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.

Install the latest version of this package by entering the following in R:
install.packages("rstpm2")
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,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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.