R: Survival Analysis

# Survival Analysis

## Documentation for package ‘survival’ version 3.7-0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J K L M N O P Q R S T U V X Y misc

## -- A --

aareg | Aalen's additive regression model for censored data
aeqSurv | Adjudicate near ties in a Surv object
aggregate.survfit | Average survival curves
agreg.fit | Cox model fitting functions
aml | Acute Myelogenous Leukemia survival data
anova.coxph | Analysis of Deviance for a Cox model.
anova.coxphlist | Analysis of Deviance for a Cox model.
anova.survreg | Regression for a Parametric Survival Model
anova.survreglist | Regression for a Parametric Survival Model
anyDuplicated.Surv | Methods for Surv objects
as.character.Surv | Methods for Surv objects
as.data.frame.Surv | Methods for Surv objects
as.matrix.Surv | Methods for Surv objects
attrassign | Create new-style "assign" attribute
attrassign.default | Create new-style "assign" attribute
attrassign.lm | Create new-style "assign" attribute

## -- B --

basehaz | Alias for the survfit function
bcloglog | Bounded link functions
bladder | Bladder Cancer Recurrences
bladder1 | Bladder Cancer Recurrences
bladder2 | Bladder Cancer Recurrences
blog | Bounded link functions
blogit | Bounded link functions
bprobit | Bounded link functions
brier | Compute the Brier score for a Cox model

## -- C --

c.Surv | Methods for Surv objects
cancer | NCCTG Lung Cancer Data
capacitor | Reliability data sets
cch | Fits proportional hazards regression model to case-cohort data
cgd | Chronic Granulotamous Disease data
cgd.raw | Chronic Granulotamous Disease data
cgd0 | Chronic Granulotomous Disease data
cipoisson | Confidence limits for the Poisson
clogit | Conditional logistic regression
cluster | Identify clusters.
colon | Chemotherapy for Stage B/C colon cancer
concordance | Compute the concordance statistic for data or a model
concordance.coxph | Compute the concordance statistic for data or a model
concordance.formula | Compute the concordance statistic for data or a model
concordance.lm | Compute the concordance statistic for data or a model
concordance.survreg | Compute the concordance statistic for data or a model
concordancefit | Compute the concordance
cox.zph | Test the Proportional Hazards Assumption of a Cox Regression
coxph | Fit Proportional Hazards Regression Model
coxph.control | Ancillary arguments for controlling coxph fits
coxph.detail | Details of a Cox Model Fit
coxph.fit | Cox model fitting functions
coxph.getdata | Fit Proportional Hazards Regression Model
coxph.object | Proportional Hazards Regression Object
coxph.penalty | Fit Proportional Hazards Regression Model
coxph.wtest | Compute a quadratic form
coxphms.object | Multi-state Proportional Hazards Regression Object
coxsurv.fit | A direct interface to the 'computational engine' of survfit.coxph
cracks | Reliability data sets

## -- D --

diabetic | Ddiabetic retinopathy
dsurvreg | Distributions available in survreg.
duplicated.Surv | Methods for Surv objects

## -- E --

extractAIC.coxph.penal | Proportional Hazards Regression Object

## -- F --

finegray | Create data for a Fine-Gray model
flchain | Assay of serum free light chain for 7874 subjects.
format.Surv | Methods for Surv objects
frailty | Random effects terms
frailty.gamma | Random effects terms
frailty.gaussian | Random effects terms
frailty.t | Random effects terms

## -- G --

gbsg | Breast cancer data sets used in Royston and Altman (2013)
genfan | Reliability data sets

## -- H --

head.Surv | Methods for Surv objects
heart | Stanford Heart Transplant data
hoel | Mouse cancer data

## -- I --

ifluid | Reliability data sets
imotor | Reliability data sets
is.na.Surv | Methods for Surv objects
is.ratetable | Verify that an object is of class ratetable.
is.Surv | Create a Survival Object

