Flexible Parametric Survival and Multi-State Models

Documentation for package ‘flexsurv’ version 2.3

Help Pages

flexsurv: Flexible parametric survival and multi-state models

-- A --

AIC.fmsm	Akaike's information criterion from a flexible parametric multistate model
AICC	Second-order Akaike information criterion
AICc	Second-order Akaike information criterion
AICC.flexsurvreg	Second-order Akaike information criterion
AICc.flexsurvreg	Second-order Akaike information criterion
ajfit	Aalen-Johansen nonparametric estimates comparable to a fitted flexsurvmix model
ajfit_flexsurvmix	Forms a tidy data frame for plotting the fit of parametric mixture multi-state models against nonparametric estimates
ajfit_fmsm	Check the fit of Markov flexible parametric multi-state models against nonparametric estimates.
augment.flexsurvreg	Augment data with information from a flexsurv model object

-- B --

basis	Natural cubic spline basis
bc	Breast cancer survival data
BIC.flexsurvreg	Bayesian Information Criterion (BIC) for comparison of flexsurvreg models
bootci.fmsm	Bootstrap confidence intervals for flexsurv output functions
bos	Bronchiolitis obliterans syndrome after lung transplants
bosms3	Bronchiolitis obliterans syndrome after lung transplants
bosms4	Bronchiolitis obliterans syndrome after lung transplants

-- C --

coef.flexsurvreg	Extract model coefficients from fitted flexible survival models
coxsnell_flexsurvreg	Cox-Snell residuals from a parametric survival model

-- D --

dbasis	Natural cubic spline basis
dfss	Natural cubic spline basis
dgenf	Generalized F distribution
dgenf.orig	Generalized F distribution (original parameterisation)
dgengamma	Generalized gamma distribution
dgengamma.orig	Generalized gamma distribution (original parameterisation)
dgompertz	The Gompertz distribution
dllogis	The log-logistic distribution
dsurvspline	Royston/Parmar spline survival distribution
dsurvspline0	Royston/Parmar spline survival distribution functions with one argument per parameter
dsurvspline1	Royston/Parmar spline survival distribution functions with one argument per parameter
dsurvspline2	Royston/Parmar spline survival distribution functions with one argument per parameter
dsurvspline3	Royston/Parmar spline survival distribution functions with one argument per parameter
dsurvspline4	Royston/Parmar spline survival distribution functions with one argument per parameter
dsurvspline5	Royston/Parmar spline survival distribution functions with one argument per parameter
dsurvspline6	Royston/Parmar spline survival distribution functions with one argument per parameter
dsurvspline7	Royston/Parmar spline survival distribution functions with one argument per parameter
dweibullPH	Weibull distribution in proportional hazards parameterisation

-- F --

flexsurv	flexsurv: Flexible parametric survival and multi-state models
flexsurv.dists	Flexible parametric regression for time-to-event data
flexsurvmix	Flexible parametric mixture models for times to competing events
flexsurvreg	Flexible parametric regression for time-to-event data
flexsurvrtrunc	Flexible parametric models for right-truncated, uncensored data defined by times of initial and final events.
flexsurvspline	Flexible survival regression using the Royston/Parmar spline model.
fmixmsm	Constructor for a mixture multi-state model based on flexsurvmix
fmsm	Construct a multi-state model from a set of parametric survival models
fss	Natural cubic spline basis

-- G --

GenF	Generalized F distribution
GenF.orig	Generalized F distribution (original parameterisation)
GenGamma	Generalized gamma distribution
GenGamma.orig	Generalized gamma distribution (original parameterisation)
get_basepars	Evaluate baseline time-to-event distribution parameters given covariate values in a flexsurvmix model
glance.flexsurvreg	Glance at a flexsurv model object
Gompertz	The Gompertz distribution

