lmeNB

Package: lmeNB
Type: Package
Title: Compute the Personalized Activity Index Based on a Negative
Binomial Model
Version: 1.3
Date: 2015-01-14
Author: Yinshan Zhao and Yumi Kondo (with contributions from Steven G. Johnson, Rudolf Schuerer and Brian Gough on the integration subroutines)
Maintainer: Yumi Kondo <y.kondo@stat.ubc.ca>
Description: 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.
License: GPL (>= 2)
Copyright: The portion of numerical integration is based on Cubature,
Copyright (c) 2005-2013 Steven G. Johnson
(http://ab-initio.mit.edu/wiki/index.php/Cubature), which in
turn is based on HIntLib (also distributed under * the GNU GPL,
v2 or later), copyright (c) 2002-2005 Rudolf Schuerer and GNU
GSL (also distributed under the GNU GPL, v2 or later),
copyright (c) 1996-2000 Brian
Gough.(http://www.gnu.org/software/gsl/).
LazyData: true
Depends: numDeriv, statmod, lmeNBBayes
Packaged: 2015-02-02 20:00:39 UTC; yumikondo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-02-02 22:40:23

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'lmeNB' ...
** package 'lmeNB' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ARlk.c -o ARlk.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o lmeNB.so ARlk.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/lmeNB/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'lmeNB'
    finding HTML links ... done
    CP_se                                   html  
    RElmeNB                                 html  
    fitParaAR1                              html  
    fitParaIND                              html  
    fitSemiAR1                              html  
    fitSemiIND                              html  
    index_batch                             html  
    jCP_ar1                                 html  
    lmeNB-internal                          html  
    lmeNB                                   html  
    rNBME_R                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (lmeNB)
Making 'packages.html' ... done