survival: Survival Analysis

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Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

Author
Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Date of publication
2016-10-30 20:29:44
Maintainer
Terry M Therneau <therneau.terry@mayo.edu>
License
LGPL (>= 2)
Version
2.40-1
URLs

View on CRAN

Man pages

aareg
Aalen's additive regression model for censored data
agreg.fit
Cox model fitting functions
aml
Acute Myelogenous Leukemia survival data
anova.coxph
Analysis of Deviance for a Cox model.
attrassign
Create new-style "assign" attribute
basehaz
Alias for the survfit function
bladder
Bladder Cancer Recurrences
cch
Fits proportional hazards regression model to case-cohort...
cgd
Chronic Granulotomous Disease data
cgd0
Chronic Granulotomous Disease data
clogit
Conditional logistic regression
cluster
Identify clusters.
colon
Chemotherapy for Stage B/C colon cancer
coxph
Fit Proportional Hazards Regression Model
coxph.control
Ancillary arguments for controling coxph fits
coxph.detail
Details of a Cox Model Fit
coxph.object
Proportional Hazards Regression Object
coxph.wtest
Compute a quadratic form
cox.zph
Test the Proportional Hazards Assumption of a Cox Regression
dsurvreg
Distributions available in survreg.
finegray
Create data for a Fine-Gray model
flchain
Assay of serum free light chain for 7874 subjects.
frailty
Random effects terms
genfan
Generator fans
heart
Stanford Heart Transplant data
is.ratetable
Verify that an object is of class ratetable.
kidney
Kidney catheter data
lines.survfit
Add Lines or Points to a Survival Plot
logan
Data from the 1972-78 GSS data used by Logan
logLik.coxph
logLik method for a Cox model
lung
NCCTG Lung Cancer Data
mgus
Monoclonal gammapothy data
mgus2
Monoclonal gammapothy data
model.frame.coxph
Model.frame method for coxph objects
model.matrix.coxph
Model.matrix method for coxph models
myeloid
Acute myeloid leukemia
neardate
Find the index of the closest value in data set 2, for each...
nwtco
Data from the National Wilm's Tumor Study
ovarian
Ovarian Cancer Survival Data
pbc
Mayo Clinic Primary Biliary Cirrhosis Data
pbcseq
Mayo Clinic Primary Biliary Cirrhosis, sequential data
plot.aareg
Plot an aareg object.
plot.cox.zph
Graphical Test of Proportional Hazards
plot.survfit
Plot method for 'survfit' objects
predict.coxph
Predictions for a Cox model
predict.survreg
Predicted Values for a 'survreg' Object
print.aareg
Print an aareg object
print.summary.coxph
Print method for summary.coxph objects
print.summary.survexp
Print Survexp Summary
print.summary.survfit
Print Survfit Summary
print.survfit
Print a Short Summary of a Survival Curve
pspline
Smoothing splines using a pspline basis
pyears
Person Years
quantile.survfit
Quantiles from a survfit object
ratetable
Ratetable reference in formula
ratetableDate
Convert date objects to ratetable form
rats
Rat treatment data from Mantel et al
rats2
Rat data from Gail et al.
residuals.coxph
Calculate Residuals for a 'coxph' Fit
residuals.survreg
Compute Residuals for 'survreg' Objects
retinopathy
Diabetic Retinopathy
rhDNase
rhDNASE data set
ridge
Ridge regression
stanford2
More Stanford Heart Transplant data
statefig
Draw a state space figure.
strata
Identify Stratification Variables
summary.aareg
Summarize an aareg fit
summary.coxph
Summary method for Cox models
summary.survexp
Summary function for a survexp object
summary.survfit
Summary of a Survival Curve
Surv
Create a Survival Object
survConcordance
Compute a concordance measure.
survdiff
Test Survival Curve Differences
survexp
Compute Expected Survival
survexp.fit
Compute Expected Survival
survexp.object
Expected Survival Curve Object
survexp.us
Census Data Sets for the Expected Survival and Person Years...
survfit
Create survival curves
survfit.coxph
Compute a Survival Curve from a Cox model
survfitcoxph.fit
A direct interface to the 'computational engine' of...
