lmeNB: Compute the Personalized Activity Index Based on a Negative Binomial Model

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The functions in this package implement the safety monitoring procedures proposed in the paper titled "Detection of unusual increases in MRI lesion counts in individual multiple sclerosis patients" by Zhao, Y., Li, D.K.B., Petkau, A.J., Riddehough, A., Traboulsee, A., published in Journal of the American Statistical Association in 2013. 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 can be modelled with a gamma or log-normal distributions. One can also choose the semi-parametric option which does not assume any distribution for the random effect. These mixed-effect models could be useful beyond the application of the safety monitoring. The maximum likelihood methods are used to estimate the unknown fixed effect parameters of the model. Based on the fitted model, the personalized activity index is computed for each patient. Lastly, this package is companion to R package lmeNBBayes, which contains the functions to compute the Personalized Activity Index in Bayesian framework.

Author
Yinshan Zhao and Yumi Kondo (with contributions from Steven G. Johnson, Rudolf Schuerer and Brian Gough on the integration subroutines)
Date of publication
2015-02-02 22:40:23
Maintainer
Yumi Kondo <y.kondo@stat.ubc.ca>
License
GPL (>= 2)
Version
1.3

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Man pages

CP_se
Compute a conditional probability of observing a set of...
fitParaAR1
Performs the maximum likelihood estimation for the negative...
fitParaIND
Performs the maximum likelihood estimation for the negative...
fitSemiAR1
Fit the semi-parametric negative binomial mixed-effect AR(1)...
fitSemiIND
Fit the semi-parametric negative binomial mixed-effect...
index_batch
The main function to compute the point estimates and 95%...
jCP_ar1
Compute a conditional probability of observing a set of...
lmeNB
Performs the maximum likelihood estimation for the negative...
lmeNB-internal
Internal lmeNB functions
RElmeNB
Calculate predicted values of E(Gi|Yi) given the estimates of...
rNBME_R
Simulate a dataset from the negative binomial mixed-effect...

Files in this package

lmeNB
lmeNB/src
lmeNB/src/ARlk.c
lmeNB/src/converged.h
lmeNB/src/vwrapper.h
lmeNB/src/cubature.h
lmeNB/NAMESPACE
lmeNB/R
lmeNB/R/oldCode.R
lmeNB/R/CPI.R
lmeNB/R/AR1models.R
lmeNB/R/INDmodels.R
lmeNB/R/Simulation.R
lmeNB/R/nbinomRE-internal.R
lmeNB/MD5
lmeNB/DESCRIPTION
lmeNB/man
lmeNB/man/fitSemiIND.Rd
lmeNB/man/index_batch.Rd
lmeNB/man/rNBME_R.Rd
lmeNB/man/fitParaAR1.Rd
lmeNB/man/fitParaIND.Rd
lmeNB/man/fitSemiAR1.Rd
lmeNB/man/jCP_ar1.Rd
lmeNB/man/CP_se.Rd
lmeNB/man/lmeNB.Rd
lmeNB/man/lmeNB-internal.Rd
lmeNB/man/RElmeNB.Rd