Package: survival 3.7-3

Terry M Therneau

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.

Authors:Terry M Therneau [aut, cre], Thomas Lumley [ctb, trl], Atkinson Elizabeth [ctb], Crowson Cynthia [ctb]

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survival.pdf |survival.html✨
survival/json (API)
NEWS

# Install 'survival' in R:
install.packages('survival', repos = c('https://therneau.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/therneau/survival/issues

Datasets:
  • aml - Acute Myelogenous Leukemia survival data
  • bladder - Bladder Cancer Recurrences
  • bladder1 - Bladder Cancer Recurrences
  • bladder2 - Bladder Cancer Recurrences
  • braking - Reliability data sets
  • cancer - NCCTG Lung Cancer Data
  • capacitor - Reliability data sets
  • cgd - Chronic Granulotamous Disease data
  • cgd0 - Chronic Granulotomous Disease data
  • colon - Chemotherapy for Stage B/C colon cancer
  • cracks - Reliability data sets
  • diabetic - Ddiabetic retinopathy
  • flchain - Assay of serum free light chain for 7874 subjects.
  • gbsg - Breast cancer data sets used in Royston and Altman
  • genfan - Reliability data sets
  • heart - Stanford Heart Transplant data
  • hoel - Mouse cancer data
  • ifluid - Reliability data sets
  • imotor - Reliability data sets
  • jasa - Stanford Heart Transplant data
  • jasa1 - Stanford Heart Transplant data
  • kidney - Kidney catheter data
  • leukemia - Acute Myelogenous Leukemia survival data
  • logan - Data from the 1972-78 GSS data used by Logan
  • lung - NCCTG Lung Cancer Data
  • mgus - Monoclonal gammopathy data
  • mgus1 - Monoclonal gammopathy data
  • mgus2 - Monoclonal gammopathy data
  • myeloid - Acute myeloid leukemia
  • myeloma - Survival times of patients with multiple myeloma
  • nafld1 - Non-alcoholic fatty liver disease
  • nafld2 - Non-alcoholic fatty liver disease
  • nafld3 - Non-alcoholic fatty liver disease
  • nwtco - Data from the National Wilm's Tumor Study
  • ovarian - Ovarian Cancer Survival Data
  • pbc - Mayo Clinic Primary Biliary Cholangitis Data
  • pbcseq - Mayo Clinic Primary Biliary Cirrhosis, sequential data
  • rats - Rat treatment data from Mantel et al
  • rats2 - Rat data from Gail et al.
  • retinopathy - Diabetic Retinopathy
  • rhDNase - RhDNASE data set
  • rotterdam - Breast cancer data set used in Royston and Altman
  • solder - Data from a soldering experiment
  • stanford2 - More Stanford Heart Transplant data
  • survexp.mn - Census Data Sets for the Expected Survival and Person Years Functions
  • survexp.us - Census Data Sets for the Expected Survival and Person Years Functions
  • survexp.usr - Census Data Sets for the Expected Survival and Person Years Functions
  • tobin - Tobin's Tobit data
  • transplant - Liver transplant waiting list
  • turbine - Reliability data sets
  • udca - Data from a trial of usrodeoxycholic acid
  • udca1 - Data from a trial of usrodeoxycholic acid
  • udca2 - Data from a trial of usrodeoxycholic acid
  • uspop2 - Projected US Population
  • valveSeat - Reliability data sets
  • veteran - Veterans' Administration Lung Cancer study

On CRAN:

20.22 score 391 stars 3.8k packages 26k scripts 121k downloads 1.7k mentions 79 exports 2 dependencies

Last updated 20 hours agofrom:99b14543e2. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-win-x86_64OKNov 05 2024
R-4.5-linux-x86_64OKNov 05 2024
R-4.4-win-x86_64OKNov 05 2024
R-4.4-mac-x86_64OKNov 05 2024
R-4.4-mac-aarch64OKNov 05 2024
R-4.3-win-x86_64OKNov 05 2024
R-4.3-mac-x86_64OKNov 05 2024
R-4.3-mac-aarch64OKNov 05 2024

Exports:aaregaeqSurvagexact.fitagreg.fitattrassignbasehazbcloglogblogblogitbprobitbriercchcipoissonclogitclusterconcordanceconcordancefitcox.zphcoxphcoxph.controlcoxph.detailcoxph.fitcoxph.wtestcoxsurv.fitdsurvregfinegrayformat.Survfrailtyfrailty.gammafrailty.gaussianfrailty.tfromtimelineis.na.Survis.ratetableis.Survmatch.ratetableneardatenskpseudopsplinepsurvregpyearsqsurvregratetableratetableDateridgeroystonrsurvregrttrightstatefigstrataSurvSurv2Surv2datasurvchecksurvConcordancesurvConcordance.fitsurvcondensesurvdiffsurvexpsurvfitsurvfit.formulasurvfit0survfitcoxph.fitsurvfitKMsurvobriensurvpenal.fitsurvregsurvreg.controlsurvreg.distributionssurvreg.fitsurvregDtestsurvSplittcuttmergetotimelineuntangle.specialsyatesyates_setup

