survival v3.1-7

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by Terry Therneau View Source

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.

Functions in survival

Name	Description
basehaz	Alias for the survfit function
agreg.fit	Cox model fitting functions
aareg	Aalen's additive regression model for censored data
anova.coxph	Analysis of Deviance for a Cox model.
Surv	Create a Survival Object
Surv-methods	Methods for Surv objects
cox.zph	Test the Proportional Hazards Assumption of a Cox Regression
concordancefit	Compute the concordance
cch	Fits proportional hazards regression model to case-cohort data
cgd	Chronic Granulotamous Disease data
concordance	Compute the concordance statistic for data or a model
colon	Chemotherapy for Stage B/C colon cancer
cgd0	Chronic Granulotomous Disease data
diabetic	Ddiabetic retinopathy
dsurvreg	Distributions available in survreg.
cipoisson	Confidence limits for the Poisson
coxph.object	Proportional Hazards Regression Object
coxph.detail	Details of a Cox Model Fit
coxph.wtest	Compute a quadratic form
coxsurv.fit	A direct interface to the `computational engine' of survfit.coxph
lung	NCCTG Lung Cancer Data
logLik.coxph	logLik method for a Cox model
levels.Surv	Return the states of a multi-state Surv object
lines.survfit	Add Lines or Points to a Survival Plot
flchain	Assay of serum free light chain for 7874 subjects.
cluster	Identify clusters.
finegray	Create data for a Fine-Gray model
clogit	Conditional logistic regression
frailty	Random effects terms
model.frame.coxph	Model.frame method for coxph objects
mgus	Monoclonal gammopathy data
mgus2	Monoclonal gammopathy data
model.matrix.coxph	Model.matrix method for coxph models
myeloid	Acute myeloid leukemia
logan	Data from the 1972-78 GSS data used by Logan
nwtco	Data from the National Wilm's Tumor Study
nafld	Non-alcohol fatty liver disease
print.summary.coxph	Print method for summary.coxph objects
neardate	Find the index of the closest value in data set 2, for each entry in data set one.
heart	Stanford Heart Transplant data
print.summary.survexp	Print Survexp Summary
coxph.control	Ancillary arguments for controlling coxph fits
pbcseq	Mayo Clinic Primary Biliary Cirrhosis, sequential data
pbc	Mayo Clinic Primary Biliary Cirrhosis Data
coxph	Fit Proportional Hazards Regression Model
is.ratetable	Verify that an object is of class ratetable.
rats2	Rat data from Gail et al.
reliability	Reliability data sets
residuals.coxph	Calculate Residuals for a `coxph' Fit
plot.cox.zph	Graphical Test of Proportional Hazards
plot.aareg	Plot an aareg object.
residuals.survreg	Compute Residuals for `survreg' Objects
print.aareg	Print an aareg object
predict.survreg	Predicted Values for a `survreg' Object
quantile.survfit	Quantiles from a survfit object
kidney	Kidney catheter data
ovarian	Ovarian Cancer Survival Data
ratetable	Rate table structure
ratetableDate	Convert date objects to ratetable form
statefig	Draw a state space figure.
survConcordance	Compute a concordance measure.
stanford2	More Stanford Heart Transplant data
survSplit	Split a survival data set at specified times
survcheck	Checks of a survival data set
ridge	Ridge regression
solder	Data from a soldering experiment
rats	Rat treatment data from Mantel et al
survdiff	Test Survival Curve Differences
survfitcoxph.fit	A direct interface to the `computational engine' of survfit.coxph
survival-internal	Internal survival functions
survfit0	Convert the format of a survfit object.
survfit.object	Survival Curve Object
summary.survexp	Summary function for a survexp object
plot.survfit	Plot method for survfit objects
transplant	Liver transplant waiting list
predict.coxph	Predictions for a Cox model
pspline	Smoothing splines using a pspline basis
tobin	Tobin's Tobit data
survreg	Regression for a Parametric Survival Model
pyears	Person Years
summary.survfit	Summary of a Survival Curve
survobrien	O'Brien's Test for Association of a Single Variable with Survival
print.summary.survfit	Print Survfit Summary
udca	Data from a trial of usrodeoxycholic acid
untangle.specials	Help Process the `specials' Argument of the `terms' Function.
strata	Identify Stratification Variables
summary.aareg	Summarize an aareg fit
print.survfit	Print a Short Summary of a Survival Curve
summary.coxph	Summary method for Cox models
retinopathy	Diabetic Retinopathy
rhDNase	rhDNASE data set
summary.pyears	Summary function for pyears objecs
ratetables	Census Data Sets for the Expected Survival and Person Years Functions
survreg.control	Package options for survreg and coxph
survreg.distributions	Parametric Survival Distributions
survfit.formula	Compute a Survival Curve for Censored Data
survexp.object	Expected Survival Curve Object
survreg.object	Parametric Survival Model Object
survexp	Compute Expected Survival
survfit.matrix	Create Aalen-Johansen estimates of multi-state survival from a matrix of hazards.
xtfrm.Surv	Sorting order for Surv objects
veteran	Veterans' Administration Lung Cancer study
vcov.coxph	Variance-covariance matrix
uspop2	Projected US Population
survregDtest	Verify a survreg distribution
yates_setup	Method for adding new models to the yates function.
survfit	Create survival curves
yates	Population prediction
survexp.fit	Compute Expected Survival
survfit.coxph	Compute a Survival Curve from a Cox model
tcut	Factors for person-year calculations
tmerge	Time based merge for survival data
aml	Acute Myelogenous Leukemia survival data
bladder	Bladder Cancer Recurrences
aeqSurv	Adjudicate near ties in a Surv object
attrassign	Create new-style "assign" attribute
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Vignettes of survival

Name
adjcurve.Rnw
approximate.Rnw
compete.Rnw
concordance.Rnw
multi.Rnw
other.Rnw
population.Rnw
refer.bib
splines.Rnw
survival.Rnw
tiedtimes.Rnw
timedep.Rnw
validate.Rnw
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Details

Priority	recommended
Date	2019-11-08
LazyData	Yes
LazyLoad	Yes
ByteCompile	Yes
License	LGPL (>= 2)
URL	https://github.com/therneau/survival
NeedsCompilation	yes
Packaged	2019-11-08 22:04:52 UTC; therneau
Repository	CRAN
Date/Publication	2019-11-09 05:30:02 UTC

imports	graphics , Matrix , methods , splines , stats , utils
depends	R (>= 3.4.0)
Contributors	Thomas Lumley