
# supported distribution names are: Normal, LogNormal, Uniform, Beta
# Modalities are: Mammo, Tomo, MRI, CT

Scenario:
                                # use true for variable spreading
    spread:                 false

    iterations:             1

                                # random generator behavior:
                                # random, fixed, increasing
    generator:              fixed

                                # initial seed unless using generator: random
    seed:                   1

                                # n cases to simulate
    cases:                  1000

    death:                  #death.txt
      1: .00000 .00000 .00000 .00000 .00000 .00000 .00000 .00000 .00000 .00000
     11: .00000 .00000 .00000 .00000 .00000 .00000 .00000 .00000 .00000 .00000
     21: .00000 .00014 .00028 .00042 .00056 .00070 .00106 .00142 .00178 .00214
     31: .00250 .00382 .00514 .00646 .00778 .00910 .01118 .01326 .01534 .01742
     41: .01950 .02312 .02674 .03036 .03398 .03760 .04414 .05068 .05722 .06376
     51: .07030 .07776 .08522 .09268 .10014 .10760 .11564 .12368 .13172 .13976
     61: .14780 .15718 .16656 .17594 .18532 .19470 .20658 .21846 .23034 .24222
     71: .25410 .27560 .29710 .31860 .34010 .36160 .39368 .42576 .45784 .48992
     81: .52200 .56240 .60280 .64320 .68360 .72400 .75826 .79252 .82678 .86104
     91: .89530 .90962 .92394 .93826 .95258 .96690 .97104 .97518 .97932 .98346
    101: .98760

    #   ref.age proportion  biop  specs (first diameter must be 0)
    # Lungcancer costs: configured at Modalities: CT: costs:
Costs:
    biop:       176
    diameters:  0: 6438  20: 7128  50: 7701
    Discount:       # breast    lung
        proportion:      0      .04
        age:            50

BreastDensities:
    #                bi-rad:  a      b      c      d
    ageGroup:    0  - 40:    .05    .30    .48    .17
    ageGroup:    40 - 50:    .06    .34    .47    .13
    ageGroup:    50 - 60:    .08    .50    .37    .05
    ageGroup:    60 - 70:    .15    .53    .29    .03
    ageGroup:    70 - * :    .18    .54    .26    .02

Modalities:

    CT:
        #        screening    diagnosis    M0      M1   (M0, M1: Table S3)
        costs:      176         1908      37909   56556


        dose:  1

        #               diam.   value (must be integral 0..100 or -1)
        sensitivity:    0 - 3:  0
        sensitivity:    3 - 5:  -1  # formula: (.5 * diam - 1.5) * 100
        sensitivity:    5 - *:  100

        #               mean    stddev  dist
        specificity:    .992    .076    Normal

    Mammo:
        costs:          64

        #      bi-rad:  a       b       c       d
        dose:           3       3       3       3
        m:             .136    .136    .136    .136

        #             ageGroup
        specificity:  0 - 40:  .961     40 - *: .965

        #       1       2       3        4
        beta:  -4.38    .49     -1.34    -7.18

        systematicError:  0.1

    Tomo:
        costs:         64

        #      bi-rad:  a       b       c       d
        dose:           3       3       3       3
        sensitivity:    .87     .84     .73     .65

        #             ageGroup
        specificity:  0 - 40:  .961     40 - *: .965

    MRI:
        costs:          280
        sensitivity:    .94
        specificity:    .95

Screening:
    # round: age    space separated modalities.
    # subsequent ages must exceed the last age by at least 1
    # with lung cancer simulations only CT can be specified,
    # with breast cancer simulations CT cannot be specified,
#    round:     50  CT
#    round:     52  CT
#    round:     54  CT
#    round:     56  CT
#    round:     58  CT
#    round:     60  CT
#    round:     62  CT
#    round:     64  CT
#    round:     66  CT
#    round:     68  CT
#    round:     70  CT
#    round:     72  CT
#    round:     74  CT

    round:     50  Mammo
    round:     52  Mammo
    round:     54  Mammo
    round:     56  Mammo
    round:     58  Mammo
    round:     60  Mammo
    round:     62  Mammo
    round:     64  Mammo
    round:     66  Mammo
    round:     68  Mammo
    round:     70  Mammo
    round:     72  Mammo
    round:     74  Mammo