Dependencies:latticeMatrix

Adjusted Survival Curves

Rendered fromadjcurve.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-04-24
Started: 2022-04-06

Approximating a Cox Model

Rendered fromapproximate.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2022-04-06
Started: 2022-04-06

Brier scores and the redistribute-to-the-right algorithm

Rendered fromredistribute.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2023-04-01
Started: 2023-04-01

Concordance

Rendered fromconcordance.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-02-14
Started: 2022-04-06

Matrix exponentials

Rendered frommatrix.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-02-14
Started: 2024-02-14

Multi-state models and competing risks

Rendered fromcompete.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-04-24
Started: 2022-04-06

Multi-state survival curves

Rendered frommulti.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2022-04-06
Started: 2022-04-06

Other vignettes

Rendered fromother.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-04-26
Started: 2022-04-06

Population contrasts

Rendered frompopulation.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2022-04-06
Started: 2022-04-06

Roundoff error and tied times

Rendered fromtiedtimes.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2022-04-06
Started: 2022-04-06

Splines, plots, and interactions

Rendered fromsplines.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2022-06-07
Started: 2022-04-06

Survival package methods

Rendered frommethods.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-11-01
Started: 2024-04-15

The survival package

Rendered fromsurvival.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-04-24
Started: 2022-04-06

Using Time Dependent Covariates

Rendered fromtimedep.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-07-04
Started: 2022-04-06

Validation

Rendered fromvalidate.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-02-14
Started: 2022-04-06

