rstpm2: Generalized Survival Models

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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.

Author
Mark Clements [aut, cre], Xing-Rong Liu [aut], Paul Lambert [ctb]
Date of publication
2016-10-09 09:19:38
Maintainer
Mark Clements <mark.clements@ki.se>
License
GPL-2 | GPL-3
Version
1.3.4
URLs

View on CRAN

Man pages

brcancer
German breast cancer data from Stata.
coef
Generic method to update the coef in an object.
colon
Colon cancer.
cox.tvc
Test for a time-varying effect in the 'coxph' model
grad
gradient function (internal function)
incrVar
Utility that returns a function to increment a variable in a...
legendre.quadrature.rule.200
Legendre quadrature rule for n=200.
nsx
Generate a Basis Matrix for Natural Cubic Splines (with...
numDeltaMethod
Calculate numerical delta method for non-linear predictions.
plot-methods
plots for an stpm2 fit
popmort
Background mortality rates for the colon dataset.
predict-methods
Predicted values for an stpm2 or pstpm2 fit
predictnl
Generic function for non-linear prediction.
predictnl.default
Default implementation of the 'predictnl' generic function.
predictnl-methods
~~ Methods for Function predictnl ~~
predict.nsx
Evaluate a Spline Basis
pstpm2
Penalised generalised survival model
pstpm2-class
Class "pstpm2"
rstpm2-internal
Internal functions for the rstpm2 package.
Rstpm2-package
Flexible parametric survival models.
stpm2
Fully parametric generalised survival model
stpm2-class
Class "stpm2" ~~~
tvcCoxph-class
Class '"tvcCoxph"'

Files in this package

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