stpm: Stochastic Process Model for Analysis of Longitudinal and Time-to-Event Outcomes

Share:

Utilities to estimate parameters of the models with survival functions induced by stochastic covariates. Miscellaneous functions for data preparation and simulation are also provided. For more information, see: (i) "Life tables with covariates: Dynamic model for nonlinear analysis of longitudinal data" by Akushevich, I. et al. (2005), Mathematical Population Studies 12(2), 51(80), <DOI:10.1080/08898480590932296>; (ii) "Stochastic model for analysis of longitudinal data on aging and mortality" by Yashin A. et al. (2007), Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>; (iii) "Health decline, aging and mortality: how are they related?" by Yashin A. et al. (2007), Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.

Author
I. Y. Zhbannikov, I. V. Akushevich, K. G. Arbeev, A. I. Yashin.
Date of publication
2016-10-17 19:00:09
Maintainer
Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
License
GPL
Version
1.4.2

View on CRAN

Man pages

func1
An internal function to compute m and gamma based on...
getNextY
An internal function to compute next value of physiological...
getNextY.cont
An internal function to compute next Y based on...
getNextY.discr
An internal function to compute the next value of...
getNextY.discr.m
An internal function to compute next m based on dicrete-time...
getPrevY.discr
An internal function to compute previous value of...
getPrevY.discr.m
An internal function to compute previous m based on...
longdat
This is the longitudinal dataset.
m
An internal function to compute m from
mu
An internal function to compute mu
prepare_data
Data pre-processing for analysis with stochastic process...
prepare_data_cont
Prepares continuouts-time dataset.
prepare_data_discr
Prepares discrete-time dataset.
sigma_sq
An internal function to compute sigma square analytically
simdata_cont
Multi-dimensional simulation function for continuous-time...
simdata_discr
Multi-dimension simulation function
simdata_gamma_frailty
This script simulates data using familial frailty model. We...
simdata_time_dep
Simulation function for continuous trait with time-dependant...
sim_pobs
Multi-dimension simulation function for data with partially...
spm
A central function that estimates Stochastic Process Model...
spm_continuous
Continuous multi-dimensional optimization
spm_discrete
Discrete multi-dimensional optimization
spm.impute
Multiple Data Imputation with SPM
spm_pobs
Continuous-time multi-dimensional optimization for SPM with...
spm_projection
A data projection with previously estimated or user-defined...
spm_time_dep
spm_time_dep : a function that estimates parameters from the...
stpm
Stochastic Process Model for Analysis of Longitudinal and...
trim
Returns string w/o leading or trailing whitespace
trim.leading
Returns string w/o leading whitespace
trim.trailing
Returns string w/o trailing whitespace
vitstat
Vital (mortality) statistics.

Files in this package

stpm
stpm/inst
stpm/inst/doc
stpm/inst/doc/stpm-vignette.R
stpm/inst/doc/stpm-vignette.Rmd
stpm/inst/doc/stpm-vignette.html
stpm/src
stpm/src/Makevars
stpm/src/spm_integral_MD.cpp
stpm/src/spm_1D.cpp
stpm/src/simdataND.cpp
stpm/src/spm_discrete.cpp
stpm/src/Makevars.win
stpm/NAMESPACE
stpm/data
stpm/data/vitstat.csv
stpm/data/longdat.csv
stpm/R
stpm/R/simdata_cont.R
stpm/R/simdata_time-dep.R
stpm/R/simdata_gamma_frailty.R
stpm/R/simdata_discr.R
stpm/R/spm.impute.R
stpm/R/spm_projection.R
stpm/R/spm_pobs.R
stpm/R/prepare_data.R
stpm/R/spm_discrete.R
stpm/R/longdat.R
stpm/R/vitstat.R
stpm/R/spm.R
stpm/R/simdata_pobs_cont.R
stpm/R/spm_continuous.R
stpm/R/stpm-package.R
stpm/R/spm_time-dependent.R
stpm/vignettes
stpm/vignettes/stpm-vignette.Rmd
stpm/README.md
stpm/MD5
stpm/build
stpm/build/vignette.rds
stpm/DESCRIPTION
stpm/man
stpm/man/sim_pobs.Rd
stpm/man/stpm.Rd
stpm/man/simdata_gamma_frailty.Rd
stpm/man/m.Rd
stpm/man/mu.Rd
stpm/man/func1.Rd
stpm/man/getNextY.cont.Rd
stpm/man/prepare_data.Rd
stpm/man/getPrevY.discr.m.Rd
stpm/man/trim.trailing.Rd
stpm/man/prepare_data_discr.Rd
stpm/man/simdata_discr.Rd
stpm/man/longdat.Rd
stpm/man/spm_projection.Rd
stpm/man/prepare_data_cont.Rd
stpm/man/simdata_time_dep.Rd
stpm/man/spm_pobs.Rd
stpm/man/spm.Rd
stpm/man/spm_continuous.Rd
stpm/man/simdata_cont.Rd
stpm/man/trim.leading.Rd
stpm/man/getNextY.Rd
stpm/man/spm_time_dep.Rd
stpm/man/trim.Rd
stpm/man/getPrevY.discr.Rd
stpm/man/spm.impute.Rd
stpm/man/sigma_sq.Rd
stpm/man/vitstat.Rd
stpm/man/getNextY.discr.Rd
stpm/man/getNextY.discr.m.Rd
stpm/man/spm_discrete.Rd