By Stuart G. Baker, 2019
Introduction
This software supports the mathematical investigation into estimating the fraction of cancers detected on screening that are overdiagnosed.
References
Baker SG and Prorok PC. Overdiagnosis in cancer screening: Improved excess incidence estimation.
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 | <<overdiag.m |
| Estimate mean Lead time |
MeanLeadTime[datavec,m,NewFitQ->True, MaxBoot->1000,Method->2] where m is unassigned symbol |
| To reproduce all analyses | Overdiag[{y,m},Fig->0,NewFitQ->True] where y and m are unassigned symbols |
MeanLeadTime[data, m, options] where
| Option | Default | Explanation |
|---|---|---|
| MaxBoot | 25 | Number of bootstrap iterations |
| NewFitQ | True | True (first fit) or False (later fit) |
data = {{n1,n2, n3, n4}, name,k0, z0, age},
| nj | Number of clinical cancers in time interval j after last screen. |
|---|---|
| name | Name of data set |
| k0 | Number of years between last screen and penultimate screen |
| k0 | maximum time since randomization (not relevant for basic analysis here) |
| z0 | Time interval length in years (usually 1 year) |
m is an unassigned symbol
File Contents
Download All (ZIP, 34 KB)
| File name | Description |
|---|---|
| overdiag.m | Main program to download (calls others) |
| overdiagsof.m | Data analyses for CNBSS and Norway data |
| overdiagleadtime.m | Mean lead time estimation |
| overdiagleadtimeboot.m | Mean lead time estimation bootstrap |
| overdiagleadtimecore.m | Core calculations for mean lead time estimation |
| overdiagsoftimeplot.m | Plot SOF and SIOF versus time |
| overdiagsoftimeplotcore.m | Core calculations for plots of SOF and SIOF versus time |
| overdiagsofmodelplot.m | Plot of SOFM and SIOFM versus mean lead time |
| overdiagsoftable.m | Tables of SOFM and SIOFM |
| overdiagsofstop.m | Stop screen analysis |
| overdiagsofcont.m | Continued screen analysis |
| overdiagsofpop.m | Population screen analysis |
| overdiagformula.m | Key formulas |
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.
Last modified: August 18, 2019