pbcseq: Mayo Clinic Primary Biliary Cirrhosis, sequential data

Description Usage Format Source References See Also Examples


This data is a continuation of the PBC data set, and contains the follow-up laboratory data for each study patient. An analysis based on the data can be found in Murtagh, et. al.

The primary PBC data set contains only baseline measurements of the laboratory parameters. This data set contains multiple laboratory results, but only on the 312 randomized patients. Some baseline data values in this file differ from the original PBC file, for instance, the data errors in prothrombin time and age which were discovered after the original analysis (see Fleming and Harrington, figure 4.6.7).

One "feature" of the data deserves special comment. The last observation before death or liver transplant often has many more missing covariates than other data rows. The original clinical protocol for these patients specified visits at 6 months, 1 year, and annually thereafter. At these protocol visits lab values were obtained for a large pre-specified battery of tests. "Extra" visits, often undertaken because of worsening medical condition, did not necessarily have all this lab work. The missing values are thus potentially informative.


data(pbc, package="survival")


id: case number
age: in years
sex: m/f
trt: 1/2/NA for D-penicillmain, placebo, not randomised
time: number of days between registration and the earlier of death,
transplantion, or study analysis in July, 1986
status: status at endpoint, 0/1/2 for censored, transplant, dead
day: number of days between enrollment and this visit date
all measurements below refer to this date
albumin: serum albumin (mg/dl)
alk.phos: alkaline phosphotase (U/liter)
ascites: presence of ascites
ast: aspartate aminotransferase, once called SGOT (U/ml)
bili: serum bilirunbin (mg/dl)
chol: serum cholesterol (mg/dl)
copper: urine copper (ug/day)
edema: 0 no edema, 0.5 untreated or successfully treated
1 edema despite diuretic therapy
hepato: presence of hepatomegaly or enlarged liver
platelet: platelet count
protime: standardised blood clotting time
spiders: blood vessel malformations in the skin
stage: histologic stage of disease (needs biopsy)
trig: triglycerides (mg/dl)


T Therneau and P Grambsch, "Modeling Survival Data: Extending the Cox Model", Springer-Verlag, New York, 2000. ISBN: 0-387-98784-3.


Murtaugh PA. Dickson ER. Van Dam GM. Malinchoc M. Grambsch PM. Langworthy AL. Gips CH. "Primary biliary cirrhosis: prediction of short-term survival based on repeated patient visits." Hepatology. 20(1.1):126-34, 1994.

Fleming T and Harrington D., "Counting Processes and Survival Analysis", Wiley, New York, 1991.

See Also



# Create the start-stop-event triplet needed for coxph
first <- with(pbcseq, c(TRUE, diff(id) !=0)) #first id for each subject
last  <- c(first[-1], TRUE)  #last id

time1 <- with(pbcseq, ifelse(first, 0, day))
time2 <- with(pbcseq, ifelse(last,  futime, c(day[-1], 0)))
event <- with(pbcseq, ifelse(last,  status, 0))

fit1 <- coxph(Surv(time1, time2, event) ~ age + sex + log(bili), pbcseq)

Example output

Warning message:
In Surv(time1, time2, event) : Invalid status value, converted to NA

survival documentation built on Aug. 24, 2021, 5:06 p.m.