"Nested Partially Latent Class Models"
add likelihood for a BrS measurement slice among cases (conditional de...
add likelihood for a BrS measurement slice among cases (conditional de...
add likelihood component for a BrS measurement slice among cases
add likelihood component for a BrS measurement slice among cases
add a likelihood component for a BrS measurement slice among cases (co...
add a likelihood component for a BrS measurement slice among cases (co...
add likelihood for a BrS measurement slice among controls (conditional...
add a likelihood component for a BrS measurement slice among controls
add a likelihood component for a BrS measurement slice among controls
add a likelihood component for a BrS measurement slice among controls ...
add parameters for a BrS measurement slice among cases and controls
add parameters for a BrS measurement slice among cases and controls (c...
add parameters for a BrS measurement slice among cases and controls (c...
add parameters for a BrS measurement slice among cases and controls
add parameters for a BrS measurement slice among cases and controls
add parameters for a BrS measurement slice among cases and controls (c...
add parameters for a BrS measurement slice among cases and controls (c...
add subclass indicators for a BrS measurement slice among cases and co...
add likelihood for a SS measurement slice among cases (conditional ind...
add parameters for a SS measurement slice among cases (conditional ind...
convert one column data frame to a vector
Interpret the specified model structure
baker: B ayesian A nalytic K it for E tiology R esearch
Pick parameters in the Beta distribution to match the specified range
Plot beta density
Convert a 0/1 binary-coded sequence into decimal digits
check existence and create folder if non-existent
Combine subsites in raw PERCH data set
Clean PERCH data
combine multiple data_nplcm (useful when simulating data from regressi...
Calculate marginal log odds ratios
compute positive rates for nested model with subclass mixing weights t...
compute positive rates for nested model with subclass mixing weights t...
create regressor summation equation used in regression for etiology
create regressor summation equation used in regression for FPR
Deletes a pattern from the start of a string, or each of a vector of s...
Make etiology design matrix for dates with R format.
Make FPR design matrix for dates with R format.
expit function
Import Raw PERCH Dataextract_data_raw imports and converts the raw d...
Obtain coverage status from a result folder
Obtain direct bias that measure the discrepancy of a posterior distrib...
get fitted mean for nested model with subclass mixing weights that are...
get model fitted mean for conditional independence model
get individual data
get individual prediction (Bayesian posterior)
get index of latent status
get marginal TPR and FPR for nested model
get marginal TPR and FPR for no nested model
Obtain Integrated Squared Aitchison Distance, Squared Bias and Varianc...
get etiology samples by names (no regression)
get the plotting positions (numeric) for the fitted means; 3 positions...
get a list of measurement index where to look for data
Obtain posterior standard deviation from a result folder
get top patterns from a slice of bronze-standard measurement
Shannon entropy for multivariate discrete data
test if a formula has terms not created by [s_date_Eti() or `s_date_FP...
Convert 0/1 coding to pathogen/combinations
Convert a matrix of binary indicators to categorical variables
Initialize individual latent status (for JAGS)
insert distribution for latent status code chunk into .bug file
Insert measurement likelihood (without regression) code chunks into .b...
insert etiology regression for latent status code chunk into .bug file...
Insert measurement likelihood (with regression; discrete) code chunks ...
insert etiology regression for latent status code chunk into .bug file
Insert measurement likelihood (nested model+regression) code chunks in...
Insert measurement likelihood (with regression) code chunks into .bug ...
Test for 'try-error' class
Check if covariates are discrete
check if the formula is intercept only
See if a result folder is obtained by JAGS
check if a list has elements all of length one
Run JAGS from R
convert line to user coordinates
load an object from .RDATA file
logit function
calculate pairwise log odds ratios
log sum exp trick
Get position to store in data_nplcm$Mobs:
Create new file name
Create new folder name
Takes any number of R objects as arguments and returns a list whose na...
Make measurement slice
Make a list with numbered names
make a mapping template for model fitting
Shannon entropy for binary data
Match latent causes that might have the same combo but different speci...
For a list of many sublists each of which has matrices as its member, ...
Reorder the measurement dimensions to match the order for display
convert 'NA' to '.'
Fit nested partially-latent class models (highest-level wrapper functi...
Fit nested partially-latent class model (low-level)
Fit nested partially-latent class model with regression (low-level)
Fit nested partially-latent class model with regression (low-level)
Fit nested partially-latent class model with regression (low-level)
Read data and other model information from a folder that stores model ...
Convert NULL to zero.
order latent status by posterior mean
specify overall uniform (symmetric Dirichlet distribution) for etiolog...
parse regression components (either false positive rate or etiology re...
plot.nplcm plot the results from nplcm().
Plot bronze-standard (BrS) panel
visualize the PERCH etiology regression with a continuous covariate
Posterior predictive checking for the nested partially class models - ...
Posterior predictive checking for nested partially latent class models...
visualize the etiology regression with a continuous covariate
visualize the etiology estimates for each discrete levels
plotting the labels on the left margin for panels plot
Visualize pairwise log odds ratios (LOR) for data that are available i...
Plot three-panel figures for nested partially-latent model results
Plot etiology (pie) panel
Plot silver-standard (SS) panel
visualize the subclass weight regression with a continuous covariate
print.nplcm summarizes the results from nplcm().
Compact printing of nplcm() model fits
Compact printing of nplcm() model fits
Compact printing of nplcm() model fits
Compact printing of nplcm() model fits
Compact printing of nplcm() model fits
Read measurement slices
Sample a vector of Bernoulli variables.
Make Etiology design matrix for dates with R format.
Make false positive rate (FPR) design matrix for dates with R format.
Set true positive rate (TPR) prior ranges for bronze-standard (BrS) da...
Set true positive rate (TPR) prior ranges for silver-standard data.
Stratification setup by covariates
Show function dependencies
get an individual's data from the output of clean_perch_data()
Simulate Bronze-Standard (BrS) Data
Simulate Latent Status:
Simulate data from nested partially-latent class model (npLCM) family
Simulate Silver-Standard (SS) Data
softmax
subset data from the output of clean_perch_data()
summarize bronze-standard data
silver-standard data summary
summary.nplcm summarizes the results from nplcm().
get symmetric difference of months from two vector of R-format dates
Convert names of pathogen/combinations into 0/1 coding
generate stick-breaking prior (truncated) from a vector of random prob...
Convert factor to numeric without losing information on the label
get unique causes, regardless of the actual order in combo
Get unique month from Date
Visualize matrix for a quantity measured on cases and controls (a sing...
visualize trend of pathogen observation rate for NPPCR data (both case...
function to write bugs model (copied from R2WinBUGS)
Write .bug model file for model without regression
Write .bug model file for regression model without nested subclasses
Write .bug model file for regression model WITH nested subclasses
Write .bug model file for regression model without nested subclasses
Provides functions to specify, fit and visualize nested partially-latent class models ( Wu, Deloria-Knoll, Hammitt, and Zeger (2016) <doi:10.1111/rssc.12101>; Wu, Deloria-Knoll, and Zeger (2017) <doi:10.1093/biostatistics/kxw037>; Wu and Chen (2021) <doi:10.1002/sim.8804>) 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.
Useful links