survival v3.2-7

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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
Surv2data	Convert data from timecourse to (time1,time2) style
agreg.fit	Cox model fitting functions
aml	Acute Myelogenous Leukemia survival data
Surv	Create a Survival Object
Surv2	Create a survival object
aareg	Aalen's additive regression model for censored data
Surv-methods	Methods for Surv objects
aeqSurv	Adjudicate near ties in a Surv object
basehaz	Alias for the survfit function
anova.coxph	Analysis of Deviance for a Cox model.
colon	Chemotherapy for Stage B/C colon cancer
concordance	Compute the concordance statistic for data or a model
coxph.detail	Details of a Cox Model Fit
coxph.object	Proportional Hazards Regression Object
cch	Fits proportional hazards regression model to case-cohort data
attrassign	Create new-style "assign" attribute
cluster	Identify clusters.
clogit	Conditional logistic regression
cipoisson	Confidence limits for the Poisson
cgd0	Chronic Granulotomous Disease data
diabetic	Ddiabetic retinopathy
coxph.wtest	Compute a quadratic form
cgd	Chronic Granulotamous Disease data
frailty	Random effects terms
lines.survfit	Add Lines or Points to a Survival Plot
cox.zph	Test the Proportional Hazards Assumption of a Cox Regression
concordancefit	Compute the concordance
coxsurv.fit	A direct interface to the `computational engine' of survfit.coxph
logLik.coxph	logLik method for a Cox model
gbsg	Breast cancer data sets used in Royston and Altman (2013)
bladder	Bladder Cancer Recurrences
coxph	Fit Proportional Hazards Regression Model
coxph.control	Ancillary arguments for controlling coxph fits
heart	Stanford Heart Transplant data
mgus2	Monoclonal gammopathy data
finegray	Create data for a Fine-Gray model
is.ratetable	Verify that an object is of class ratetable.
logan	Data from the 1972-78 GSS data used by Logan
mgus	Monoclonal gammopathy data
print.aareg	Print an aareg object
lung	NCCTG Lung Cancer Data
dsurvreg	Distributions available in survreg.
model.frame.coxph	Model.frame method for coxph objects
print.summary.coxph	Print method for summary.coxph objects
ratetable	Rate table structure
ratetableDate	Convert date objects to ratetable form
rttright	Compute redistribute-to-the-right weights
survConcordance	Compute a concordance measure.
solder	Data from a soldering experiment
myeloid	Acute myeloid leukemia
flchain	Assay of serum free light chain for 7874 subjects.
pbcseq	Mayo Clinic Primary Biliary Cirrhosis, sequential data
nafld	Non-alcohol fatty liver disease
kidney	Kidney catheter data
levels.Surv	Return the states of a multi-state Surv object
model.matrix.coxph	Model.matrix method for coxph models
plot.aareg	Plot an aareg object.
neardate	Find the index of the closest value in data set 2, for each entry in data set one.
pyears	Person Years
print.summary.survexp	Print Survexp Summary
pbc	Mayo Clinic Primary Biliary Cirrhosis Data
ovarian	Ovarian Cancer Survival Data
print.summary.survfit	Print Survfit Summary
survcheck	Checks of a survival data set
survdiff	Test Survival Curve Differences
plot.cox.zph	Graphical Test of Proportional Hazards
survSplit	Split a survival data set at specified times
nwtco	Data from the National Wilm's Tumor Study
survregDtest	Verify a survreg distribution
quantile.survfit	Quantiles from a survfit object
survreg.object	Parametric Survival Model Object
residuals.coxph	Calculate Residuals for a `coxph' Fit
residuals.survreg	Compute Residuals for `survreg' Objects
summary.coxph	Summary method for Cox models
retinopathy	Diabetic Retinopathy
reliability	Reliability data sets
survexp.object	Expected Survival Curve Object
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
tcut	Factors for person-year calculations
uspop2	Projected US Population
survreg.distributions	Parametric Survival Distributions
vcov.coxph	Variance-covariance matrix
rats	Rat treatment data from Mantel et al
predict.coxph	Predictions for a Cox model
rotterdam	Breast cancer data set used in Royston and Altman (2013)
rats2	Rat data from Gail et al.
plot.survfit	Plot method for survfit objects
rhDNase	rhDNASE data set
pspline	Smoothing splines using a pspline basis
royston	Compute Royston's D for a Cox model
print.survfit	Print a Short Summary of a Survival Curve
summary.survexp	Summary function for a survexp object
survfit.formula	Compute a Survival Curve for Censored Data
strata	Identify Stratification Variables
predict.survreg	Predicted Values for a `survreg' Object
summary.aareg	Summarize an aareg fit
survfit.matrix	Create Aalen-Johansen estimates of multi-state survival from a matrix of hazards.
ridge	Ridge regression
statefig	Draw a state space figure.
stanford2	More Stanford Heart Transplant data
tmerge	Time based merge for survival data
survobrien	O'Brien's Test for Association of a Single Variable with Survival
survfit	Create survival curves
yates	Population prediction
yates_setup	Method for adding new models to the yates function.
summary.survfit	Summary of a Survival Curve
survfitcoxph.fit	A direct interface to the `computational engine' of survfit.coxph
survreg	Regression for a Parametric Survival Model
survfit.coxph	Compute a Survival Curve from a Cox model
survexp	Compute Expected Survival
survival-internal	Internal survival functions
untangle.specials	Help Process the `specials' Argument of the `terms' Function.
survexp.fit	Compute Expected Survival
udca	Data from a trial of usrodeoxycholic acid
veteran	Veterans' Administration Lung Cancer study
xtfrm.Surv	Sorting order for Surv objects
survfit0	Convert the format of a survfit object.
survfit.object	Survival Curve Object
tobin	Tobin's Tobit data
transplant	Liver transplant waiting list
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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	2020-09-24
LazyData	Yes
LazyLoad	Yes
ByteCompile	Yes
License	LGPL (>= 2)
URL	https://github.com/therneau/survival
NeedsCompilation	yes
Packaged	2020-09-25 17:55:24 UTC; therneau
Repository	CRAN
Date/Publication	2020-09-28 08:20:02 UTC

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