    #                   proportion:
    attendanceRate:     .8

Tumor:

    Beir7:
            #    eta   beta  spread   dist.
        breast:  -2.0   0.51   0.32  Normal

        #                            Beta-distribution parameters:
        # LC:    eta   beta  dist    constant factor   aParam    bParam
        male:    -1.4   .32  Beta    .234091  1.72727  2.664237  5.184883
        female:  -1.4  1.40  Beta    .744828   .818966 3.366115  4.813548

    Growth:
            #  breast   lung
        start:    5       3

        #selfDetect:      # stdev       mean    spread  dist
        breast:             .70         2.92    .084    Normal
        lung:               .014        3.037   .61     Normal

        DoublingTime:
            #                   stdev   mean  spread  dist.
            ageGroup:  1 - 50:   .61    4.38   .43    Normal
            ageGroup: 50 - 70:   .26    5.06   .17    Normal
            ageGroup: 70 - * :   .45    5.24   .23    Normal

            #     all ages      stdev   mean  spread  dist.
            lung:                .21    4.59   .74    Normal

    Incidence:
        Male:
            #                   value   spread  distr.
            lifetimeRisk:         .22   .005    Normal
            meanAge:            72.48  1.08     Normal
            stdDev:              9.28  1.62     Normal

        Female:
            #                   value   spread  distr.
            lifetimeRisk:         .20   .004    Normal
            meanAge:            69.62  1.49     Normal
            stdDev:              9.73  1.83     Normal

        Breast:
            probability:    1
            #                   value   spread  distr.
            lifetimeRisk:         .226  .0053   Normal
            meanAge:            72.9    .552    Normal
            stdDev:             21.1

        BRCA1:
            probability:    0
            #                   value   spread  distr.
            lifetimeRisk:         .96
            meanAge:            53.9
            stdDev:             16.51

         BRCA2:
            probability:    0
            #                   value   spread  distr.
            lifetimeRisk:         .96
            meanAge:            53.9
            stdDev:             16.51

    Survival:
        #              value        spread      dist:
        type:  a        .00004475   .000004392  Normal
        type:  b       1.85867      .0420       Normal
        type:  c       -.271        .0101       Normal
        type:  d       2.0167       .0366       Normal

       # table S4: 4 columns per a..d parameter
       # lungX: X is table S4's column index
       lung0: a        .00143      .00095      Normal
       lung0: b       1.84559      .33748      Normal
       lung0: c       -.22794      .07823      Normal
       lung0: d       1.06799      .16226      Normal

       lung1: a        .01530      .00381      Normal
       lung1: b       1.69434      .10979      Normal
       lung1: c       -.19358      .02105      Normal
       lung1: d        .66690      .03869      Normal

       lung2: a        .78600      .29815      Normal
       lung2: b        .69791      .05425      Normal
       lung2: c        .0          .0          Normal
       lung2: d        .0          .0          Normal

       lung3: a       1.25148      .32305      Normal
       lung3: b        .77852      .34149      Normal
       lung3: c        .0          .0          Normal
       lung3: d        .0          .0          Normal

    S3:
       #      diameter (mm)
       # T-row    <=       N0,M0   N1-3,M0   N1-3,M1a-b   N0-3M1c
       prob:      10:       .756    .157      .048        .039       # T1a
       prob:      20:       .703    .197      .055        .045       # T1b
       prob:      30:       .559    .267      .095        .078       # T1c
       prob:      50:       .345    .351      .167        .137       # T2a,b
       prob:      70:       .196    .408      .218        .178       # T3
       prob:       *:       .187    .347      .256        .210       # T4

    #  BC TNM categories thru (<=) diameters (mm):
    bc:        20  50   *
    #  TNM:    T1  T2  T3