survfit.formula
Compute a Survival Curve for Censored Data
survfit.matrix
Create Aalen-Johansen estimates of multi-state survival from...
survfit.object
Survival Curve Object
survival-internal
Internal survival functions
survobrien
O'Brien's Test for Association of a Single Variable with...
survreg
Regression for a Parametric Survival Model
survreg.control
Package options for survreg and coxph
survreg.distributions
Parametric Survival Distributions
survregDtest
Verify a survreg distribution
survreg.object
Parametric Survival Model Object
survSplit
Split a survival data set at specified times
tcut
Factors for person-year calculations
tmerge
Time based merge for survival data
tobin
Tobin's Tobit data
transplant
Liver transplant waiting list
untangle.specials
Help Process the 'specials' Argument of the 'terms' Function.
uspop2
Projected US Population
veteran
Veterans' Administration Lung Cancer study

Files in this package

survival
survival/inst
survival/inst/CITATION
survival/inst/NEWS.Rd
survival/inst/COPYRIGHTS
survival/inst/doc
survival/inst/doc/splines.pdf
survival/inst/doc/adjcurve.Rnw
survival/inst/doc/compete.R
survival/inst/doc/tests.pdf
survival/inst/doc/multi.pdf
survival/inst/doc/multi.Rnw
survival/inst/doc/timedep.R
survival/inst/doc/adjcurve.pdf
survival/inst/doc/compete.Rnw
survival/inst/doc/compete.pdf
survival/inst/doc/validate.pdf
survival/inst/doc/tests.Rnw
survival/inst/doc/adjcurve.R
survival/inst/doc/multi.R
survival/inst/doc/timedep.Rnw
survival/inst/doc/splines.Rnw
survival/inst/doc/timedep.pdf
survival/inst/doc/splines.R
survival/inst/doc/validate.R
survival/inst/doc/tests.R
survival/inst/doc/validate.Rnw
survival/ToDo
survival/tests
survival/tests/singtest.Rout.save
survival/tests/anova.R
survival/tests/model.matrix.Rout.save
survival/tests/expected.Rout.save
survival/tests/factor2.Rout.save
survival/tests/strata2.Rout.save
survival/tests/r_capacitor.R
survival/tests/fr_cancer.Rout.save
survival/tests/data.rat2
survival/tests/quantile.R
survival/tests/fr_ovarian.Rout.save
survival/tests/difftest.Rout.save
survival/tests/turnbull.Rout.save
survival/tests/aareg.R
survival/tests/jasa.R
survival/tests/model.matrix.R
survival/tests/fr_simple.R
survival/tests/difftest.R
survival/tests/ovarian.R
survival/tests/quantile.Rout.save
survival/tests/cancer.Rout.save
survival/tests/r_peterson.R
survival/tests/rounding.Rout.save
survival/tests/r_capacitor.Rout.save
survival/tests/summary_survfit.R
survival/tests/survSplit.R
survival/tests/data.interval
survival/tests/testnull.Rout.save
survival/tests/bladder.R
survival/tests/stratatest.Rout.save
survival/tests/gray1.rda
survival/tests/strata2.R
survival/tests/rounding.R
survival/tests/r_tdist.R
survival/tests/frank.R
survival/tests/tmerge.R
survival/tests/expected2.R
survival/tests/concordance.R
survival/tests/book4.R
survival/tests/turnbull.R
survival/tests/mstate.R
survival/tests/coxsurv4.Rout.save
survival/tests/r_strata.Rout.save
survival/tests/r_strata.R
survival/tests/book4.Rout.save
survival/tests/r_tdist.Rout.save
survival/tests/jasa.Rout.save
survival/tests/book6.R
survival/tests/finegray.R
survival/tests/data.motor
survival/tests/fr_resid.R
survival/tests/mstate.Rout.save
survival/tests/testci.R
survival/tests/coxsurv.Rout.save
