flexsurv: Flexible Parametric Survival and Multi-State Models
Version 1.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorChristopher Jackson [aut, cre], Paul Metcalfe [ctb], Jordan Amdahl [ctb]
Date of publication2017-03-27 14:03:47 UTC
MaintainerChristopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
LicenseGPL (>= 2)
Version1.1
URL https://github.com/chjackson/flexsurv-dev
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("flexsurv")

Man pages

basis: Natural cubic spline basis
bc: Breast cancer survival data
bos: Bronchiolitis obliterans syndrome after lung transplants
coef.flexsurvreg: Extract model coefficients from fitted flexible survival...
flexsurv-package: flexsurv: Flexible parametric survival and multi-state models
flexsurvreg: Flexible parametric regression for time-to-event data
flexsurvspline: Flexible survival regression using the Royston/Parmar spline...
GenF: Generalized F distribution
GenF.orig: Generalized F distribution (original parameterisation)
GenGamma: Generalized gamma distribution
GenGamma.orig: Generalized gamma distribution (original parameterisation)
Gompertz: The Gompertz distribution
hazard: Hazard and cumulative hazard functions
lines.flexsurvreg: Add fitted flexible survival curves to a plot
Llogis: The log-logistic distribution
means: Mean and restricted mean survival functions
model.frame.flexsurvreg: Extract original data from 'flexsurvreg' objects.
msfit.flexsurvreg: Cumulative intensity function for parametric multi-state...
normboot.flexsurvreg: Simulate from the asymptotic normal distribution of parameter...
pars.fmsm: Transition-specific parameters in a flexible parametric...
plot.flexsurvreg: Plots of fitted flexible survival models
pmatrix.fs: Transition probability matrix from a fully-parametric,...
pmatrix.simfs: Transition probability matrix from a fully-parametric,...
qgeneric: Generic function to find quantiles of a distribution
rmst_generic: Generic function to find restricted mean survival of a...
sim.fmsm: Simulate paths through a fully parametric semi-Markov...
summary.flexsurvreg: Summaries of fitted flexible survival models
Survspline: Royston/Parmar spline survival distribution
totlos.fs: Total length of stay in particular states for a...
totlos.simfs: Expected total length of stay in specific states, from a...
unroll.function: Convert a function with matrix arguments to a function with...
WeibullPH: Weibull distribution in proportional hazards parameterisation

