By Stuart G. Baker, 2017
Introduction
This software fits a zero-intercept random effects linear model to data on surrogate and true endpoints in previous trials.
Requirement: Mathematica Version 11 or later.
To run the program
| copy | all files into some folder called "FOLDER" |
|---|---|
| start | a new Mathematica session |
| type | SetDirectory["FOLDER"] |
| type | << sfit.m |
| type | SFit[data,options] |
Key Function: SFit[data, options] where
| Option | Default | Explanation |
|---|---|---|
| SizeNewTrial | Automatic (median size of previous trials) | Size of new trial with only surrogate endpoint |
| ShowCalc | False | Show intermediate calculations |
dataset={xvec,yvec,nvec,wvec,name},
| xvec | lists of differences in surrogate endpoints over all trials |
|---|---|
| yvec | lists of differences in true endpoints over all trials |
| nvec | list of sample sizes over all trials |
| wvec | lists of estimated variances of true endpoint over all trials |
| name | name of data set |
File Contents
Download All (ZIP, 25 KB)
| File name | Description |
|---|---|
| sfit.m | main packages |
| sfitplot.m | core plotting program |
| sfitsimplot.m | plotting hypothetical data |
| sfitsim.m | simulations |
| sfitlik.m | fitting model with simple estimates and MLE’s |
| sfitdata.m | generates data examples from the literature |
As an example, type SFit[dataMANU]
Disclaimer
This code is provided "as is", without warranty of any kind, express or implied, including but not limited to the warranties of merchantability, fitness for a particular purpose and non-infringement. In no event shall the NCI or the individual developers be liable for any claim, damages or other liability of any kind. Use of this code by recipient is at recipient's own risk. NCI makes no representations that the use of the code will not infringe any patent or proprietary rights of third parties.
The data were obtained from the following studies:
Sargent, DJ, Wieand, S, Haller, DG, Gray, R, Benedetti, J, Buyse, M, Labianca, R, Seitz, J F, Callaghan, C J O, Francini, G, Grothey, A, O'Connell, M, Catalano, PJ, Blanke, CD, Kerr D, Green, E, Wolmark, N, Andre, T, Goldberg, RM, and De Gramont A (2005) Disease-free survival (DFS) vs overall survival (OS) as a primary endpoint for adjuvant colon cancer studies: Individual patient data from 20,898 patients on 18 randomized trials J Clin Oncol 23, 8664-8670
Meta-Analysis Group in Cancer (2004) Modulation of fluorouracil by leucovorin in patients with advanced colorectal cancer: an updated meta-analysis J Clin Oncol 22, 3766-3775
Buyse, M, Burzykowski, T, Carroll, K, Michiels, S, Sargent, D, Miller, LL, Elfring, GL, Pignon, JP, and Piedbois, P (2007) Progression-free survival is a surrogate for survival in advanced colorectal cancer J Clin Oncol 25, 5218-5224
Last updated: May 03, 2017