-- H --

hazard	Hazard and cumulative hazard functions
Hexp	Hazard and cumulative hazard functions
hexp	Hazard and cumulative hazard functions
Hgamma	Hazard and cumulative hazard functions
hgamma	Hazard and cumulative hazard functions
Hgenf	Generalized F distribution
hgenf	Generalized F distribution
Hgenf.orig	Generalized F distribution (original parameterisation)
hgenf.orig	Generalized F distribution (original parameterisation)
Hgengamma	Generalized gamma distribution
hgengamma	Generalized gamma distribution
Hgengamma.orig	Generalized gamma distribution (original parameterisation)
hgengamma.orig	Generalized gamma distribution (original parameterisation)
Hgompertz	The Gompertz distribution
hgompertz	The Gompertz distribution
Hllogis	The log-logistic distribution
hllogis	The log-logistic distribution
Hlnorm	Hazard and cumulative hazard functions
hlnorm	Hazard and cumulative hazard functions
hr_flexsurvreg	Hazard ratio as a function of time from a parametric survival model
Hsurvspline	Royston/Parmar spline survival distribution
hsurvspline	Royston/Parmar spline survival distribution
Hsurvspline0	Royston/Parmar spline survival distribution functions with one argument per parameter
hsurvspline0	Royston/Parmar spline survival distribution functions with one argument per parameter
Hsurvspline1	Royston/Parmar spline survival distribution functions with one argument per parameter
hsurvspline1	Royston/Parmar spline survival distribution functions with one argument per parameter
Hsurvspline2	Royston/Parmar spline survival distribution functions with one argument per parameter
hsurvspline2	Royston/Parmar spline survival distribution functions with one argument per parameter
Hsurvspline3	Royston/Parmar spline survival distribution functions with one argument per parameter
hsurvspline3	Royston/Parmar spline survival distribution functions with one argument per parameter
Hsurvspline4	Royston/Parmar spline survival distribution functions with one argument per parameter
hsurvspline4	Royston/Parmar spline survival distribution functions with one argument per parameter
Hsurvspline5	Royston/Parmar spline survival distribution functions with one argument per parameter
hsurvspline5	Royston/Parmar spline survival distribution functions with one argument per parameter
Hsurvspline6	Royston/Parmar spline survival distribution functions with one argument per parameter
hsurvspline6	Royston/Parmar spline survival distribution functions with one argument per parameter
Hsurvspline7	Royston/Parmar spline survival distribution functions with one argument per parameter
hsurvspline7	Royston/Parmar spline survival distribution functions with one argument per parameter
Hweibull	Hazard and cumulative hazard functions
hweibull	Hazard and cumulative hazard functions
HweibullPH	Weibull distribution in proportional hazards parameterisation
hweibullPH	Weibull distribution in proportional hazards parameterisation

-- L --

lines.flexsurvreg	Add fitted flexible survival curves to a plot
lines.survrtrunc	Plot nonparametric estimates of survival from right-truncated data.
Llogis	The log-logistic distribution
logLik.flexsurvreg	Log likelihood from a flexsurvreg model

-- M --

meanfinal_fmixmsm	Mean time to final state in a mixture multi-state model
means	Mean and restricted mean survival functions
mean_exp	Mean and restricted mean survival functions
mean_flexsurvmix	Mean times to events from a flexsurvmix model
mean_gamma	Mean and restricted mean survival functions
mean_genf	Mean and restricted mean survival functions
mean_genf.orig	Mean and restricted mean survival functions
mean_gengamma	Mean and restricted mean survival functions
mean_gengamma.orig	Mean and restricted mean survival functions
mean_gompertz	Mean and restricted mean survival functions
mean_llogis	Mean and restricted mean survival functions
mean_lnorm	Mean and restricted mean survival functions
mean_survspline	Royston/Parmar spline survival distribution
mean_survspline0	Royston/Parmar spline survival distribution functions with one argument per parameter
mean_survspline1	Royston/Parmar spline survival distribution functions with one argument per parameter
mean_survspline2	Royston/Parmar spline survival distribution functions with one argument per parameter
mean_survspline3	Royston/Parmar spline survival distribution functions with one argument per parameter
mean_survspline4	Royston/Parmar spline survival distribution functions with one argument per parameter
mean_survspline5	Royston/Parmar spline survival distribution functions with one argument per parameter
mean_survspline6	Royston/Parmar spline survival distribution functions with one argument per parameter
mean_survspline7	Royston/Parmar spline survival distribution functions with one argument per parameter
mean_weibull	Mean and restricted mean survival functions
mean_weibullPH	Mean and restricted mean survival functions
model.frame.flexsurvmix	Model frame from a flexsurvmix object
model.frame.flexsurvreg	Extract original data from 'flexsurvreg' objects.
model.matrix.flexsurvreg	Extract original data from 'flexsurvreg' objects.
msfit.flexsurvreg	Cumulative intensity function for parametric multi-state models