survival/tests/r_user.Rout.save
survival/tests/tiedtime.R
survival/tests/r_sas.Rout.save
survival/tests/finegray.Rout.save
survival/tests/r_resid.R
survival/tests/fr_lung.R
survival/tests/pspline.R
survival/tests/book6.Rout.save
survival/tests/anova.Rout.save
survival/tests/testci2.Rout.save
survival/tests/prednew.R
survival/tests/survreg2.Rout.save
survival/tests/survfit2.Rout.save
survival/tests/fr_rat1.Rout.save
survival/tests/survreg2.R
survival/tests/book3.R
survival/tests/book1.Rout.save
survival/tests/nested.R
survival/tests/book1.R
survival/tests/fr_kidney.R
survival/tests/r_sas.R
survival/tests/fr_ovarian.R
survival/tests/survtest.R
survival/tests/mrtest.R
survival/tests/r_stanford.Rout.save
survival/tests/clogit.R
survival/tests/factor.R
survival/tests/book7.Rout.save
survival/tests/r_donnell.R
survival/tests/book2.Rout.save
survival/tests/testreg.Rout.save
survival/tests/doaml.R
survival/tests/coxsurv2.R
survival/tests/r_donnell.Rout.save
survival/tests/prednew.Rout.save
survival/tests/r_user.R
survival/tests/ratetable.Rout.save
survival/tests/book2.R
survival/tests/r_scale.R
survival/tests/tt.Rout.save
survival/tests/ovarian.Rout.save
survival/tests/fr_kidney.Rout.save
survival/tests/singtest.R
survival/tests/data.cracks
survival/tests/testci2.R
survival/tests/fr_rat2.Rout.save
survival/tests/testnull.R
survival/tests/fr_cancer.R
survival/tests/coxsurv4.R
survival/tests/coxsurv3.Rout.save
survival/tests/data.valve
survival/tests/survSplit.Rout.save
survival/tests/survtest.Rout.save
survival/tests/factor2.R
survival/tests/ratetable.R
survival/tests/data.donnell
survival/tests/nested.Rout.save
survival/tests/fr_simple.Rout.save
survival/tests/r_scale.Rout.save
survival/tests/fr_rat1.R
survival/tests/book5.Rout.save
survival/tests/r_lung.R
survival/tests/detail.Rout.save
survival/tests/expected2.Rout.save
survival/tests/bladder.Rout.save
survival/tests/infcox.Rout.save
survival/tests/data.capacitor
survival/tests/ties.rda
survival/tests/coxsurv2.Rout.save
survival/tests/surv.Rout.save
survival/tests/doaml.Rout.save
survival/tests/r_resid.Rout.save
survival/tests/pspline.Rout.save
survival/tests/clogit.Rout.save
survival/tests/summary_survfit.Rout.save
survival/tests/book3.Rout.save
survival/tests/frank.Rout.save
survival/tests/r_stanford.R
survival/tests/infcox.R
survival/tests/cancer.R
survival/tests/detail.R
survival/tests/fr_rat2.R
survival/tests/data.peterson
survival/tests/frailty.Rout.save
survival/tests/tmerge.Rout.save
survival/tests/counting.R
survival/tests/testci.Rout.save
survival/tests/data.fluid
survival/tests/r_lung.Rout.save
survival/tests/r_peterson.Rout.save
survival/tests/mrtest.Rout.save
survival/tests/aareg.Rout.save
survival/tests/surv.R
survival/tests/factor.Rout.save
survival/tests/pyear.R
survival/tests/fr_resid.Rout.save
survival/tests/frailty.R
survival/tests/counting.Rout.save
survival/tests/tt.R
survival/tests/fr_lung.Rout.save
survival/tests/testreg.R
survival/tests/book5.R
survival/tests/data.smoke
survival/tests/concordance.Rout.save
survival/tests/pyear.Rout.save
survival/tests/stratatest.R
survival/tests/survfit2.R
survival/tests/doweight.R
survival/tests/tiedtime.Rout.save
survival/tests/coxsurv3.R
survival/tests/book7.R
