Software for WNAR2008 Short Course
Davis, California, June 2008
Logistic Regression Analysis of Stratified Case-Control Data
R functions for the analysis of two-phase stratified data with binary
(case-control) outcomes as described by N.E. Breslow and
N. Chatterjee, ``Design and analysis of two-phase studies with binary
outcome applied to Wilms tumour prognosis,"
Applied Statistics 48:457-68, 1999.
Converted from the S-Plus functions by Jon Wakefield and Sebastien
Haneuse. For the original S-Plus functions, documentation and grouped datasets see
Software for IBC2004 Satellite Workshop .
Also provided is some R code showing how to analyze the data using both
the stand alone R functions and Lumley's survey package (see below).
Cox Regression Analysis of Stratified Case-Cohort Data
Dataset from the National Wilms Tumor Study (NWTS) originally used by M.
Kulich and D.Y. Lin: Improving the
efficiency of relative-risk estimation in case-cohort studies.
J Amer Statis Assoc 99:832-844, 2004.
R code for the analysis of the NWTS data using weighted likelihood or
Horvitz-Thompson estimating equations, with weights possibly adjusted
by calibration or estimation.
The code is to be used in conjunction with Thomas Lumley's
R Survey Package
For theoretical background see
- Mark SK, Katki HA: Specifying and implementing nonparametric and
semiparametric survival estimators in two-stage (nested) cohort studies
with missing data. J Amer Statist Assoc 101:460-71, 2006
- Breslow NE, Wellner JA: Weighted likelihood for semiparametric models and two-phase stratified samples, with application to Cox regression.
Scand J Statist 34:86-102, 2007
- Breslow NE, Wellner JA. A Z-theorem with estimated nuisance parameters and correction note for `Weighted likelihood for semiparametric models and two-phase stratified samples, with application to Cox regression'. Scand J Statist 34:86-102, 2008
The dataset is drawn from the third and fourth Wilms tumor studies
(NWTS-3 and NWTS-4). Please reference this website
together with the following publications in any work that makes use of the data:
- D'Angio GJ, Breslow N, Beckwith JB, Evans A, Baum H, de Lorimier A,
Ferbach D, Hrabovsky E, Jones G, Kelalis P, et al. Treatment of Wilms' tumor.
Results of the Third National Wilms Tumor Study.
Cancer 64(2):349-60, 1989
- Green DM, Breslow NE, Beckwith JB, Finklestein JZ, Grundy PG, Thomas PRM,
Kim T, Shochat S, Haase GM, Ritchey ML, Kelalis PP, D'Angio GJ:
Comparison between single-dose and divided-dose administration of
dactinomycin and doxorubicin for patients with Wilms' tumor: A report
from the National Wilms' Tumor Study Group.
J Clin Oncol 16:237-245, 1998
Results of a simulation study comparing properties of estimates obtained from
these data using adjusted (calibrated or estimated) weights in comparison with
standard methods of analysis of (stratified) case-cohort data are available
in a manuscript currently under consideration for publication.