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

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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.

Author
Yumi Kondo
Date of publication
2015-02-21 01:31:16
Maintainer
Yumi Kondo <y.kondo@stat.ubc.ca>
License
GPL (>= 2)
Version
1.3.1

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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

Files in this package

lmeNBBayes
lmeNBBayes/src
lmeNBBayes/src/nbinDPmix.c
lmeNBBayes/NAMESPACE
lmeNBBayes/R
lmeNBBayes/R/nbinDPmix_C.R
lmeNBBayes/MD5
lmeNBBayes/DESCRIPTION
lmeNBBayes/man
lmeNBBayes/man/dqmix.Rd
lmeNBBayes/man/lmeNBBayes.Rd
lmeNBBayes/man/lmeNBBayes-internal.Rd
lmeNBBayes/man/getDIC.Rd
lmeNBBayes/man/getS.StatInMed.Rd
lmeNBBayes/man/index_batch_Bayes.Rd