survival/tests/data.turbine
survival/tests/coxsurv.R
survival/tests/doweight.Rout.save
survival/tests/expected.R
survival/src
survival/src/pystep.c
survival/src/survfit4.c
survival/src/coxcount1.c
survival/src/chinv2.c
survival/src/pyears3b.c
survival/src/survS.h
survival/src/chsolve2.c
survival/src/survproto.h
survival/src/agmart2.c
survival/src/survregc2.c
survival/src/coxexact.c
survival/src/survdiff2.c
survival/src/pyears1.c
survival/src/coxmart2.c
survival/src/coxfit5.c
survival/src/agfit4.c
survival/src/survreg6.c
survival/src/agscore.c
survival/src/survpenal.c
survival/src/concordance1.c
survival/src/coxmart.c
survival/src/agsurv4.c
survival/src/cox_Rcallback.c
survival/src/coxfit6.c
survival/src/tmerge.c
survival/src/cholesky2.c
survival/src/agsurv5.c
survival/src/chsolve3.c
survival/src/coxph_wtest.c
survival/src/pyears2.c
survival/src/finegray.c
survival/src/coxdetail.c
survival/src/agsurv3.c
survival/src/coxscho.c
survival/src/agexact.c
survival/src/survregc1.c
survival/src/survsplit.c
survival/src/doloop.c
survival/src/survfitci.c
survival/src/init.c
survival/src/survConcordance.c
survival/src/agmart3.c
survival/src/agfit5.c
survival/src/cholesky3.c
survival/src/coxscore.c
survival/src/coxsafe.c
survival/src/dmatrix.c
survival/src/chinv3.c
survival/src/agmart.c
survival/src/survreg7.c
survival/NAMESPACE
survival/noweb
survival/noweb/plot.Rnw.orig
survival/noweb/survfitKM.Rnw
survival/noweb/Makefile
survival/noweb/agreg.Rnw
survival/noweb/msurv.nw
survival/noweb/survfitCI.Rnw
survival/noweb/plot.Rnw
survival/noweb/finegray.Rnw
survival/noweb/main.Rnw
survival/noweb/residuals.survreg.Rnw
survival/noweb/concordance.Rnw
survival/noweb/refer.bib
survival/noweb/survfitms.Rnw
survival/noweb/coxsurv2.Rnw
survival/noweb/pyears.Rnw
survival/noweb/coxph.Rnw
survival/noweb/zzz
survival/noweb/statefig.Rnw
survival/noweb/tmerge.Rnw
survival/noweb/rates
survival/noweb/rates/minn2004.dat
survival/noweb/rates/minndecennial.dat
survival/noweb/rates/us2004.dat
survival/noweb/rates/minn2000.dat
survival/noweb/rates/us2003.dat
survival/noweb/rates/usinfant.dat
survival/noweb/rates/us2002.dat
survival/noweb/rates/us1996.dat
survival/noweb/rates/us1997.dat
survival/noweb/rates/us1998.dat
survival/noweb/rates/us2005.dat
survival/noweb/rates/usdecennial.dat
survival/noweb/rates/us1999.dat
survival/noweb/rates/us2001.dat
survival/noweb/rates/us2006.dat
survival/noweb/rates/us2000.dat
survival/noweb/survexp.Rnw
survival/noweb/coxsurv.Rnw
survival/noweb/survfit.Rnw
survival/noweb/tail
survival/noweb/exact.nw
survival/noweb/Readme
survival/data
survival/data/rats.rda
survival/data/ovarian.rda
survival/data/flchain.rda
survival/data/pbc.rda
survival/data/veteran.rda
survival/data/retinopathy.rda
survival/data/mgus2.rda
survival/data/leukemia.rda
survival/data/bladder.rda
survival/data/survexp.rda
survival/data/rhDNase.rda
survival/data/cgd.rda
survival/data/mgus.rda
survival/data/nwtco.rda
survival/data/myeloid.rda
survival/data/genfan.rda
survival/data/logan.rda
survival/data/datalist
survival/data/cancer.rda
survival/data/tobin.txt.gz
survival/data/transplant.rda
survival/data/lung.rda
survival/data/stanford2.rda
survival/data/kidney.rda
survival/data/heart.rda
survival/data/colon.rda
survival/data/uspop2.rda
