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flexsurv (version 2.3.2)

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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Version

Install

install.packages('flexsurv')

Monthly Downloads

8,143

Version

2.3.2

License

GPL (>= 2)

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Repository

https://github.com/chjackson/flexsurv

Homepage

http://chjackson.github.io/flexsurv/

Maintainer

Christopher Jackson

Last Published

August 17th, 2024

Functions in flexsurv (2.3.2)

AICc.flexsurvreg

Second-order Akaike information criterion

BIC.flexsurvreg

Bayesian Information Criterion (BIC) for comparison of flexsurvreg models

Plot standardized metrics from a fitted flexsurv model

The log-logistic distribution

Second-order Akaike information criterion

quantile_flexsurvmix

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

Weibull distribution in proportional hazards parameterisation

Royston/Parmar spline survival distribution

meanfinal_fmixmsm

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

The Gompertz distribution

Royston/Parmar spline survival distribution functions with one argument per parameter

plot.flexsurvreg

Plots of fitted flexible survival models

Generalized F distribution

Generalized gamma distribution (original parameterisation)

Generalized gamma distribution

Bronchiolitis obliterans syndrome after lung transplants

augment.flexsurvreg

Augment data with information from a flexsurv model object

flexsurv-package

flexsurv: Flexible parametric survival and multi-state models

Akaike's information criterion from a flexible parametric multistate model

pdf_flexsurvmix

Fitted densities for times to events in a flexsurvmix model

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

unroll.function

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

Natural cubic spline basis

Constructor for a mixture multi-state model based on flexsurvmix

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

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

logLik.flexsurvreg

Log likelihood from a flexsurvreg model

Flexible survival regression using the Royston/Parmar spline model.

lines.flexsurvreg

Add fitted flexible survival curves to a plot

Transition probabilities from a flexsurvmix model

Aalen-Johansen nonparametric estimates comparable to a fitted flexsurvmix model

simt_flexsurvmix

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

Generalized F distribution (original parameterisation)

Hazard and cumulative hazard functions

coxsnell_flexsurvreg

Cox-Snell residuals from a parametric survival model

plot.survrtrunc

Plot nonparametric estimates of survival from right-truncated data.

Breast cancer survival data

Bootstrap confidence intervals for flexsurv output functions

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

model.frame.flexsurvreg

Extract original data from flexsurvreg objects.

residuals.flexsurvreg

Calculate residuals for flexible survival models

Objects exported from other packages

ajfit_flexsurvmix

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

vcov.flexsurvreg

Variance-covariance matrix from a flexsurvreg model

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

msfit.flexsurvreg

Cumulative intensity function for parametric multi-state models

glance.flexsurvreg

Glance at a flexsurv model object

model.frame.flexsurvmix

Model frame from a flexsurvmix object

helper function to safely convert a Hessian matrix to covariance matrix

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

summary.flexsurvrtrunc

Summarise quantities of interest from fitted flexsurvrtrunc models

mean_flexsurvmix

Mean times to events from a flexsurvmix model

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

Probabilities of final states in a flexible parametric competing risks model

Mean and restricted mean survival functions

Flexible parametric mixture models for times to competing events

tidy.flexsurvreg

Tidy a flexsurv model object

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

Flexible parametric regression for time-to-event data

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

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

Nonparametric estimator of survival from right-truncated, uncensored data

Generic function to find restricted mean survival time for some distribution

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

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

probs_flexsurvmix

Probabilities of competing events from a flexsurvmix model

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

coef.flexsurvreg

Extract model coefficients from fitted flexible survival models

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

summary.flexsurvreg

Summaries of fitted flexible survival models

Marginal survival and hazards of fitted flexsurvreg models

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

predict.flexsurvreg

Predictions from flexible survival models

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

rmst_flexsurvmix

Restricted mean times to events from a flexsurvmix model

nobs.flexsurvreg

Number of observations contributing to a fitted flexible survival model

normboot.flexsurvreg

Simulate from the asymptotic normal distribution of parameter estimates.

Generic function to find quantiles of a distribution

simulate.flexsurvreg

Simulate censored time-to-event data from a fitted flexsurvreg model

Tidy a standsurv object.