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survival (version 3.5-0)

Survival Analysis

Description

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.

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install.packages('survival')

Monthly Downloads

98,782

Version

3.5-0

License

LGPL (>= 2)

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Maintainer

Terry Therneau

Last Published

January 9th, 2023

Functions in survival (3.5-0)

Surv-methods

Methods for Surv objects
Surv

Create a Survival Object
aggregate.survfit

Average survival curves
aeqSurv

Adjudicate near ties in a Surv object
Surv2data

Convert data from timecourse to (time1,time2) style
agreg.fit

Cox model fitting functions
anova.coxph

Analysis of Deviance for a Cox model.
attrassign

Create new-style "assign" attribute
basehaz

Alias for the survfit function
cch

Fits proportional hazards regression model to case-cohort data
bladder

Bladder Cancer Recurrences
cipoisson

Confidence limits for the Poisson
cgd

Chronic Granulotamous Disease data
cgd0

Chronic Granulotomous Disease data
blogit

Bounded link functions
clogit

Conditional logistic regression
cluster

Identify clusters.
coxph.wtest

Compute a quadratic form
coxphms.object

Multi-state Proportional Hazards Regression Object
colon

Chemotherapy for Stage B/C colon cancer
concordance

Compute the concordance statistic for data or a model
coxph.object

Proportional Hazards Regression Object
coxph.detail

Details of a Cox Model Fit
coxph

Fit Proportional Hazards Regression Model
coxph.control

Ancillary arguments for controlling coxph fits
coxsurv.fit

A direct interface to the `computational engine' of survfit.coxph
finegray

Create data for a Fine-Gray model
dsurvreg

Distributions available in survreg.
diabetic

Ddiabetic retinopathy
levels.Surv

Return the states of a multi-state Surv object
is.ratetable

Verify that an object is of class ratetable.
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
frailty

Random effects terms
cox.zph

Test the Proportional Hazards Assumption of a Cox Regression
concordancefit

Compute the concordance
gbsg

Breast cancer data sets used in Royston and Altman (2013)
plot.aareg

Plot an aareg object.
kidney

Kidney catheter data
nwtco

Data from the National Wilm's Tumor Study
mgus

Monoclonal gammopathy data
myeloma

Survival times of patients with multiple myeloma
pbc

Mayo Clinic Primary Biliary Cholangitis Data
model.matrix.coxph

Model.matrix method for coxph models
flchain

Assay of serum free light chain for 7874 subjects.
lung

NCCTG Lung Cancer Data
plot.cox.zph

Graphical Test of Proportional Hazards
myeloid

Acute myeloid leukemia
neardate

Find the index of the closest value in data set 2, for each entry in data set one.
ovarian

Ovarian Cancer Survival Data
heart

Stanford Heart Transplant data
print.summary.survfit

Print Survfit Summary
nsk

Natural splines with knot heights as the basis.
print.summary.coxph

Print method for summary.coxph objects
pbcseq

Mayo Clinic Primary Biliary Cirrhosis, sequential data
print.summary.survexp

Print Survexp Summary
mgus2

Monoclonal gammopathy data
model.frame.coxph

Model.frame method for coxph objects
ratetableDate

Convert date objects to ratetable form
ratetable

Rate table structure
pseudo

Pseudo values for survival.
residuals.survfit

IJ residuals from a survfit object.
print.aareg

Print an aareg object
retinopathy

Diabetic Retinopathy
residuals.survreg

Compute Residuals for `survreg' Objects
predict.survreg

Predicted Values for a `survreg' Object
pyears

Person Years
print.survfit

Print a Short Summary of a Survival Curve
quantile.survfit

Quantiles from a survfit object
royston

Compute Royston's D for a Cox model
rhDNase

rhDNASE data set
solder

Data from a soldering experiment
reliability

Reliability data sets
nafld

Non-alcohol fatty liver disease
rttright

Compute redistribute-to-the-right weights
summary.pyears

Summary function for pyears objecs
residuals.coxph

Calculate Residuals for a `coxph' Fit
predict.coxph

Predictions for a Cox model
survcondense

Shorten a (time1, time2) survival dataset
survcheck

Checks of a survival data set
plot.survfit

Plot method for survfit objects
ridge

Ridge regression
pspline

Smoothing splines using a pspline basis
stanford2

More Stanford Heart Transplant data
survfit.matrix

Create Aalen-Johansen estimates of multi-state survival from a matrix of hazards.
summary.survexp

Summary function for a survexp object
survexp.fit

Compute Expected Survival
survexp.object

Expected Survival Curve Object
survfit.object

Survival Curve Object
summary.survfit

Summary of a Survival Curve
survfit.formula

Compute a Survival Curve for Censored Data
survfit.coxph

Compute a Survival Curve from a Cox model
rats

Rat treatment data from Mantel et al
rotterdam

Breast cancer data set used in Royston and Altman (2013)
survSplit

Split a survival data set at specified times
summary.coxph

Summary method for Cox models
summary.aareg

Summarize an aareg fit
rats2

Rat data from Gail et al.
survreg.object

Parametric Survival Model Object
survival-deprecated

Deprecated functions in package survival
survival-internal

Internal survival functions
xtfrm.Surv

Sorting order for Surv objects
survfitcoxph.fit

A direct interface to the `computational engine' of survfit.coxph
survfit0

Convert the format of a survfit object.
survobrien

O'Brien's Test for Association of a Single Variable with Survival
vcov.coxph

Variance-covariance matrix
survreg

Regression for a Parametric Survival Model
uspop2

Projected US Population
veteran

Veterans' Administration Lung Cancer study
survreg.distributions

Parametric Survival Distributions
survreg.control

Package options for survreg and coxph
statefig

Draw a state space figure.
strata

Identify Stratification Variables
survexp

Compute Expected Survival
udca

Data from a trial of usrodeoxycholic acid
untangle.specials

Help Process the `specials' Argument of the `terms' Function.
survdiff

Test Survival Curve Differences
survregDtest

Verify a survreg distribution
yates

Population prediction
yates_setup

Method for adding new models to the yates function.
survfit

Create survival curves
tcut

Factors for person-year calculations
tmerge

Time based merge for survival data
ratetables

Census Data Sets for the Expected Survival and Person Years Functions
transplant

Liver transplant waiting list
tobin

Tobin's Tobit data
aml

Acute Myelogenous Leukemia survival data
Surv2

Create a survival object
aareg

Aalen's additive regression model for censored data