survival/R
survival/R/survreg.control.S
survival/R/print.summary.coxph.S
survival/R/print.coxph.penal.S
survival/R/summary.coxph.S
survival/R/summary.pyears.S
survival/R/residuals.survreg.penal.S
survival/R/frailty.gaussian.S
survival/R/survpenal.fit.S
survival/R/tcut.S
survival/R/print.coxph.S
survival/R/survSplit.R
survival/R/print.aareg.S
survival/R/plot.aareg.S
survival/R/print.survexp.S
survival/R/cox.zph.S
survival/R/survregDtest.S
survival/R/survdiff.S
survival/R/coxph.fit.S
survival/R/coxph.control.S
survival/R/frailty.controlgam.S
survival/R/statefig.R
survival/R/anova.survreglist.S
survival/R/survfitms.R
survival/R/survfit.matrix.R
survival/R/tmerge.R
survival/R/predict.survreg.S
survival/R/print.survfit.S
survival/R/predict.coxph.R
survival/R/model.matrix.coxph.R
survival/R/print.survreg.S
survival/R/coxph.detail.S
survival/R/residuals.coxph.null.S
survival/R/model.frame.survreg.R
survival/R/residuals.survreg.R
survival/R/finegray.R
survival/R/survreg.S
survival/R/summary.coxph.penal.S
survival/R/frailty.brent.S
survival/R/plot.cox.zph.S
survival/R/survexp.fit.S
survival/R/coxph.rvar.S
survival/R/print.coxph.null.S
survival/R/ratetableDate.S
survival/R/pspline.R
survival/R/anova.survreg.S
survival/R/survexp.cfit.R
survival/R/frailty.t.S
survival/R/residuals.coxph.S
survival/R/is.ratetable.S
survival/R/normalizetime.R
survival/R/survobrien.S
survival/R/print.ratetable.S
survival/R/summary.ratetable.S
survival/R/agsurv.R
survival/R/untangle.specials.S
survival/R/match.ratetable.S
survival/R/ridge.S
survival/R/clogit.R
survival/R/survexp.R
survival/R/pyears.R
survival/R/summary.survreg.S
survival/R/coxph.wtest.S
survival/R/survcallback.S
survival/R/Surv.S
survival/R/is.na.coxph.penalty.S
survival/R/neardate.R
survival/R/survfitCI.R
survival/R/quantile.survfit.R
survival/R/ratetable.S
survival/R/cluster.S
survival/R/aareg.taper.S
survival/R/coxexact.fit.R
survival/R/anova.coxph.R
survival/R/lines.survexp.R
survival/R/plot.survfit.R
survival/R/survfitKM.S
survival/R/survConcordance.R
survival/R/frailty.controlaic.S
survival/R/strata.S
survival/R/survfit.R
survival/R/predict.survreg.penal.S
survival/R/coxph.getdata.S
survival/R/basehaz.R
survival/R/frailty.controlgauss.S
survival/R/print.survreg.penal.S
survival/R/survreg.fit.S
survival/R/survreg.distributions.S
survival/R/summary.aareg.S
survival/R/predict.coxph.penal.S
survival/R/frailty.gamma.S
survival/R/survConcordance.fit.R
survival/R/print.survdiff.S
survival/R/lines.survfit.coxph.S
survival/R/coxph.R
survival/R/agexact.fit.S
survival/R/print.summary.survexp.R
survival/R/summary.survexp.R
survival/R/survfitcoxph.fit.R
survival/R/frailty.S
survival/R/format.Surv.S
survival/R/logLik.coxph.R
survival/R/lines.aareg.S
survival/R/print.summary.survfitms.S
survival/R/aareg.S
survival/R/cch.R
survival/R/print.pyears.R
survival/R/frailty.controldf.S
survival/R/agreg.fit.R
survival/R/print.summary.survreg.S
survival/R/coxpenal.df.S
survival/R/firstlib.R
survival/R/survfitTurnbull.S
survival/R/survdiff.fit.S
survival/R/print.summary.coxph.penal.S
survival/R/print.summary.survfit.S
survival/R/dsurvreg.S
survival/R/anova.coxphlist.S
survival/R/survfit.coxph.R
survival/R/frailty.gammacon.S
survival/R/xtras.R
survival/R/print.cox.zph.S
