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flexsurv (version 2.2)

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

7,794

Version

2.2

License

GPL (>= 2)

Issues

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Repository

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

Maintainer

Christopher Jackson

Last Published

June 17th, 2022

Functions in flexsurv (2.2)

Weibull distribution in proportional hazards parameterisation

Generalized gamma distribution

Aalen-Johansen nonparametric estimates comparable to a fitted flexsurvmix model

The log-logistic distribution

The Gompertz distribution

Generalized gamma distribution (original parameterisation)

Generalized F distribution

Royston/Parmar spline survival distribution

Bronchiolitis obliterans syndrome after lung transplants

Generalized F distribution (original parameterisation)

coef.flexsurvreg

Extract model coefficients from fitted flexible survival models

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

ajfit_flexsurvmix

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

Royston/Parmar spline survival distribution functions

Bootstrap confidence intervals for flexsurv output functions

Breast cancer survival data

Constructor for a mixture multi-state model based on flexsurvmix

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

helper function to safely convert a Hessian matrix to covariance matrix

coxsnell_flexsurvreg

Cox-Snell residuals from a parametric survival model

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

Flexible survival regression using the Royston/Parmar spline model.

model.frame.flexsurvreg

Extract original data from flexsurvreg objects.

msfit.flexsurvreg

Cumulative intensity function for parametric multi-state models

Natural cubic spline basis

augment.flexsurvreg

Augment data with information from a flexsurv model object

Flexible parametric mixture models for times to competing events

Hazard and cumulative hazard functions

normboot.flexsurvreg

Simulate from the asymptotic normal distribution of parameter estimates.

nobs.flexsurvreg

Number of observations contributing to a fitted flexible survival model

lines.flexsurvreg

Add fitted flexible survival curves to a plot

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

glance.flexsurvreg

Glance at a flexsurv model object

Flexible parametric regression for time-to-event data

meanfinal_fmixmsm

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

pdf_flexsurvmix

Fitted densities for times to events in a flexsurvmix model

Probabilities of final states in a flexible parametric competing risks model

Hazard ratio as a function of time from a parametric survival model

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

plot.survrtrunc

Plot nonparametric estimates of survival from right-truncated data.

predict.flexsurvreg

Predictions from flexible survival models

Plot standardized metrics from a fitted flexsurv model

plot.flexsurvreg

Plots of fitted flexible survival models

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

mean_flexsurvmix

Mean times to events from a flexsurvmix model

Transition probabilities from a flexsurvmix model

residuals.flexsurvreg

Calculate residuals for flexible survival models

probs_flexsurvmix

Probabilities of competing events from a flexsurvmix model

Marginal survival and hazards of fitted flexsurvreg models

Objects exported from other packages

quantile_flexsurvmix

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

tidy.flexsurvreg

Tidy a flexsurv model object

flexsurv-package

flexsurv: Flexible parametric survival and multi-state models

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

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

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

Tidy a standsurv object.

summary.flexsurvreg

Summaries of fitted flexible survival models

Mean and restricted mean survival functions

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

summary.flexsurvrtrunc

Summarise quantities of interest from fitted flexsurvrtrunc models

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

Nonparametric estimator of survival from right-truncated, uncensored data

Generic function to find quantiles of a distribution

simt_flexsurvmix

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

rmst_flexsurvmix

Restricted mean times to events from a flexsurvmix model

simulate.flexsurvreg

Simulate datasets from a fitted flexsurvreg model

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

Generic function to find restricted mean survival of a distribution

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

unroll.function

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

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

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