Functions

DLSexp Source code
DLSgompertz Source code
DLSllogis Source code
DLSsurvspline Source code
DLSweibull Source code
DLdexp Source code
DLdgompertz Source code
DLdllogis Source code
DLdsurvspline Source code
DLdweibull Source code
Dcov Source code
Dminusloglik.flexsurv Source code
GenF Man page
GenF.orig Man page
GenGamma Man page
GenGamma.orig Man page
Gompertz Man page
Hexp Man page Source code
Hgamma Man page Source code
Hgenf Man page Source code
Hgenf.orig Man page Source code
Hgengamma Man page Source code
Hgengamma.orig Man page Source code
Hgompertz Man page Source code
Hlink Source code
Hllogis Man page Source code
Hlnorm Man page Source code
Hsurvspline Man page Source code
Hweibull Man page Source code Source code
Hweibull.quiet Source code
HweibullPH Man page Source code
Llogis Man page
Slink Source code
Survspline Man page
WeibullPH Man page
_PACKAGE Man page
absorbing Source code
add.covs Source code
ancpar.formula Source code
basis Man page Source code
basis_matrix Source code
basis_vector Source code
bc Man page
bfp Source code
bootci.fmsm Source code
bos Man page
bosms3 Man page
bosms4 Man page
buildAuxParms Source code
buildTransformer Source code
check.dlist Source code
check.exp Source code
check.flexsurv.response Source code
check.formula Source code
check.gamma Source code
check.genf Source code
check.genf.orig Source code
check.gengamma Source code
check.gengamma.orig Source code
check.gompertz Source code
check.llogis Source code
check.lnorm Source code
check.weibull Source code Source code
cisumm.flexsurvreg Source code
coef.flexsurvreg Man page Source code
compress.model.matrices Source code
concat.formulae Source code
dbase Source code
dbase.survspline Source code
dbasis Man page Source code
dbasis_matrix Source code
dbasis_vector Source code
dbfp Source code
dderiv Source code
deriv.test Source code
dexph Source code
dfss Man page Source code
dgenf Man page Source code
dgenf.orig Man page Source code
dgenf_work Source code
dgengamma Man page Source code
dgengamma.orig Man page Source code
dgengamma_work Source code
dgompertz Man page Source code
dgompertz_work Source code
dlink Source code
dllogis Man page Source code
dllogis_work Source code
dsurvspline Man page Source code
dtsfn Source code
dweibull.quiet Source code
dweibullPH Man page Source code
expand.inits.args Source code
expand.summfn.args Source code
exph Source code
flexsurv Man page
flexsurv-package Man page
flexsurv.dists Man page
flexsurv.splineinits Source code
flexsurv.splineinits.cox Source code
flexsurvreg Man page Source code
flexsurvspline Man page Source code
form.basepars.tcovs Source code
form.dp Source code
form.model.matrix Source code
form.msm.newdata Source code
format.ci Source code
fss Man page Source code
get.locform Source code
hazard Man page
hexp Man page Source code
hgamma Man page Source code
hgenf Man page Source code
hgenf.orig Man page Source code
hgengamma Man page Source code
hgengamma.orig Man page Source code
hgompertz Man page Source code
hlink Source code
hllogis Man page Source code
hlnorm Man page Source code
hsurvspline Man page Source code
hweibull Man page Source code Source code
hweibull.quiet Source code Source code
hweibullPH Man page Source code
integrate.dh Source code
is.flexsurvlist Source code
ldlink Source code
lines.flexsurvreg Man page Source code
logLik.flexsurvreg Source code
logLikFactory Source code
logh Source code
mean_exp Man page Source code
mean_gamma Man page Source code
mean_genf Man page Source code
mean_genf.orig Man page Source code
mean_gengamma Man page Source code
mean_gengamma.orig Man page Source code
mean_gompertz Man page Source code
mean_llogis Man page Source code
mean_lnorm Man page Source code
mean_survspline Man page Source code
mean_weibull Man page Source code
mean_weibull.quiet Source code
mean_weibullPH Man page Source code
means Man page
minusloglik.flexsurv Source code
model.frame.flexsurvreg Man page Source code
model.matrix.flexsurvreg Man page Source code
msfit.flexsurvreg Man page Source code
normboot.flexsurvreg Man page Source code
normbootfn.flexsurvreg Source code
onLoad Source code
onUnload Source code
pars.fmsm Man page Source code
pgenf Man page Source code
pgenf.orig Man page Source code
pgenf_work Source code
pgengamma Man page Source code
pgengamma.orig Man page Source code
pgengamma_work Source code
pgompertz Man page Source code
pgompertz_work Source code
pllogis Man page Source code
pllogis_work Source code
plot.flexsurvreg Man page Source code
pmatrix.fs Man page Source code
pmatrix.simfs Man page Source code
print.ci Source code
print.flexsurvreg Source code
print.fs.msm.est Source code
print.summary.flexsurvreg Source code
print.totlos.fs Source code
psurvspline Man page Source code
pweibull.quiet Source code
pweibullPH Man page Source code
qgeneric Man page Source code
qgenf Man page Source code
qgenf.orig Man page Source code
qgengamma Man page Source code
qgengamma.orig Man page Source code
qgompertz Man page Source code
qllogis Man page Source code
qsurvspline Man page Source code
qweibull.quiet Source code
qweibullPH Man page Source code
rbase Source code
rgenf Man page Source code
rgenf.orig Man page Source code
rgengamma Man page Source code
rgengamma.orig Man page Source code
rgompertz Man page Source code
rllogis Man page Source code
rmst_exp Man page Source code
rmst_gamma Man page Source code
rmst_generic Man page Source code
rmst_genf Man page Source code
rmst_genf.orig Man page Source code
rmst_gengamma Man page Source code
rmst_gengamma.orig Man page Source code
rmst_gompertz Man page Source code
rmst_llogis Man page Source code
rmst_lnorm Man page Source code
rmst_survspline Man page Source code
rmst_weibull Man page Source code
rmst_weibull.quiet Source code
rmst_weibullPH Man page Source code
rsurvspline Man page Source code
rweibullPH Man page Source code
sim.fmsm Man page Source code
sr.exp.inits Source code
sr.llog.inits Source code
sr.ln.inits Source code
sr.weib.inits Source code
sr.weibPH.inits Source code
sr2fsexp Source code
sr2fsllog Source code
sr2fsln Source code
sr2fswei Source code
summary.flexsurvreg Man page Source code
summary.fns Source code
totlos.fs Man page Source code
totlos.simfs Man page Source code
transient Source code
tsfn Source code
unroll.function Man page Source code
var.exp Source code
var.gamma Source code
var.llogis Source code
var.lnorm Source code
var.weibull Source code
var.weibull.quiet Source code
vcov.flexsurvreg Source code