## -- J --

jasa | Stanford Heart Transplant data
jasa1 | Stanford Heart Transplant data

## -- K --

kidney | Kidney catheter data

## -- L --

labels.survreg | Regression for a Parametric Survival Model
length.Surv | Methods for Surv objects
leukemia | Acute Myelogenous Leukemia survival data
levels.Surv | Return the states of a multi-state Surv object
levels.tcut | Factors for person-year calculations
lines.survexp | Add Lines or Points to a Survival Plot
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
logLik.survreg | logLik method for a Cox model
lung | NCCTG Lung Cancer Data

## -- M --

Math.ratetable | Verify that an object is of class ratetable.
Math.Surv | Methods for Surv objects
mean.Surv | Methods for Surv objects
median.Surv | Methods for Surv objects
median.survfit | Quantiles from a survfit object
mgus | Monoclonal gammopathy data
mgus1 | Monoclonal gammopathy data
mgus2 | Monoclonal gammopathy data
model.frame.coxph | Model.frame method for coxph objects
model.frame.survreg | Regression for a Parametric Survival Model
model.matrix.coxph | Model.matrix method for coxph models
myeloid | Acute myeloid leukemia
myeloma | Survival times of patients with multiple myeloma

## -- N --

nafld1 | Non-alcoholic fatty liver disease
nafld2 | Non-alcoholic fatty liver disease
nafld3 | Non-alcoholic fatty liver disease
names.Surv | Methods for Surv objects
names<-.Surv | Methods for Surv objects
neardate | Find the index of the closest value in data set 2, for each entry in data set one.
nsk | Natural splines with knot heights as the basis.
nwtco | Data from the National Wilm's Tumor Study

## -- O --

Ops.ratetable | Verify that an object is of class ratetable.
Ops.Surv | Methods for Surv objects
order.Surv | Sorting order for Surv objects
ovarian | Ovarian Cancer Survival Data

## -- P --

pbc | Mayo Clinic Primary Biliary Cholangitis Data
pbcseq | Mayo Clinic Primary Biliary Cirrhosis, sequential data
plot.aareg | Plot an aareg object.
plot.cox.zph | Graphical Test of Proportional Hazards
plot.Surv | Methods for Surv objects
plot.survfit | Plot method for 'survfit' objects
points.survfit | Add Lines or Points to a Survival Plot
predict.coxph | Predictions for a Cox model
predict.coxph.penal | Predictions for a Cox model
predict.survreg | Predicted Values for a 'survreg' Object
predict.survreg.penal | Predicted Values for a 'survreg' Object
print.aareg | Print an aareg object
print.cox.zph | Test the Proportional Hazards Assumption of a Cox Regression
print.coxph | Proportional Hazards Regression Object
print.coxph.null | Fit Proportional Hazards Regression Model
print.coxph.penal | Fit Proportional Hazards Regression Model
print.summary.coxph | Print method for summary.coxph objects
print.summary.survexp | Print Survexp Summary
print.summary.survfit | Print Survfit Summary
print.summary.survreg | Regression for a Parametric Survival Model
print.survdiff | Test Survival Curve Differences
print.survexp | Compute Expected Survival
print.survfit | Print a Short Summary of a Survival Curve
print.survreg | Parametric Survival Model Object
print.survreg.penal | Regression for a Parametric Survival Model
pseudo | Pseudo values for survival.
pspline | Smoothing splines using a pspline basis
psplineinverse | Smoothing splines using a pspline basis
psurvreg | Distributions available in survreg.
pyears | Person Years

## -- Q --

qsurvreg | Distributions available in survreg.
quantile.Surv | Methods for Surv objects
quantile.survfit | Quantiles from a survfit object
quantile.survfitms | Quantiles from a survfit object

