survival: Survival Analysis

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.

AuthorTerry M Therneau [aut, cre], Thomas Lumley [ctb, trl] (original S->R port and maintainer until 2009)
Date of publication2016-10-30 20:29:44
MaintainerTerry M Therneau <therneau.terry@mayo.edu>
LicenseLGPL (>= 2)
Version2.40-1
https://github.com/therneau/survival

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

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