Estimating the Overdiagnosis Fraction in Cancer Screening

By Stuart G. Baker, 2019


This software supports the mathematical investigation into estimating the fraction of cancers detected on screening that are overdiagnosed.


Baker SG and Prorok PC. Overdiagnosis in cancer screening: Improved excess incidence estimation.


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


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