survival/R/labels.survreg.S
survival/R/coxpenal.fit.R
survival/R/anova.coxph.penal.R
survival/R/residuals.coxph.penal.S
survival/R/attrassign.R
survival/vignettes
survival/vignettes/adjcurve.Rnw
survival/vignettes/refer.bib
survival/vignettes/multi.Rnw
survival/vignettes/.install_extras
survival/vignettes/compete.Rnw
survival/vignettes/tests.Rnw
survival/vignettes/timedep.Rnw
survival/vignettes/splines.Rnw
survival/vignettes/mstate.rda
survival/vignettes/validate.Rnw
survival/MD5
survival/build
survival/build/vignette.rds
survival/DESCRIPTION
survival/man
survival/man/survexp.Rd
survival/man/survreg.control.Rd
survival/man/mgus2.Rd
survival/man/lines.survfit.Rd
survival/man/print.summary.survfit.Rd
survival/man/colon.Rd
survival/man/survreg.distributions.Rd
survival/man/attrassign.Rd
survival/man/rats2.Rd
survival/man/rats.Rd
survival/man/survreg.Rd
survival/man/uspop2.Rd
survival/man/survfitcoxph.fit.Rd
survival/man/ratetable.Rd
survival/man/residuals.survreg.Rd
survival/man/survfit.matrix.Rd
survival/man/print.survfit.Rd
survival/man/summary.survexp.Rd
survival/man/survdiff.Rd
survival/man/bladder.Rd
survival/man/pbcseq.Rd
survival/man/frailty.Rd
survival/man/myeloid.Rd
survival/man/print.summary.coxph.Rd
survival/man/cluster.Rd
survival/man/tobin.Rd
survival/man/is.ratetable.Rd
survival/man/survexp.fit.Rd
survival/man/ovarian.Rd
survival/man/anova.coxph.Rd
survival/man/summary.survfit.Rd
survival/man/quantile.survfit.Rd
survival/man/transplant.Rd
survival/man/flchain.Rd
survival/man/survival-internal.Rd
survival/man/survfit.formula.Rd
survival/man/ridge.Rd
survival/man/survregDtest.Rd
survival/man/predict.survreg.Rd
survival/man/survConcordance.Rd
survival/man/model.frame.coxph.Rd
survival/man/coxph.detail.Rd
survival/man/rhDNase.Rd
survival/man/retinopathy.Rd
survival/man/agreg.fit.Rd
survival/man/strata.Rd
survival/man/finegray.Rd
survival/man/stanford2.Rd
survival/man/lung.Rd
survival/man/cgd0.Rd
survival/man/survreg.object.Rd
survival/man/survexp.object.Rd
survival/man/untangle.specials.Rd
survival/man/summary.aareg.Rd
survival/man/survexp.us.Rd
survival/man/tmerge.Rd
survival/man/ratetableDate.Rd
survival/man/predict.coxph.Rd
survival/man/cgd.Rd
survival/man/plot.survfit.Rd
survival/man/summary.coxph.Rd
survival/man/mgus.Rd
survival/man/kidney.Rd
survival/man/survfit.object.Rd
survival/man/pspline.Rd
survival/man/pyears.Rd
survival/man/genfan.Rd
survival/man/nwtco.Rd
survival/man/survfit.Rd
survival/man/model.matrix.coxph.Rd
survival/man/plot.aareg.Rd
survival/man/coxph.Rd
survival/man/logLik.coxph.Rd
survival/man/statefig.Rd
survival/man/survfit.coxph.Rd
survival/man/residuals.coxph.Rd
survival/man/coxph.control.Rd
survival/man/cox.zph.Rd
survival/man/print.summary.survexp.Rd
survival/man/tcut.Rd
survival/man/aml.Rd
survival/man/pbc.Rd
survival/man/Surv.Rd
survival/man/coxph.object.Rd
survival/man/veteran.Rd
survival/man/coxph.wtest.Rd
survival/man/survobrien.Rd
survival/man/basehaz.Rd
survival/man/aareg.Rd
survival/man/plot.cox.zph.Rd
survival/man/dsurvreg.Rd
survival/man/survSplit.Rd
survival/man/clogit.Rd
survival/man/print.aareg.Rd
survival/man/logan.Rd
survival/man/cch.Rd
survival/man/neardate.Rd
survival/man/heart.Rd
survival/cleanup
survival/.Rinstignore
survival/cleanup.win