-- N --

nobs.flexsurvreg	Number of observations contributing to a fitted flexible survival model
normboot.flexsurvreg	Simulate from the asymptotic normal distribution of parameter estimates.

-- P --

pars.fmsm	Transition-specific parameters in a flexible parametric multi-state model
pdf_flexsurvmix	Fitted densities for times to events in a flexsurvmix model
pfinal_fmsm	Probabilities of final states in a flexible parametric competing risks model
pgenf	Generalized F distribution
pgenf.orig	Generalized F distribution (original parameterisation)
pgengamma	Generalized gamma distribution
pgengamma.orig	Generalized gamma distribution (original parameterisation)
pgompertz	The Gompertz distribution
pllogis	The log-logistic distribution
plot.flexsurvreg	Plots of fitted flexible survival models
plot.standsurv	Plot standardized metrics from a fitted flexsurv model
plot.survrtrunc	Plot nonparametric estimates of survival from right-truncated data.
pmatrix.fs	Transition probability matrix from a fully-parametric, time-inhomogeneous Markov multi-state model
pmatrix.simfs	Transition probability matrix from a fully-parametric, semi-Markov multi-state model
ppath_fmixmsm	Probability of each pathway taken through a mixture multi-state model
predict.flexsurvreg	Predictions from flexible survival models
probs_flexsurvmix	Probabilities of competing events from a flexsurvmix model
psurvspline	Royston/Parmar spline survival distribution
psurvspline0	Royston/Parmar spline survival distribution functions with one argument per parameter
psurvspline1	Royston/Parmar spline survival distribution functions with one argument per parameter
psurvspline2	Royston/Parmar spline survival distribution functions with one argument per parameter
psurvspline3	Royston/Parmar spline survival distribution functions with one argument per parameter
psurvspline4	Royston/Parmar spline survival distribution functions with one argument per parameter
psurvspline5	Royston/Parmar spline survival distribution functions with one argument per parameter
psurvspline6	Royston/Parmar spline survival distribution functions with one argument per parameter
psurvspline7	Royston/Parmar spline survival distribution functions with one argument per parameter
pweibullPH	Weibull distribution in proportional hazards parameterisation
p_flexsurvmix	Transition probabilities from a flexsurvmix model

-- Q --

qfinal_fmixmsm	Quantiles of the distribution of the time until reaching a final state in a mixture multi-state model
qgeneric	Generic function to find quantiles of a distribution
qgenf	Generalized F distribution
qgenf.orig	Generalized F distribution (original parameterisation)
qgengamma	Generalized gamma distribution
qgengamma.orig	Generalized gamma distribution (original parameterisation)
qgompertz	The Gompertz distribution
qllogis	The log-logistic distribution
qsurvspline	Royston/Parmar spline survival distribution
qsurvspline0	Royston/Parmar spline survival distribution functions with one argument per parameter
qsurvspline1	Royston/Parmar spline survival distribution functions with one argument per parameter
qsurvspline2	Royston/Parmar spline survival distribution functions with one argument per parameter
qsurvspline3	Royston/Parmar spline survival distribution functions with one argument per parameter
qsurvspline4	Royston/Parmar spline survival distribution functions with one argument per parameter
qsurvspline5	Royston/Parmar spline survival distribution functions with one argument per parameter
qsurvspline6	Royston/Parmar spline survival distribution functions with one argument per parameter
qsurvspline7	Royston/Parmar spline survival distribution functions with one argument per parameter
quantile_flexsurvmix	Quantiles of time-to-event distributions in a flexsurvmix model
qweibullPH	Weibull distribution in proportional hazards parameterisation

