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>.

AuthorI. Y. Zhbannikov, Liang He, K. G. Arbeev, A. I. Yashin.
Date of publication2017-03-05 08:47:31
MaintainerIlya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
LicenseGPL
Version1.6.4

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: 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_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 Man page
getNextY.cont 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
stpm-package Man page
trim Man page
trim.leading Man page
trim.trailing Man page
vitstat Man page

Files

stpm
stpm/inst
stpm/inst/NEWS
stpm/inst/extdata
stpm/inst/extdata/vitstat.csv
stpm/inst/extdata/longdat.csv
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/devlik_g.cpp
stpm/src/spm_integral_MD.cpp
stpm/src/spm_1D.cpp
stpm/src/simdataND.cpp
stpm/src/loglik.cpp
stpm/src/hes_spm_g.cpp
stpm/src/devlik.cpp
stpm/src/registerDynamicSymbol.c
stpm/src/loglik_g_2.cpp
stpm/src/loglik_g.cpp
stpm/src/devlik_g_2.cpp
stpm/src/spm_discrete.cpp
stpm/src/Makevars.win
stpm/NAMESPACE
stpm/data
stpm/data/ex_spmcon1dg.rda
stpm/R
stpm/R/simdata_cont.R
stpm/R/lik_con_1d.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_con_1d.r
stpm/R/spm_projection.R
stpm/R/spm_con_1d_g.r
stpm/R/general.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/lik_con_1d_g.r
stpm/R/hes_spm.r
stpm/R/spm_continuous.R stpm/R/stpm-package.R
stpm/R/hes_spm_g.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_con_1d.Rd stpm/man/spm_continuous.Rd stpm/man/ex_data.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/spm_con_1d_g.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

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