Translations of symbols used in the original sources to currently used symbols
==============================================================================

mammoCosts, MRICosts, TomoCosts = mammotomo.h, mri.h
biopsyCosts, treatmentCosts[3] = costs.h

fpctrl          - input/control.txt oid
fpin            - not used
fpout           - not used
fpcosts         - input/costs.txt
fpdeath         - test3/data-?.txt
fpsensitivity   - test3/sensitivity.txt
fpdist          - test3/dist-?.txt
fp              = test3/rounds-?.txt

Nmam                = loop.d_nMam
Ntomo               = loop.d_nTomo
NfalseP             = loop.d_nRoundFP
NfalseN             = loop.d_nRoundFN
Ndect               = loop.d_nDetections
screeningRoundCosts = loop.d_roundCost

naturalDeathAge     = loop.d_naturalDeathAge
deathStatus         = loop.d_status
deathAge            = loop.d_deathAge
AgeOfDetection      = loop.d_detectionAge

Nscr    - scenario.rounds().size()

scr[].age = scenario.age(idx)
src[].T0  = scenario.round(idx).mammo()
src[].T1  = scenario.round(idx).tomo()

fpdist, distFileName:   options::d_cumTotalRiskFile

calcTotalRisk   = tumorinfo/cumtotalrisk
cumTotRisk      = tumorinfo/d_cumRisk
                  tumorinfo: DoubleVect const &cumTotalRisk() const

beir      = tumorInfo.induction()

dose      = modalities.mammoParams().dose()
tomodose  = modalities.tomoParams().dose()

                                [a][b]: a = type (xray) b = id(Mammo, Tomo)
specMam[?] =        - d_modality.mammoParams()[?].value()
                    - d_modality[XRAY][MAMMO][?].value()

specTomo[?] =       - d_modality.tomoParams[?].value()
                    - d_modality[XRAY][TOMO][?].value()



tumorSurvival[0..4] = Survival 
tumorRisk_f =   incidence.risk().value()   params(): vector of nCarriers values
tumorRisk_m =   incidence.mean().value()
tumorRisk_s =   incidence.stdDev().value()
tumorRisk   =   incidence

tumor.selfDetectAge()   - d_tumor.age()
tumor.deathAge(...)     - d_tumor.deathAge()    - wrt tumor.age()
                          d_tumor.deathAge(x)   - wrt age x
                                                    (e.g. tumor.selfDetect() 

tumorConfig.startDiameter           = growth.start()        (VSD's)
tumorConfig.selfDetectDiameterMu    = growth.selfMu()
tumorConfig.selfDetectDiameterSigma = growth.selfSigma()
    
tumorConfig.doublingTimeMu[ageGroupIndex]     - growth.group[idx].mean()
tumorConfig.doublingTimeSigma[ageGroupIndex]  - growth.group[idx].stdDev()


RoundVect rounds()    - vector of screening rounds:
                        uint16_t age(), mammo() tomo()

womenYears          - Loop:d_sumDeathAge

womenCosts          - Loop:d_caseCost   (was: Loop:d_totalCost)

Ninterval           - Loop:d_nIntervals     (vector)
womencost           - Loop:d_roundCost      (vector)
screeningRoundCosts - Loop:d_screeningCost  (vector)

attendanceRate      -  Screening:d_attentanceRate

densities           - d_densities.indices() -> Loop:d_indices

                     Breast density index at screening rounds
int density[Nscr]   - Loop:d_indices



Ndect               - Loop:d_nDetected;


filenames:

scenarioName is, e.g. 'noscreening', defined in control.txt
iter is the string converted iteration index
all filenames end in scenarioName + -i + iter + .txt (not used below)

settingsFileName = "output/settings-
        writeSettings(settingsFileName);
outputFileName = "output/summary-
deathFileName = "./output/women-
sensitivityFileName = ./output/sensitivity-

        
resetRandomNumberGenerator  - d_random.reset
