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

# (Sub)section names to which # is prefixed are optional
#=======================================================

#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 may be omitted with LC simulations:
    biop:       176

    diameters:  0: 6438  20: 7128  50: 7701

        # if one proportion value is specified it's the proportion value used 
        # for the configured simulation. E.g., for just LC simulations:
        #       proportion .04 
        # if two values are specified (as shown below) the 1st proportion
        # is used for BC simulations, the 2nd proportion for LC simulations
    #Discount:      # breast   lung
        proportion:      0      .04
        age:            50

BreastDensities:
    #                bi-rad:  a      b      c      d
    ageGroup:    0  - 40:    .05    .30    .48    .17
        #optionally the following lines may start with ageGroup:
                 40 - 50:    .06    .34    .47    .13
                 50 - 60:    .08    .50    .37    .05
                 60 - 70:    .15    .53    .29    .03
                 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
            #optionally the following lines may start with sensitivity:
                        3 - 5:  -1  # formula: (.5 * diam - 1.5) * 100
                        5 - *:  100

        #               mean    stddev  dist
        specificity:    .992    .076    Normal



# defining outside could be OK. If also defined inside then that 
#   definition takes precedence (also if defined in Mammo in the config file,
#   but stand-alone in an Analysis specification), see mammo/setbeta.cc, 
#        #       1       2       3        4
#       beta:  -4.38    .49     -1.34    -7.18

    Mammo:
        costs:          64

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

        #             ageGroups:
        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

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

    MRI:
        costs:       280
        #               proportion:
        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
#       #optionally the following lines may start with round:
#               52  CT
#               54  CT
#               56  CT
#               58  CT
#               60  CT
#               62  CT
#               64  CT
#               66  CT
#               68  CT
#               70  CT
#               72  CT
#               74  CT

    round:     50  Mammo
        #optionally the following lines may start with round:
               52  Mammo
               54  Mammo
               56  Mammo
               58  Mammo
               60  Mammo
               62  Mammo
               64  Mammo
               66  Mammo
               68  Mammo
               70  Mammo
               72  Mammo
               74  Mammo

    #                   proportion:
    attendanceRate:     .8

#Tumor:

    Beir7:
        # only used with BC simulations:
            #    eta   beta  spread   dist.
        breast:  -2.0   0.51   0.32  Normal

        #only used with LC simulations:
        #                            Beta-distribution parameters:
        #        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:

            # if one start value is specified it's the start value used 
            # for the configured simulation. E.g., for just LC simulations:
            #       start: 3
            # if two values are specified (as shown below) the 1st value
            # is used for BC simulations, the 2nd value for LC simulations
            #  breast   lung
        start:    5       3

        # the following parameter values are now exp(old-values)
        #   the original values are FOR NOW shown in comment lines

        #selfDetect:      # stdev       mean    spread  dist
        #                     .70         2.92    .084    Normal
        breast:             2.01375     18.5413   2.31637   Normal

        #                   .014        3.037     .61     Normal
        lung:               1.0141      20.8426   1.84043  Normal

        DoublingTime:
            #                   stdev   mean  spread  dist.

            #           1 - 50:   .61        4.38   .43    Normal
            ageGroup:  1 - 50:   1.84043    79.838 1.53726  Normal
                #optionally the following lines may start with ageGroup:
                    # 50 - 70:   .26       5.06    .17     Normal
                      50 - 70:   1.29693    157.591 1.1853  Normal
                    # 70 - * :   .45       5.24    .23     Normal
                      70 - * :   1.56831    188.67  1.2586  Normal

            #  LC: all ages       stdev     mean    spread  dist.
            #                     .21       4.59    .74     Normal
            lung:                 1.23368   98.4944 2.09594 Normal

    #Incidence:
        Male:
            # riskTable: consisting of >= 2 age cum.prob pairs may be
            #            specified. If specified, lifetimeRisk:, meanAge: and
            #            stdDev: specifications are ignored
            #                   value   spread  distr.

            # fictious example riskTable:
            #   riskTable: 
            #           40 .01      50 .1       55 .15 
            #           60 .22      65 .55      70 .62  
            #           75 .67

            lifetimeRisk:         .22   .005    Normal
            meanAge:            72.48  1.08     Normal
            stdDev:              9.28  1.62     Normal

        Female:
            # riskTable: may be specified as described at subsection Male:
            #                   value   spread  distr.
            lifetimeRisk:         .20   .004    Normal
            meanAge:            69.62  1.49     Normal
            stdDev:              9.73  1.83     Normal

        Breast:
            # riskTable: may be specified as described at subsection Male:
            probability:    1
            #                   value   spread  distr.
            lifetimeRisk:         .226  .0053   Normal
            meanAge:            72.9    .552    Normal
            stdDev:             21.1

        BRCA1:
            # riskTable: may be specified as described at subsection Male:
            probability:    0
            #                   value   spread  distr.
            lifetimeRisk:         .96
            meanAge:            53.9
            stdDev:             16.51

         BRCA2:
            # riskTable: may be specified as described at subsection Male:
            probability:    0
            #                   value   spread  distr.
            lifetimeRisk:         .96
            meanAge:            53.9
            stdDev:             16.51

    #Survival:

    # For LC simulations the type paramaters and the bc parameters can be
    # omitted 
        #              value        spread      dist:
        type:  a        .00004475   .000004392  Normal
            #optionally the following lines may start with type:
               b       1.85867      .0420       Normal
               c       -.271        .0101       Normal
               d       2.0167       .0366       Normal
               e       1.00         .01         Normal

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


    # For BC simulations the lung[0-4] and S3 paramaters can be omitted
       # table S4: 4 columns per a..d parameter
       # lungX: X is table S4's column index
       lung0: a        .00143      .00095      Normal
            #optionally the following lines may start with lung0:
              b       1.84559      .33748      Normal
              c       -.22794      .07823      Normal
              d       1.06799      .16226      Normal
              e       1.00         .01         Normal

       lung1: a        .01530      .00381      Normal
            #optionally the following lines may start with lung1:
              b       1.69434      .10979      Normal
              c       -.19358      .02105      Normal
              d        .66690      .03869      Normal
              e       1.00         .01         Normal

       lung2: a        .78600      .29815      Normal
            #optionally the following lines may start with lung2:
              b        .69791      .05425      Normal
              c        .0          .0          Normal
              d        .0          .0          Normal
              e       1.00         .01         Normal

       lung3: a       1.25148      .32305      Normal
            #optionally the following lines may start with lung3:
              b        .77852      .34149      Normal
              c        .0          .0          Normal
              d        .0          .0          Normal
              e       1.00         .01         Normal

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