Channing House Data

Description

The ChanningHouse data frame has 457 rows and 5 columns. This is 5 fewer than the parent channing data frame in the boot package. These 5 were removed because the exit time was not smaller than the entry time.

Channing House is a retirement centre in Palo Alto, California. These data were collected between the opening of the house in 1964 until July 1, 1975. In that time 97 men and 365 women passed through the centre. For each of these, their age on entry and also on leaving or death was recorded. A large number of the observations were censored mainly due to the resident being alive on July 1, 1975 when the data was collected. Over the time of the study 130 women and 46 men died at Channing House. Differences between the survival of the sexes, taking age into account, was one of the primary concerns of this study.

Usage

data("ChanningHouse")

Format

A data frame with 457 observations on the following 5 variables.

sex

a factor for the sex of each resident with levels Female Male

entry

The residents age (in months) on entry to the center)

exit

The age (in months) of the resident on death, leaving the center or July 1, 1975, whichever event occurred first.)

time

The length of time (in months) that the resident spent at Channing House. (time=exit-entry)))

cens

The indicator of reight censoring. 1 indicates that the resident died at Channing House, 0 indicates that they left the house prior to July 1, 1975 or that they were still alive and living in the center at that date.

Source

The current data were derived from the "channing" data frame in the "boot" package. The original source for the data was

Hyde, J. (1980) Testing survival with incomplete observations. Biostatistics Casebook. R.G. Miller, B. Efron, B.W. Brown and L.E. Moses (editors), 31-46. John Wiley.

References

Davison, A.C. and Hinkley, D.V. (1997) Bootstrap Methods and Their Application. Cambridge University Press.

Canty, A. and Ripley, B. (2015) boot package.

Examples

data(ChanningHouse)
  

ashkenazi

Description

This is a random subset of data from the Struewing et al. (1997) study of Ashkenazi jews and breast cancer. The subset consists of pairs of first-degree female relatives who are also first degree relatives of a proband.

Usage

data("ashkenazi")

Format

A data frame with 3920 observations on the following 4 variables.

famID

family ID indicator

brcancer

1 if subject had breast cancer, 0 if not

age

Age at onset of breast cancer, or current age if no breast cancer

mutant

1 if first degree relative proband was a BRCA mutation carrier, 0 if not

References

Moore DF, Chatterjee N, Pee D, and Gail MH (2001) Pseudo-likelihood estimates of the cumulative risk of an autosomal dominant disease from a kin-cohort study. Genetic Epidemiology 20, 210-227.)

Struewing JP, Hartge P, Wacholder S, Baker SM, Berlin M, McAdams M, Timmerman MM, Brody LC, and Tucker MA (1997) The risk of cancer associated with specific mutations of BRCA1 and BRCA2 among ashkenazi jews. New England Journal of Medicine 336, 1401-1408.)

Examples

data(ashkenazi)

gasticXelox

Description

Data from a Phase II clinical trial of Xeloda and exaliplatin given before surgery to advanced gastric cancer patients with para-aortic lymph node metastasis.

Usage

data("gastricXelox")

Format

A data frame with 48 observations on the following 2 variables.

timeWeeks

survival time in weeks

delta

1 for death, 0 for censored

Details

The data were extracted from the Kaplan-Meier survival plot.

References

Wang Y, Yu Y-Y, Li W, Feng Y, Hou J, Ji Y, Sun Y-H, Shen K-T, Shen Z-B, Qin X-Y, and Liu T-S. (2014) A phase II trial of xeloda and oxaliplatin (XELOX) neo-adjuvant chemotherapy followed by surgery for advanced gastric cancer patients with para-aortic lymph node metastasis. Cancer Chemotherapy and Pharmacology 73(6), 1155-1161.))

Examples

data(gastricXelox)

hepatoCellular

Description

Overall and recurrence-free survival of patients with hepatocellular carcinoma.

Usage

data("hepatoCellular")

Format

A data frame with 227 observations on 48 clinical and biomarker variables

Number

Patient ID number

Age

a numeric vector

Gender

a numeric vector

HBsAg

a numeric vector

Cirrhosis

a numeric vector

ALT

a numeric vector

AST

a numeric vector

AFP

a numeric vector

Tumorsize

a numeric vector

Tumordifferentiation

a numeric vector

Vascularinvasion

a numeric vector

Tumormultiplicity

a numeric vector

Capsulation

a numeric vector

TNM

a numeric vector

BCLC

a numeric vector

OS

Overall survival

Death

1 denotes death, 0 censored

RFS

Recurrence-free survival

Recurrence

1 denotes recurrence, 0 censored

CXCL17T

a numeric vector

CXCL17P

a numeric vector

CXCL17N

a numeric vector

CD4T

a numeric vector

CD4N

a numeric vector

CD8T

a numeric vector

CD8N

a numeric vector

CD20T

a numeric vector

CD20N

a numeric vector

CD57T

a numeric vector

CD57N

a numeric vector

CD15T

a numeric vector

CD15N

a numeric vector

CD68T

a numeric vector

CD68N

a numeric vector

CD4NR

a numeric vector

CD8NR

a numeric vector

CD20NR

a numeric vector

CD57NR

a numeric vector

CD15NR

a numeric vector

CD68NR

a numeric vector

CD4TR

a numeric vector

CD8TR

a numeric vector

CD20TR

a numeric vector

CD57TR

a numeric vector

CD15TR

a numeric vector

CD68TR

a numeric vector

Ki67

a numeric vector

CD34

a numeric vector

References

Li L, Yan J, Xu J, Liu C-Q, Zhen Z-J, Chen H-W, Ji Y, Wu Z-P, Hu J-Y, Zheng L, Lau WY (2014) Cxcl17 expression predicts poor prognosis and correlates with adverse immune infiltration in hepatocellular carcinoma. Plos One 9 (10) e110064.