-- R --

residuals.flexsurvreg	Calculate residuals for flexible survival models
rgenf	Generalized F distribution
rgenf.orig	Generalized F distribution (original parameterisation)
rgengamma	Generalized gamma distribution
rgengamma.orig	Generalized gamma distribution (original parameterisation)
rgompertz	The Gompertz distribution
rllogis	The log-logistic distribution
rmst_exp	Mean and restricted mean survival functions
rmst_flexsurvmix	Restricted mean times to events from a flexsurvmix model
rmst_gamma	Mean and restricted mean survival functions
rmst_generic	Generic function to find restricted mean survival time for some distribution
rmst_genf	Mean and restricted mean survival functions
rmst_genf.orig	Mean and restricted mean survival functions
rmst_gengamma	Mean and restricted mean survival functions
rmst_gengamma.orig	Mean and restricted mean survival functions
rmst_gompertz	Mean and restricted mean survival functions
rmst_llogis	Mean and restricted mean survival functions
rmst_lnorm	Mean and restricted mean survival functions
rmst_survspline	Royston/Parmar spline survival distribution
rmst_survspline0	Royston/Parmar spline survival distribution functions with one argument per parameter
rmst_survspline1	Royston/Parmar spline survival distribution functions with one argument per parameter
rmst_survspline2	Royston/Parmar spline survival distribution functions with one argument per parameter
rmst_survspline3	Royston/Parmar spline survival distribution functions with one argument per parameter
rmst_survspline4	Royston/Parmar spline survival distribution functions with one argument per parameter
rmst_survspline5	Royston/Parmar spline survival distribution functions with one argument per parameter
rmst_survspline6	Royston/Parmar spline survival distribution functions with one argument per parameter
rmst_survspline7	Royston/Parmar spline survival distribution functions with one argument per parameter
rmst_weibull	Mean and restricted mean survival functions
rmst_weibullPH	Mean and restricted mean survival functions
rsurvspline	Royston/Parmar spline survival distribution
rsurvspline0	Royston/Parmar spline survival distribution functions with one argument per parameter
rsurvspline1	Royston/Parmar spline survival distribution functions with one argument per parameter
rsurvspline2	Royston/Parmar spline survival distribution functions with one argument per parameter
rsurvspline3	Royston/Parmar spline survival distribution functions with one argument per parameter
rsurvspline4	Royston/Parmar spline survival distribution functions with one argument per parameter
rsurvspline5	Royston/Parmar spline survival distribution functions with one argument per parameter
rsurvspline6	Royston/Parmar spline survival distribution functions with one argument per parameter
rsurvspline7	Royston/Parmar spline survival distribution functions with one argument per parameter
rweibullPH	Weibull distribution in proportional hazards parameterisation

-- S --

sim.fmsm	Simulate paths through a fully parametric semi-Markov multi-state model
simfinal_fmsm	Simulate and summarise final outcomes from a flexible parametric multi-state model
simfs_bytrans	Reformat simulated multi-state data with one row per simulated transition
simt_flexsurvmix	Simulate times to competing events from a mixture multi-state model
simulate.flexsurvreg	Simulate censored time-to-event data from a fitted flexsurvreg model
standsurv	Marginal survival and hazards of fitted flexsurvreg models
summary.flexsurvreg	Summaries of fitted flexible survival models
summary.flexsurvrtrunc	Summarise quantities of interest from fitted flexsurvrtrunc models
survrtrunc	Nonparametric estimator of survival from right-truncated, uncensored data
Survspline	Royston/Parmar spline survival distribution
Survsplinek	Royston/Parmar spline survival distribution functions with one argument per parameter

-- T --

tidy.flexsurvreg	Tidy a flexsurv model object
tidy.standsurv	Tidy a standsurv object.
totlos.fs	Total length of stay in particular states for a fully-parametric, time-inhomogeneous Markov multi-state model
totlos.simfs	Expected total length of stay in specific states, from a fully-parametric, semi-Markov multi-state model

-- U --

unroll.function

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

-- V --

vcov.flexsurvreg

Variance-covariance matrix from a flexsurvreg model

-- W --

WeibullPH

Weibull distribution in proportional hazards parameterisation