PBC: Primary biliary cirrhosis (PBC) of the liver data

Description Usage Format Details Source References Examples

Description

A subset of primary biliary cirrhosis (PBC) of the liver data in the book "Counting Process & Survival Analysis" by Fleming & Harrington (1991). This subset is used in Tibshirani (1997).

Usage

1

Format

A data frame with 276 observations on the following 19 variables.

T

Survival times (either time to death or censoring) in days

d

Censoring indicator, 1=death, 0=censoring

trt

Treatment indicator, 1=treatment by D-penicillamine, 0=placebo

age

Age in years (days divided by 365.25)

sex

Sex, 0=male, 1=female

asc

Presence of ascites, 0=no, 1=yes

hep

Presence of hepatomegaly, 0=no, 1=yes

spi

Presence of spiders, 0=no, 1=yes

ede

Presence of edema, 0=no edema, 0.5=edema resolved by therapy, 1=edema not resolved by therapy

bil

log(bililubin, mg/dl)

cho

log(cholesterol, mg/dl)

alb

log(albumin, gm/dl)

cop

log(urine copper, mg/day)

alk

log(alkarine, U/liter)

SGO

log(SGOT, in U/ml)

tri

log(triglycerides, in mg/dl)

pla

log(platelet count, [the number of platelets per-cubic-milliliter of blood]/1000)

pro

log(prothrombin time, in seconds)

gra

Histologic stage of disease, graded 1, 2, 3, or 4

Details

Survival data consisting of 276 patients with 17 covariates. Among them, 111 patients died (d=1) while others were censored (d=0). The covariates consist of a treatment indicator (trt), age, sex, 5 categorical variables (ascites, hepatomegaly, spider, edema, and stage of disease) and 9 log-transformed continuous variables (bilirubin, cholesterol, albumin, urine copper, alkarine, SGOT, triglycerides, platelet count, and prothrombine).

Source

Fleming & Harrignton (1991); Tibshirani (1997)

References

Tibshirani R (1997), The Lasso method for variable selection in the Cox model, Statistics in Medicine, 385-395.

Examples

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data(PBC)
PBC[1:5,] ### profiles for the first 5 patients ###
# See also Appendix D.1 of Fleming & Harrington, Counting Process & Survival Analysis (1991) # 

Example output

Loading required package: numDeriv
Loading required package: survival
     T d trt      age sex asc hep spi ede        bil      cho       alb
1  400 1   1 58.76523   1   1   1   1 1.0 2.67414865 5.564520 0.9555114
2 4500 0   1 56.44627   1   0   1   1 0.0 0.09531018 5.710427 1.4206958
3 1012 1   1 70.07255   0   0   0   0 0.5 0.33647224 5.170484 1.2470323
4 1925 1   1 54.74059   1   0   1   1 0.5 0.58778666 5.497168 0.9321641
5 1504 0   0 38.10541   1   0   1   1 0.0 1.22377543 5.631212 1.2612979
       cop      alk      SGO      tri      pla      pro gra
1 5.049856 7.448916 4.926891 5.147494 5.247024 2.501436   4
2 3.988984 8.908532 4.731979 4.477337 5.398163 2.360854   3
3 5.347108 6.246107 4.565389 4.007333 5.017280 2.484907   4
4 4.158883 8.719611 4.104790 4.521789 5.209486 2.332144   4
5 4.962845 6.508769 4.728714 4.276666 4.912655 2.388763   3

compound.Cox documentation built on July 21, 2018, 5:01 p.m.