.
get_fitted_mean_nested | get fitted mean for nested model with subclass mixing weights that are the same among cases
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 and Variance (both on Central Log-Ratio transformed scale) that measure the discrepancy of a posterior distribution of pie and a true pie.
get_pEti_samp | get etiology samples by names (no regression)
get_plot_num | get the plotting positions (numeric) for the fitted means; 3 positions for each cell
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 --

H | Shannon entropy for multivariate discrete data
has_non_basis | test if a formula has terms not created by [s_date_Eti() or 's_date_FPR()'

## -- I --

I2symb | Convert 0/1 coding to pathogen/combinations
Imat2cat | Convert a matrix of binary indicators to categorical variables
init_latent_jags_multipleSS | Initialize individual latent status (for 'JAGS')
insert_bugfile_chunk_noreg_etiology | insert distribution for latent status code chunk into .bug file
insert_bugfile_chunk_noreg_meas | Insert measurement likelihood (without regression) code chunks into .bug model file
insert_bugfile_chunk_reg_discrete_predictor_etiology | insert etiology regression for latent status code chunk into .bug file; discrete predictors
insert_bugfile_chunk_reg_discrete_predictor_nonest_meas | Insert measurement likelihood (with regression; discrete) code chunks into .bug model file
insert_bugfile_chunk_reg_etiology | insert etiology regression for latent status code chunk into .bug file
insert_bugfile_chunk_reg_nest_meas | Insert measurement likelihood (nested model+regression) code chunks into .bug model file
insert_bugfile_chunk_reg_nonest_meas | Insert measurement likelihood (with regression) code chunks into .bug model file
is.error | Test for 'try-error' class
is_discrete | Check if covariates are discrete
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

## -- J --

jags2_baker | Run 'JAGS' from R

## -- L --

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:

## -- M --

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 whose names are derived from the names of the R objects.
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 different specifications
merge_lists | For a list of many sublists each of which has matrices as its member, we combine across the many sublists to produce a final list
my_reorder | Reorder the measurement dimensions to match the order for display

## -- N --

NA2dot | convert 'NA' to '.'
nplcm | Fit nested partially-latent class models (highest-level wrapper function)
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 (low-level)
nplcm_fit_Reg_Nest | Fit nested partially-latent class model with regression (low-level)
nplcm_fit_Reg_NoNest | Fit nested partially-latent class model with regression (low-level)
nplcm_read_folder | Read data and other model information from a folder that stores model results.
null_as_zero | Convert 'NULL' to zero.

## -- O --

order_post_eti | order latent status by posterior mean
overall_uniform | specify overall uniform (symmetric Dirichlet distribution) for etiology prior

## -- P --

parse_nplcm_reg | parse regression components (either false positive rate or etiology regression) for fitting npLCM; Only use this when formula is not 'NULL'.
pathogen_category_perch | pathogens and their categories in PERCH study (virus or bacteria)
pathogen_category_simulation | Hypothetical pathogens and their categories (virus or bacteria)
plot.nplcm | 'plot.nplcm' plot the results from 'nplcm()'.
plot_BrS_panel | Plot bronze-standard (BrS) panel
plot_case_study | visualize the PERCH etiology regression with a continuous covariate
plot_check_common_pattern | Posterior predictive checking for the nested partially class models - frequent patterns in the BrS data. (for multiple folders)
plot_check_pairwise_SLORD | Posterior predictive checking for nested partially latent class models - pairwise log odds ratio (only for bronze-standard data)
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 available in both cases and controls
plot_panels | Plot three-panel figures for nested partially-latent model results
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 covariate
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

## -- R --

read_meas_object | Read measurement slices
rvbern | Sample a vector of Bernoulli variables.

## -- S --

set_prior_tpr_BrS_NoNest | Set true positive rate (TPR) prior ranges for bronze-standard (BrS) data
set_prior_tpr_SS | Set true positive rate (TPR) prior ranges for silver-standard data.
set_strat | Stratification setup by covariates
show_dep | Show function dependencies
show_individual | get an individual's data from the output of 'clean_perch_data()'
simulate_brs | Simulate Bronze-Standard (BrS) Data
simulate_latent | Simulate Latent Status:
simulate_nplcm | Simulate data from nested partially-latent class model (npLCM) family
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 R-format dates
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 format.

## -- T --

tsb | generate stick-breaking prior (truncated) from a vector of random probabilities

## -- U --

unfactor | Convert factor to numeric without losing information on the label
unique_cause | get unique causes, regardless of the actual order in combo
unique_month | Get unique month from Date

## -- V --

visualize_case_control_matrix | Visualize matrix for a quantity measured on cases and controls (a single number)
visualize_season | visualize trend of pathogen observation rate for NPPCR data (both cases and controls)

## -- W --

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 subclasses
write_model_Reg_Nest | Write '.bug' model file for regression model WITH nested subclasses
write_model_Reg_NoNest | Write .bug model file for regression model without nested subclasses