Li L, Yan J, Xu J, Liu C-Q, Zhen Z-J, Chen H-W, Ji Y, Wu Z-P, Hu J-Y, Zheng L, Lau WY (2014) Cxcl17 expression predicts poor prognosis and correlates with adverse immune infiltration in hepatocellular carcinoma. Dryad Digital Repository datadryad.org.

Examples

data(hepatoCellular)

pancreatic

Description

Data from a Phase II clinical trial of patients with locally advanced or metastatic pancreatic cancer.

Usage

data("pancreatic")

Format

A data frame with 41 observations on the following 4 variables.

stage

a factor with levels LA (locally advanced) or M (metastatic)

onstudy

date of enrollment into the clinical trial, in month/day/year format

progression

date of progression, in month/day/year format

death

date of death, in month/day/year format

Details

Since all patients in this study have known death dates, there is no censoring.

References

Moss RA, Moore D, Mulcahy MF, Nahum K, Saraiya B, Eddy S, Kleber M, and Poplin EA (2012) A multi-institutional phase 2 study of imatinib mesylate and gemcitabine for first-line treatment of advanced pancreatic cancer. Gastrointestinal Cancer Research 5, 77 - 83.

Examples

data(pancreatic)

pancreatic2

Description

This is the same data as in 'pancreatic', with overall and progression-free survival calculated. Dates have been removed.

Usage

data("pancreatic2")

Format

A data frame with 41 observations on the following 4 variables.

pfs

Progression-free survival: Time from entry until disease progression. If no progression was observed, before death, the time to death is used.

os

Overall survival: Time from entry until death

status

This censoring indicator is 1 for all patients, since all patients died.

stage

a factor with levels LA (locally advanced) or M (metastatic)

References

Moss RA, Moore D, Mulcahy MF, Nahum K, Saraiya B, Eddy S, Kleber M, and Poplin EA (2012) A multi-institutional phase 2 study of imatinib mesylate and gemcitabine for first-line treatment of advanced pancreatic cancer. Gastrointestinal Cancer Research 5, 77 - 83.

Examples

data(pancreatic2)

pharmacoSmoking

Description

Randomized trial of triple therapy vs. patch for smoking cessation.

Usage

data("pharmacoSmoking")

Format

A data frame with 125 observations on the following 14 variables.

id

patient ID number

ttr

Time in days until relapse

relapse

Indicator of relapse (return to smoking)

grp

Randomly assigned treatment group with levels combination or patchOnly

age

Age in years at time of randomization

gender

Female or Male

race

black, hispanic, white, or other

employment

ft (full-time), pt (part-time), or other

yearsSmoking

Number of years the patient had been a smoker

levelSmoking

heavy or light

ageGroup2

Age group with levels 21-49 or 50+

ageGroup4

Age group with levels 21-34, 35-49, 50-64, or 65+

priorAttempts

The number of prior attempts to quit smoking

longestNoSmoke

The longest period of time, in days, that the patient has previously gone without smoking

Source

This data is from a clinical trial described in Steinberg et al. (2009)

References

Steinberg, M.B. Greenhaus, S. Schmelzer, A.C. Bover, M.T., Foulds, J., Hoover, D.R., and Carson, J.L. (2009) Triple-combination pharmacotherapy for medically ill smokers: A randomized trial. Annals of Internal Medicine 150, 447-454.

Examples

data(pharmacoSmoking)

prostateSurvival

Description

This data set contains survival times for two competing causes: time from prostate cancer diagnosis to death from prostate cancer, and time from prostate cancer diagnosis to death from other causes. The data set also contains information on several risk factors. The data in this data set are simulated from detailed competing risk survival curves and counts of numbers of patients per group presented in Lu-Yao et al. (2009). Thus, the simulated data presented here contain many of the characteristics of the original SEER-Medicare prostate cancer data used in Lu-Yao et al. (2009).

Usage

data("prostateSurvival")

Format

A data frame with 14294 observations on the following 5 variables.

grade

a factor with levels mode (moderately differentiated) and poor (poorly differentiated)

stage

a factor with levels T1ab (Stage T1, clinically diagnoseed), T1c (Stage T1, diagnosed via a PSA test), and T2 (Stage T2)

ageGroup

a factor with levels 66-69 70-74 75-79 80+

survTime

time from diagnosis to death or last date known alive

status

a censoring variable, 0, (censored), 1 (death from prostate cancer), and 2 (death from other causes)

Source

Lu-Yao, GL, Albertsen PC, Moore DF, Shih W, Lin Y, DiPaola RS, Barry MJ, Zietman A, O'Leary M, Walker-Corkery E, Yao S-L (2009) Outcomes of localized prostate cancer following conservative management. Journal of the American Medical Association 302, 1202 - 1209.)

Examples

data(prostateSurvival)