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

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)"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>; (ii) "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>.

Install the latest version of this package by entering the following in R:
install.packages("stpm")
AuthorI. Y. Zhbannikov, Liang He, K. G. Arbeev, A. I. Yashin.
Date of publication2017-04-07 17:54:04 UTC
MaintainerIlya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
LicenseGPL
Version1.6.6

View on CRAN

Man pages

ex_data: This is the longitudinal genetic dataset.

func1: An internal function to compute m and gamma based on...

getNextY.cont: An internal function to compute next Y based on...

getNextY.cont2: An internal function to compute next value of physiological...

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_con_1d: Fitting a 1-D SPM model with constant parameters

spm_con_1d_g: Fitting a 1-D genetic SPM model with constant parameters

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 for the model with time-dependent...

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.

Functions

ex_data Man page
func1 Man page
getNextY.cont Man page
getNextY.cont2 Man page
getNextY.discr Man page
getNextY.discr.m Man page
getPrevY.discr Man page
getPrevY.discr.m Man page
longdat Man page
m Man page
mu Man page
prepare_data Man page
prepare_data_cont Man page
prepare_data_discr Man page
sigma_sq Man page
simdata_cont Man page
simdata_discr Man page
simdata_gamma_frailty Man page
simdata_time_dep Man page
sim_pobs Man page
spm Man page
spm_con_1d Man page
spm_con_1d_g Man page
spm_continuous Man page
spm_discrete Man page
spm.impute Man page
spm_pobs Man page
spm_projection Man page
spm_time_dep Man page
stpm Man page
stpm-package Man page
trim Man page
trim.leading Man page
trim.trailing Man page
vitstat Man page

Files

inst
inst/NEWS
inst/extdata
inst/extdata/vitstat.csv
inst/extdata/longdat.csv
inst/doc
inst/doc/stpm-vignette.R
inst/doc/stpm-vignette.Rmd
inst/doc/stpm-vignette.html
src
src/Makevars
src/devlik_g.cpp
src/spm_integral_MD.cpp
src/spm_1D.cpp
src/simdataND.cpp
src/loglik.cpp
src/hes_spm_g.cpp
src/devlik.cpp
src/registerDynamicSymbol.c
src/loglik_g_2.cpp
src/loglik_g.cpp
src/devlik_g_2.cpp
src/spm_discrete.cpp
src/Makevars.win
NAMESPACE
data
data/ex_spmcon1dg.rda
R
R/simdata_cont.R R/lik_con_1d.r R/simdata_time-dep.R R/simdata_gamma_frailty.R R/simdata_discr.R R/spm.impute.R R/spm_con_1d.r R/spm_projection.R R/spm_con_1d_g.r R/general.R R/spm_pobs.R R/prepare_data.R R/spm_discrete.R R/longdat.R R/vitstat.R R/spm.R R/simdata_pobs_cont.R R/lik_con_1d_g.r R/hes_spm.r R/spm_continuous.R R/stpm-package.R R/hes_spm_g.r R/spm_time-dependent.R
vignettes
vignettes/stpm-vignette.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/sim_pobs.Rd man/stpm.Rd man/simdata_gamma_frailty.Rd man/m.Rd man/mu.Rd man/func1.Rd man/getNextY.cont.Rd man/prepare_data.Rd man/getPrevY.discr.m.Rd man/trim.trailing.Rd man/prepare_data_discr.Rd man/simdata_discr.Rd man/longdat.Rd man/spm_projection.Rd man/prepare_data_cont.Rd man/simdata_time_dep.Rd man/spm_pobs.Rd man/spm.Rd man/spm_con_1d.Rd man/spm_continuous.Rd man/getNextY.cont2.Rd man/ex_data.Rd man/simdata_cont.Rd man/trim.leading.Rd man/spm_time_dep.Rd man/trim.Rd man/spm_con_1d_g.Rd man/getPrevY.discr.Rd man/spm.impute.Rd man/sigma_sq.Rd man/vitstat.Rd man/getNextY.discr.Rd man/getNextY.discr.m.Rd man/spm_discrete.Rd
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