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BIOMETRY RESEARCH GROUP

Mathematica Packages

Periodic Screening Evaluation

(Written by Stuart G. Baker)

New Approach (Simplified Approximation): See Baker SG. Evaluating periodic cancer screening without a randomized control group: a simplified design and analysis. In: Duffy SW, Hill C, Esteve J (eds). Methods of Evaluation of Cancer Screening. To appear.

Original Approach: Periodic Screening Evaluation is a method for estimating the reduction in mortality from starting periodic cancer screening at various ages based on either data from a special nonrandomized or randomized design. The methodology is described in Baker SG. Evaluating the age to begin periodic breast cancer screening using data from a few regularly scheduled screens. Biometrics 1998;54:1569-1578. It simplifies and extends Baker SG, Chu KC. Evaluating screening for the early detection and treatment of cancer without using a randomized control group. Journal of the American Statistical Association 1990;85:321-327.

It runs in Mathematica 2.2 or 3.0 and requires the files listed below.

Filename

File Notes

pse.m

main program (which loads others)

psederiv.m

derivatives used for evaluation

psedata.m

source of data

psefit.m

fitting models to the data

psepreg.m

Poisson regression

pseplot.m

plotting program

statplot.m

plotting confidence intervals

matrixlx.m

matrix programming language

psefalse.m

computation for false positives

To reproduce calculations in the manuscript, load pse.m and use the function PSEHIP[dataHIP, a, z].

  • Data are available in psedata.m
  • dataOBS is for nonrandomized study
  • dataRAN is for a randomized study.
  • These should be modified with new data.
  • To run PSE for ages, say 40 to 50, with mortality endpoint use
  • PSEOBS[dataOBS,a,z,{40,50},"MORT"] for a nonrandomized study

PSERAN[dataRAN,a,z,{40,50},"MORT"] for a randomized study.

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