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 <email@example.com>|
|License||GPL-2 | GPL-3|
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"'