Files

inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/flexsurv-examples.pdf
inst/doc/flexsurv.R
inst/doc/flexsurv-examples.R
inst/doc/flexsurv.pdf
tests
tests/test_base.R
tests/testthat
tests/testthat/test_utils.R
tests/testthat/test_outputs.R
tests/testthat/test_flexsurvreg.R
tests/testthat/test_custom.R
tests/testthat/test_spline.R
tests/testthat/test_gengamma_orig.R
tests/testthat/test_genf.R
tests/testthat/test_gengamma.R
tests/testthat/test_deriv.R
tests/testthat/test_splinedist.R
tests/testthat/test_genf_orig.R
tests/testthat/test_mstate.R
tests/testthat/test_gompertz.R
tests/testthat/test_llogis.R
src
src/genf.cpp
src/rep_len.h
src/gengamma.h
src/splines.cpp
src/llogis.cpp
src/mapply.h
src/special.cpp
src/mapply_4.h
src/gompertz.cpp
src/flexsurv-init.c
src/gengamma.cpp
src/RcppExports.cpp
src/distribution.h
src/mapply_5.h
NAMESPACE
data
data/bc.txt
data/bc.rda
data/bosms3.rda
data/bosms4.rda
Changelog
R
R/Llogis.R
R/flexsurv-package.R
R/utils.R
R/mstate.R
R/Gompertz.R
R/custom.R
R/Exp.R
R/flexsurvreg.R
R/distributions.R
R/spline.R
R/fracpoly.R
R/RcppExports.R
R/GenGamma.R
R/unroll.function.R
R/deriv.R
R/Gamma.R
R/GenF.R
R/Weibull.R
R/Lnorm.R
R/WeibullPH.R
vignettes
vignettes/flexsurv.bib
vignettes/bosmsm.pdf
vignettes/flexsurv-examples.Rnw
vignettes/flexsurv.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/totlos.fs.Rd
man/coef.flexsurvreg.Rd
man/GenF.Rd
man/rmst_generic.Rd
man/basis.Rd
man/GenGamma.orig.Rd
man/sim.fmsm.Rd
man/model.frame.flexsurvreg.Rd
man/Gompertz.Rd
man/pmatrix.simfs.Rd
man/pars.fmsm.Rd
man/flexsurvreg.Rd
man/summary.flexsurvreg.Rd
man/Llogis.Rd
man/totlos.simfs.Rd
man/means.Rd
man/flexsurvspline.Rd
man/plot.flexsurvreg.Rd
man/bc.Rd
man/hazard.Rd
man/WeibullPH.Rd
man/normboot.flexsurvreg.Rd
man/msfit.flexsurvreg.Rd
man/pmatrix.fs.Rd
man/GenGamma.Rd
man/flexsurv-package.Rd
man/bos.Rd
man/GenF.orig.Rd
man/qgeneric.Rd
man/Survspline.Rd
man/lines.flexsurvreg.Rd
man/unroll.function.Rd
flexsurv documentation built on May 19, 2017, 11:25 a.m.