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 mixedeffect regression model. To account for the correlation among repeated measures from the same patient, the model has subjectspecific 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 mixedeffect 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 mixedeffect 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.
Author  Yumi Kondo 
Date of publication  20150221 01:31:16 
Maintainer  Yumi Kondo <y.kondo@stat.ubc.ca> 
License  GPL (>= 2) 
Version  1.3.1 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:

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 mixedeffect negative...  
index_batch_Bayes: The main function to compute the point estimates and 95%...  
lmeNBBayes: Generate posterior samples from a flexible mixed effect...  
lmeNBBayesinternal: 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/lmeNBBayesinternal.Rd  
man/getDIC.Rd  
man/getS.StatInMed.Rd  
man/index_batch_Bayes.Rd 
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