H                       Shannon entropy for multivariate discrete data
I2symb                  Convert 0/1 coding to pathogen/combinations
Imat2cat                Convert a matrix of binary indicators to
                        categorical variables
NA2dot                  convert 'NA' to '.'
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_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_case_NoNest_reg_Slice_jags
                        add likelihood component 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 cases
add_meas_BrS_ctrl_Nest_Slice
                        add likelihood for a BrS measurement slice
                        among controls (conditional independence)
add_meas_BrS_ctrl_NoNest_Slice
                        add a likelihood component for a BrS
                        measurement slice among controls (conditional
                        independence)
add_meas_BrS_ctrl_NoNest_reg_Slice_jags
                        add a likelihood component 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 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_Nest_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_param_NoNest_reg_Slice_jags
                        add parameters for a BrS measurement slice
                        among cases and controls
add_meas_BrS_param_NoNest_reg_discrete_predictor_Slice_jags
                        add parameters for a BrS measurement slice
                        among cases and controls
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
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
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
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.
expit                   expit function
extract_data_raw        Import Raw PERCH Data 'extract_data_raw'
                        imports and converts the raw data to analyzable
                        format
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
has_non_basis           test if a formula has terms not created by
                        [s_date_Eti() or 's_date_FPR()'
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
jags2_baker             Run 'JAGS' from R
line2user               convert line to user coordinates
loadOneName             load an object from .RDATA file
logOR                   calculate pairwise log odds ratios
logit                   logit function
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 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
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_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_fit_Reg_discrete_predictor_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.
order_post_eti          order latent status by posterior mean
overall_uniform         specify overall uniform (symmetric Dirichlet
                        distribution) for etiology prior
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_SS_panel           Plot silver-standard (SS) 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_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
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 format.
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()'.
sym_diff_month          get symmetric difference of months from two
                        vector of R-format dates
symb2I                  Convert names of pathogen/combinations into 0/1
                        coding
tsb                     generate stick-breaking prior (truncated) from
                        a vector of random probabilities
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
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)
write.model             function to write bugs model (copied from
                        R2WinBUGS)
write_model_NoReg       Write .bug model file for model without
                        regression
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
write_model_Reg_discrete_predictor_NoNest
                        Write .bug model file for regression model
                        without nested subclasses