## -- R --

ratetable | Allow ratetable() terms in a model
ratetableDate | Convert date objects to ratetable form
rats | Rat treatment data from Mantel et al
rats2 | Rat data from Gail et al.
reliability | Reliability data sets
rep.int.Surv | Methods for Surv objects
rep.Surv | Methods for Surv objects
rep_len.Surv | Methods for Surv objects
residuals.coxph | Calculate Residuals for a 'coxph' Fit
residuals.coxph.null | Calculate Residuals for a 'coxph' Fit
residuals.coxph.penal | Calculate Residuals for a 'coxph' Fit
residuals.coxphms | Calculate Residuals for a 'coxph' Fit
residuals.survfit | IJ residuals from a survfit object.
residuals.survreg | Compute Residuals for 'survreg' Objects
residuals.survreg.penal | Compute Residuals for 'survreg' Objects
retinopathy | Diabetic Retinopathy
rev.Surv | Methods for Surv objects
rhDNase | rhDNASE data set
ridge | Ridge regression
rotterdam | Breast cancer data set used in Royston and Altman (2013)
royston | Compute Royston's D for a Cox model
rsurvreg | Distributions available in survreg.
rttright | Compute redistribute-to-the-right weights

## -- S --

solder | Data from a soldering experiment
sort.Surv | Sorting order for Surv objects
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.coxph.penal | Fit Proportional Hazards Regression Model
summary.pyears | Summary function for pyears objecs
Summary.Surv | Methods for Surv objects
summary.survexp | Summary function for a survexp object
summary.survfit | Summary of a Survival Curve
summary.survfitms | Summary of a Survival Curve
summary.survreg | Parametric Survival Model Object
Surv | Create a Survival Object
Surv2 | Create a survival object
Surv2data | Convert data from timecourse to (time1,time2) style
survcheck | Checks of a survival data set
survConcordance | Deprecated functions in package 'survival'
survConcordance.fit | Deprecated functions in package 'survival'
survcondense | Shorten a (time1, time2) survival dataset
survdiff | Test Survival Curve Differences
survexp | Compute Expected Survival
survexp.fit | Compute Expected Survival
survexp.mn | Census Data Sets for the Expected Survival and Person Years Functions
survexp.object | Expected Survival Curve Object
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
survfit | Create survival curves
survfit.coxph | Compute a Survival Curve from a Cox model
survfit.coxphms | Compute a Survival Curve from a Cox model
survfit.formula | Compute a Survival Curve for Censored Data
survfit.matrix | Create Aalen-Johansen estimates of multi-state survival from a matrix of hazards.
survfit.object | Survival Curve Object
survfit0 | Convert the format of a survfit object.
survfitcoxph.fit | A direct interface to the 'computational engine' of survfit.coxph
survfitms.object | Survival Curve Object
survival-deprecated | Deprecated functions in package 'survival'
survobrien | O'Brien's Test for Association of a Single Variable with Survival
survReg | Regression for a Parametric Survival Model
survreg | Regression for a Parametric Survival Model
survreg.control | Package options for survreg and coxph
survreg.distributions | Parametric Survival Distributions
survreg.object | Parametric Survival Model Object
survregDtest | Verify a survreg distribution
survSplit | Split a survival data set at specified times

## -- T --

t.Surv | Methods for Surv objects
tail.Surv | Methods for Surv objects
tcut | Factors for person-year calculations
tmerge | Time based merge for survival data
tobin | Tobin's Tobit data
transplant | Liver transplant waiting list
turbine | Reliability data sets

## -- U --

udca | Data from a trial of usrodeoxycholic acid
udca1 | Data from a trial of usrodeoxycholic acid
udca2 | Data from a trial of usrodeoxycholic acid
unique.Surv | Methods for Surv objects
untangle.specials | Help Process the 'specials' Argument of the 'terms' Function.
uspop2 | Projected US Population

## -- V --

valveSeat | Reliability data sets
vcov.coxph | Variance-covariance matrix
vcov.survreg | Variance-covariance matrix
veteran | Veterans' Administration Lung Cancer study

## -- X --

xtfrm.Surv | Sorting order for Surv objects

## -- Y --

yates | Population prediction
yates_setup | Method for adding new models to the 'yates' function.

## -- misc --

[.cox.zph | Test the Proportional Hazards Assumption of a Cox Regression
[.Surv | Create a Survival Object
[.survfit | Compute a Survival Curve for Censored Data
[.tcut | Factors for person-year calculations