lmeNBBayes: Compute the Personalized Activity Index Based on a Flexible Bayesian Negative Binomial Model
Version 1.3.1

The functions in this package implement the safety monitoring procedures proposed in the paper titled "A flexible mixed effect negative binomial regression model for detecting unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Kondo, Y., Zhao, Y. and Petkau, A.J. The procedure first models longitudinally collected count variables with a negative binomial mixed-effect regression model. To account for the correlation among repeated measures from the same patient, the model has subject-specific random intercept, which is modelled with the infinite mixture of Beta distributions, very flexible distribution that theoretically allows any form. The package also has the option of a single beta distribution for random effects. These mixed-effect models could be useful beyond the application of the safety monitoring. The inference is based on MCMC samples and this package contains a Gibbs sampler to sample from the posterior distribution of the negative binomial mixed-effect regression model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNB, which contains the functions to compute the Personalized Activity Index in the frequentist framework.

AuthorYumi Kondo
Date of publication2015-02-21 01:31:16
MaintainerYumi Kondo <y.kondo@stat.ubc.ca>
LicenseGPL (>= 2)
Version1.3.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("lmeNBBayes")

Popular man pages

dqmix: Estimate the random effect distribution of the flexible mixed...
getDIC: Compute the DIC given the output from 'lmeNBBayes'.
getS.StatInMed: Generate samples from the flexible mixed-effect negative...
index_batch_Bayes: The main function to compute the point estimates and 95%...
lmeNBBayes: Generate posterior samples from a flexible mixed effect...
lmeNBBayes-internal: Internal lmeNBBayes functions
See all...

All man pages Function index File listing

Man pages

dqmix: Estimate the random effect distribution of the flexible mixed...
getDIC: Compute the DIC given the output from 'lmeNBBayes'.
getS.StatInMed: Generate samples from the flexible mixed-effect negative...
index_batch_Bayes: The main function to compute the point estimates and 95%...
lmeNBBayes: Generate posterior samples from a flexible mixed effect...
lmeNBBayes-internal: Internal lmeNBBayes functions

Functions

E.KN Man page Source code
F_inv_beta2 Source code
Nuniq Man page Source code
UsedPara Source code
adjustPosDef Man page Source code
colmeansd Man page Source code
condProbCI Man page Source code
cor2cov Source code
cov2corNA Source code
denfun.YZ Source code
denfun.norm Source code
dqmix Man page Source code
getDIC Man page Source code
getDIC.FG Source code
getDIC_aGh.rGh.G Source code
getM Man page Source code
getS.StatInMed Man page Source code
getTrueProb Source code
index.YZ Man page Source code
index.b.each Man page Source code
index.batch.Bayes Man page Source code
index.gammas Source code
int.M Man page Source code
intfun Source code
invlnpara Source code
llk.FG Source code
llk.FG_i Man page Source code
lmeNBBayes Man page Source code
lnpara Man page Source code Source code
log.choose Source code
logL.G Source code
logL.aGh.rGh Source code
mixgamma Source code
momBeta Source code
momGL Source code
newCat Man page Source code
numfun.YZ Source code
numfun.norm Source code
piM Man page Source code
plotGs Man page Source code
plotHistAcf Source code
plotbeta Man page Source code
plotgamma Man page Source code
plotlnorm Source code
plotnbinom Man page Source code
pointsgamma Man page Source code
prIndex Man page
print.IndexBatch Man page
print.LinearMixedEffectNBBayes Man page Source code
repeatAsID Man page Source code
rmvnorm Source code
slim Man page Source code
tempCdens Source code
useSamp Man page Source code

Files

src
src/nbinDPmix.c
NAMESPACE
R
R/nbinDPmix_C.R
MD5
DESCRIPTION
man
man/dqmix.Rd
man/lmeNBBayes.Rd
man/lmeNBBayes-internal.Rd
man/getDIC.Rd
man/getS.StatInMed.Rd
man/index_batch_Bayes.Rd
lmeNBBayes documentation built on May 19, 2017, 7:47 a.m.

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