Description
Usage
Arguments
Value
View source: R/nplcmfitNoRegBrSandSSNest.R
Features:
data_nplcm 

Mobs A list of measurements. The elements of the list
should include MBS , MSS , and MGS . If any of the component
is not available, please specify it as, e.g., MGS=NA or MGS=NULL
(effectively deleting MGS from Mobs ).

MBS a data frame of bronzestandard (BrS) measurements.
Rows are subjects, columns are pathogens.
They have imperfect sensitivity/specificity (e.g. nasalpharyngeal PCR).

MSS a data frame of silverstandard (SS) measurements.
Rows are subjects, columns are pathogens measured in specimen (e.g. blood culture).
These measurements have perfect specificity but imperfect sensitivity.

MGS a data frame of goldstandard (GS) measurements.
Rows are subject, columns are pathogen measurements.
These measurements have perfect sensitivity and specificity.

Y Vector of disease status: 1 for case, 0 for control.

X Covariate matrix for regression modeling. It contains raw covariate
data, not design matrix for regression models.

model_options 
A list of model options.

M_use List of measurements to be used in the model;

k_subclass The number of nested subclasses. 1 for conditional independence,
>1 for conditional dependence;

TPR_prior Description of priors for the measurements
(e.g., informative vs noninformative).
Its length should be the same with M_use ;

Eti_prior Description of etiology prior
(e.g., overall_uniform  all hyperparameters are 1; or 0_1  all hyperparameters
are 0.1);

pathogen_BrS_list The vector of pathogen names with BrS measure;

cause_list The vector of causes that are either singleton or
combinations of items in pathogen_BrS_list ; 'NoA' can also be included
at the end, meaning 'NoneofAbove';

X_reg_FPR formula for false positive rates (FPR) regressions; see
formula . You can use dm_Rdate_FPR to specify part
of the design matrix for R format enrollment date; it will produce thinplate
regression spline basis for every date (if effect="random" and num_knots_FPR is
specified to a positive integer, e.g., 10.). If effect="fixed" , dm_Rdate_FPR
will just specify a design matrix with appropirately standardized dates. Specify ~0 if no
regression is intended.

X_reg_Eti formula for etiology regressions. You can use
dm_Rdate_Eti to specify the design matrix for R format enrollment date;
it will produce natural cubic splines for every date. Specify ~0 if no
regression is intended.

pathogen_BrS_cat The twocolumn data frame that has category of pathogens: virus (V), bacteria (B)
and fungi (F);

pathogen_SSonly_list The vector of pathogens with only
SS measure;

pathogen_SSonly_cat The category of pathogens with only SS measure.

mcmc_options 
A list of Markov chain Monte Carlo (MCMC) options.

debugstatus Logical  whether to pause WinBUGS after it finishes
model fitting;

n.chains Number of MCMC chains;

n.burnin Number of burnin samples;

n.thin To keep every other n.thin samples after burnin period;

individual.pred whether to perform individual prediction;

ppd whether to perform posterior predictive (ppd) checking;

result.folder Path to folder storing the results;

bugsmodel.dir Path to WinBUGS model files;

winbugs.dir Path to where WinBUGS 1.4 is installed.

WinBUGS fit results.
zhenkewu/nplcm documentation built on May 28, 2017, 1:43 p.m.