rstpm2: Generalized Survival Models

R implementation of generalized survival models, where g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth. For fully parametric models, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects.

AuthorMark Clements [aut, cre], Xing-Rong Liu [aut], Paul Lambert [ctb]
Date of publication2016-10-09 09:19:38
MaintainerMark Clements <mark.clements@ki.se>
LicenseGPL-2 | GPL-3
Version1.3.4
http://github.com/mclements/rstpm2

View on CRAN

Functions

AICc,pstpm2-method Man page
AIC,pstpm2-method Man page
anova,pstpm2-method Man page
BIC,pstpm2-method Man page
brcancer Man page
coef<- Man page
colon Man page
cox.tvc Man page
grad Man page
incrVar Man page
legendre.quadrature.rule.200 Man page
lhs Man page
lhs<- Man page
nsx Man page
numDeltaMethod Man page
plot-methods Man page
plot,pstpm2,missing-method Man page
plot,stpm2-method Man page
plot,stpm2,missing-method Man page
plot,tvcCoxph,missing-method Man page
popmort Man page
predict-methods Man page
predictnl Man page
predictnl.default Man page
predictnl-methods Man page
predictnl,mle2-method Man page
predictnl,pstpm2-method Man page
predictnl,stpm2-method Man page
predict.nsx Man page
predict,pstpm2-method Man page
predict,pstpm2-method Man page
predict,stpm2-method Man page
predict,stpm2-method Man page
pstpm2 Man page
pstpm2-class Man page
qAICc,pstpm2-method Man page
rhs Man page
rhs<- Man page
Rstpm2 Man page
Rstpm2-package Man page
stpm2 Man page
stpm2-class Man page
summary,pstpm2-method Man page
summary,stpm2-method Man page
tvcCoxph-class Man page

Files

rstpm2
rstpm2/inst
rstpm2/inst/ihe-expected-utilites.png
rstpm2/inst/working_code.R
rstpm2/inst/ihe-expect-utilities-males.png
rstpm2/inst/fig2-README.md.jpg
rstpm2/inst/tvc-cox.R
rstpm2/inst/test.do
rstpm2/inst/Rcpp-tests.R
rstpm2/inst/model.bug
rstpm2/inst/fig1-README.md.jpg
rstpm2/inst/pstpm2.out
rstpm2/inst/doc
rstpm2/inst/doc/Introduction.Rnw
rstpm2/inst/doc/Introduction.R
rstpm2/inst/doc/Introduction.pdf
rstpm2/inst/unitTests
rstpm2/inst/unitTests/runit.Basic.R
rstpm2/inst/unitTests/runTests.R
rstpm2/inst/competing_risks.R
rstpm2/src
rstpm2/src/Makevars
rstpm2/src/cox_ph.cpp
rstpm2/src/gsl_bspline.c
rstpm2/src/gsl_bspline.h
rstpm2/src/bspline.c
rstpm2/src/RuniqueCombs.c
rstpm2/src/RuniqueCombs.h
rstpm2/src/c_optim.h
rstpm2/src/test-nmmin.cpp
rstpm2/src/c_optim.cpp
rstpm2/NAMESPACE
rstpm2/data
rstpm2/data/brcancer.rda
rstpm2/data/legendre.quadrature.rule.200.rda
rstpm2/data/colon.rda
rstpm2/data/popmort.rda
rstpm2/R
rstpm2/R/pm2-3.R rstpm2/R/tvc.coxph.R
rstpm2/vignettes
rstpm2/vignettes/Introduction.Rnw
rstpm2/vignettes/Introduction.Rnw.tex
rstpm2/vignettes/_region_.tex
rstpm2/vignettes/auto
rstpm2/vignettes/auto/Introduction.el
rstpm2/README.md
rstpm2/MD5
rstpm2/build
rstpm2/build/vignette.rds
rstpm2/DESCRIPTION
rstpm2/man
rstpm2/man/incrVar.Rd rstpm2/man/numDeltaMethod.Rd rstpm2/man/predict.nsx.Rd rstpm2/man/colon.Rd rstpm2/man/predictnl.default.Rd rstpm2/man/stpm2.Rd rstpm2/man/plot-methods.Rd rstpm2/man/pstpm2.Rd rstpm2/man/predictnl-methods.Rd rstpm2/man/pstpm2-class.Rd rstpm2/man/rstpm2-internal.Rd rstpm2/man/popmort.Rd rstpm2/man/predictnl.Rd rstpm2/man/brcancer.Rd rstpm2/man/Rstpm2-package.Rd rstpm2/man/tvcCoxph-class.Rd rstpm2/man/nsx.Rd rstpm2/man/cox.tvc.Rd rstpm2/man/stpm2-class.Rd rstpm2/man/grad.Rd rstpm2/man/predict-methods.Rd rstpm2/man/legendre.quadrature.rule.200.Rd rstpm2/man/coef.Rd

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