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flexsurv (version 2.0)

Flexible Parametric Survival and Multi-State Models

Description

Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models, based on either cause-specific hazards or mixture models.

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Install

install.packages('flexsurv')

Monthly Downloads

6,864

Version

2.0

License

GPL (>= 2)

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Repository

https://github.com/chjackson/flexsurv-dev

Maintainer

Christopher Jackson

Last Published

February 22nd, 2021

Functions in flexsurv (2.0)

Generalized gamma distribution

Royston/Parmar spline survival distribution functions

Weibull distribution in proportional hazards parameterisation

The log-logistic distribution

Generalized F distribution (original parameterisation)

Aalen-Johansen nonparametric estimates comparable to a fitted flexsurvmix model

Generalized F distribution

The Gompertz distribution

Royston/Parmar spline survival distribution

augment.flexsurvreg

Augment data with information from a flexsurv model object

Bronchiolitis obliterans syndrome after lung transplants

Generalized gamma distribution (original parameterisation)

Numerical evaluation of the hessian of a function using numDeriv::hessian

Natural cubic spline basis

ajfit_flexsurvmix

Forms a tidy data frame for plotting the fit of parametric mixture multi-state models against nonparametric estimates

Check the fit of Markov flexible parametric multi-state models against nonparametric estimates.

helper function to safely convert a Hessian matrix to covariance matrix

Flexible parametric regression for time-to-event data

flexsurv-package

flexsurv: Flexible parametric survival and multi-state models

Flexible survival regression using the Royston/Parmar spline model.

Flexible parametric mixture models for times to competing events

Constructor for a mixture multi-state model based on flexsurvmix

Flexible parametric models for right-truncated, uncensored data defined by times of initial and final events.

Breast cancer survival data

Bootstrap confidence intervals for flexsurv output functions

nobs.flexsurvreg

Number of observations contributing to a fitted flexible survival model

glance.flexsurvreg

Glance at a flexsurv model object

normboot.flexsurvreg

Simulate from the asymptotic normal distribution of parameter estimates.

Hazard and cumulative hazard functions

lines.flexsurvreg

Add fitted flexible survival curves to a plot

Transition-specific parameters in a flexible parametric multi-state model

Construct a multi-state model from a set of parametric survival models

Transition probabilities from a flexsurvmix model

Simulate paths through a fully parametric semi-Markov multi-state model

Generic function to find quantiles of a distribution

coef.flexsurvreg

Extract model coefficients from fitted flexible survival models

Evaluate baseline time-to-event distribution parameters given covariate values in a flexsurvmix model

msfit.flexsurvreg

Cumulative intensity function for parametric multi-state models

plot.flexsurvreg

Plots of fitted flexible survival models

Quantiles of the distribution of the time until reaching a final state in a mixture multi-state model

Expected total length of stay in specific states, from a fully-parametric, semi-Markov multi-state model

predict.flexsurvreg

Predictions from flexible survival models

rmst_flexsurvmix

Restricted mean times to events from a flexsurvmix model

mean_flexsurvmix

Mean times to events from a flexsurvmix model

meanfinal_fmixmsm

Mean time to final state in a mixture multi-state model

Probabilities of final states in a flexible parametric competing risks model

residuals.flexsurvreg

Calculate residuals for flexible survival models

Generic function to find restricted mean survival of a distribution

unroll.function

Convert a function with matrix arguments to a function with vector arguments.

model.frame.flexsurvreg

Extract original data from flexsurvreg objects.

Transition probability matrix from a fully-parametric, semi-Markov multi-state model

Probability of each pathway taken through a mixture multi-state model

probs_flexsurvmix

Probabilities of competing events from a flexsurvmix model

simt_flexsurvmix

Simulate times to competing events from a mixture multi-state model

Reformat simulated multi-state data with one row per simulated transition

Transition probability matrix from a fully-parametric, time-inhomogeneous Markov multi-state model

quantile_flexsurvmix

Quantiles of time-to-event distributions in a flexsurvmix model

tidy.flexsurvreg

Tidy a flexsurv model object

plot.survrtrunc

Plot nonparametric estimates of survival from right-truncated data.

Mean and restricted mean survival functions

Total length of stay in particular states for a fully-parametric, time-inhomogeneous Markov multi-state model

Simulate and summarise final outcomes from a flexible parametric multi-state model

Objects exported from other packages

summary.flexsurvrtrunc

Summarise quantities of interest from fitted flexsurvrtrunc models

summary.flexsurvreg

Summaries of fitted flexible survival models

Nonparametric estimator of survival from right-truncated, uncensored data