Readme and manuals

Help Manual

Help pageTopics
Aalen's additive regression model for censored dataaareg
Adjudicate near ties in a Surv objectaeqSurv
Average survival curvesaggregate.survfit
Cox model fitting functionsagreg.fit coxph.fit
Acute Myelogenous Leukemia survival dataaml leukemia
Analysis of Deviance for a Cox model.anova.coxph anova.coxphlist
Create new-style "assign" attributeattrassign attrassign.default attrassign.lm
Alias for the survfit functionbasehaz
Bladder Cancer Recurrencesbladder bladder1 bladder2
Bounded link functionsbcloglog blog blogit bprobit
Compute the Brier score for a Cox modelbrier
Fits proportional hazards regression model to case-cohort datacch
Chronic Granulotamous Disease datacgd cgd.raw
Chronic Granulotomous Disease datacgd0
Confidence limits for the Poissoncipoisson
Conditional logistic regressionclogit
Identify clusters.cluster
Chemotherapy for Stage B/C colon cancercolon
Compute the concordance statistic for data or a modelconcordance concordance.coxph concordance.formula concordance.lm concordance.survreg
Compute the concordanceconcordancefit
Test the Proportional Hazards Assumption of a Cox Regressioncox.zph print.cox.zph [.cox.zph
Fit Proportional Hazards Regression Modelcoxph coxph.getdata coxph.penalty print.coxph.null print.coxph.penal summary.coxph.penal
Ancillary arguments for controlling coxph fitscoxph.control
Details of a Cox Model Fitcoxph.detail
Proportional Hazards Regression Objectcoxph.object extractAIC.coxph.penal print.coxph
Compute a quadratic formcoxph.wtest
Multi-state Proportional Hazards Regression Objectcoxphms.object
A direct interface to the `computational engine' of survfit.coxphcoxsurv.fit
Ddiabetic retinopathydiabetic
Distributions available in survreg.dsurvreg psurvreg qsurvreg rsurvreg
Create data for a Fine-Gray modelfinegray
Assay of serum free light chain for 7874 subjects.flchain
Random effects termsfrailty frailty.gamma frailty.gaussian frailty.t
Breast cancer data sets used in Royston and Altman (2013)gbsg
Stanford Heart Transplant dataheart jasa jasa1
Mouse cancer datahoel
Verify that an object is of class ratetable.is.ratetable Math.ratetable Ops.ratetable
Kidney catheter datakidney
Return the states of a multi-state Surv objectlevels.Surv
Add Lines or Points to a Survival Plotlines.survexp lines.survfit points.survfit
Data from the 1972-78 GSS data used by Loganlogan
logLik method for a Cox modellogLik.coxph logLik.survreg
NCCTG Lung Cancer Datacancer lung
Monoclonal gammopathy datamgus mgus1
Monoclonal gammopathy datamgus2
Model.frame method for coxph objectsmodel.frame.coxph
Model.matrix method for coxph modelsmodel.matrix.coxph
Acute myeloid leukemiamyeloid
Survival times of patients with multiple myelomamyeloma
Non-alcoholic fatty liver diseasenafld1 nafld2 nafld3
Find the index of the closest value in data set 2, for each entry in data set one.neardate
Natural splines with knot heights as the basis.nsk
Data from the National Wilm's Tumor Studynwtco
Ovarian Cancer Survival Dataovarian
Mayo Clinic Primary Biliary Cholangitis Datapbc
Mayo Clinic Primary Biliary Cirrhosis, sequential datapbcseq
Plot an aareg object.plot.aareg
Graphical Test of Proportional Hazardsplot.cox.zph
Plot method for 'survfit' objectsplot.survfit
Predictions for a Cox modelpredict.coxph predict.coxph.penal
Predicted Values for a `survreg' Objectpredict.survreg predict.survreg.penal
Print an aareg objectprint.aareg
Print method for summary.coxph objectsprint.summary.coxph
Print Survexp Summaryprint.summary.survexp
Print Survfit Summaryprint.summary.survfit
Print a Short Summary of a Survival Curveprint.survfit
Pseudo values for survival.pseudo
Smoothing splines using a pspline basispspline psplineinverse
Person Yearspyears
Quantiles from a survfit objectmedian.survfit quantile.survfit quantile.survfitms
Allow ratetable() terms in a modelratetable
Convert date objects to ratetable formratetableDate
Census Data Sets for the Expected Survival and Person Years Functionssurvexp.mn survexp.us survexp.usr
Rat treatment data from Mantel et alrats
Rat data from Gail et al.rats2
Reliability data setsbraking capacitor cracks genfan ifluid imotor reliability turbine valveSeat
Calculate Residuals for a `coxph' Fitresiduals.coxph residuals.coxph.null residuals.coxph.penal residuals.coxphms
IJ residuals from a survfit object.residuals.survfit
Compute Residuals for `survreg' Objectsresiduals.survreg residuals.survreg.penal
Diabetic Retinopathyretinopathy
rhDNASE data setrhDNase
Ridge regressionridge
Breast cancer data set used in Royston and Altman (2013)rotterdam
Compute Royston's D for a Cox modelroyston
Compute redistribute-to-the-right weightsrttright
Data from a soldering experimentsolder
More Stanford Heart Transplant datastanford2
Draw a state space figure.statefig
Identify Stratification Variablesstrata
Summarize an aareg fitsummary.aareg
Summary method for Cox modelssummary.coxph
Summary function for pyears objecssummary.pyears
Summary function for a survexp objectsummary.survexp
Summary of a Survival Curvesummary.survfit summary.survfitms
Create a Survival Objectis.Surv Surv [.Surv
Methods for Surv objectsanyDuplicated.Surv as.character.Surv as.data.frame.Surv as.matrix.Surv c.Surv duplicated.Surv format.Surv head.Surv is.na.Surv length.Surv Math.Surv mean.Surv median.Surv names.Surv names<-.Surv Ops.Surv plot.Surv quantile.Surv rep.int.Surv rep.Surv rep_len.Surv rev.Surv Summary.Surv t.Surv tail.Surv unique.Surv
Create a survival objectSurv2
Convert data from timecourse to (time1,time2) styleSurv2data
Checks of a survival data setsurvcheck
Shorten a (time1, time2) survival datasetsurvcondense
Test Survival Curve Differencesprint.survdiff survdiff
Compute Expected Survivalprint.survexp survexp
Compute Expected Survivalsurvexp.fit
Expected Survival Curve Objectsurvexp.object
Create survival curvessurvfit
Compute a Survival Curve from a Cox modelsurvfit.coxph survfit.coxphms
Compute a Survival Curve for Censored Datasurvfit.formula [.survfit
Create Aalen-Johansen estimates of multi-state survival from a matrix of hazards.survfit.matrix
Survival Curve Objectsurvfit.object survfitms.object
Convert the format of a survfit object.survfit0
A direct interface to the `computational engine' of survfit.coxphsurvfitcoxph.fit
Deprecated functions in package 'survival'survConcordance survConcordance.fit survival-deprecated
O'Brien's Test for Association of a Single Variable with Survivalsurvobrien
Regression for a Parametric Survival Modelanova.survreg anova.survreglist labels.survreg model.frame.survreg print.summary.survreg print.survreg.penal survReg survreg
Package options for survreg and coxphsurvreg.control
Parametric Survival Distributionssurvreg.distributions
Parametric Survival Model Objectprint.survreg summary.survreg survreg.object
Verify a survreg distributionsurvregDtest
Split a survival data set at specified timessurvSplit
Factors for person-year calculationslevels.tcut tcut [.tcut
Convert to/from a timeline data set formatfromtimeline timeline totimeline
Time based merge for survival datatmerge
Tobin's Tobit datatobin
Liver transplant waiting listtransplant
Data from a trial of usrodeoxycholic acidudca udca1 udca2
Help Process the `specials' Argument of the `terms' Function.untangle.specials
Projected US Populationuspop2
Variance-covariance matrixvcov.coxph vcov.survreg
Veterans' Administration Lung Cancer studyveteran
Sorting order for Surv objectsorder.Surv sort.Surv xtfrm.Surv
Population predictionyates
Method for adding new models to the 'yates' function.yates_setup