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#ifndef INCLUDED_LOOP_
#define INCLUDED_LOOP_
#include <iosfwd>
#include "../typedefs/typedefs.h"
#include "../globals/globals.h"
#include "../scenario/scenario.h"
#include "../screening/screening.h"
#include "../densities/densities.h"
#include "../modalities/modalities.h"
#include "../tumorinfo/tumorinfo.h"
#include "../tumor/tumor.h"
#include "../costs/costs.h"
class Options;
class Scenario;
namespace FBB
{
class CSVTable;
}
class Loop: public Globals
{
//
// 2 -> 1, 5 -> 4, 9 -> 8 if the natural death is before the tumor's onset.
//
enum Status // labels in data.cc
{
PRESENT, // 0
NATURAL_PRE, // 1 natural death before the 1st screening round
UNDETECTED_PRE, // 2 nat. death, undetected tumor, before 1st scr.
SELF_PRE, // 3 self-detected tumor before 1st scr.
NATURAL_DURING, // 4 nat. death between screening rounds
UNDETECTED_DURING, // 5 nat. death, undetected tumor, between scr.
SELF_DURING, // 6 self-detected tumor between scr. rounds
SCREEN_DETECTED, // 7 screening-detected tumor
NATURAL_POST, // 8 nat. death after the last screening round
UNDETECTED_POST, // 9 nat. death, undetected tumor, afer last scr.
SELF_POST, // 10 self-detected tumor after last scr. round
Status_END
};
enum // round info (per case) '0': not attended
{
ATTENDED = '1',
FALSE_NEGATIVE = '2',
FALSE_POSITIVE = '3'
};
enum
{
N_RESULTS = 13 // weird... used in results()
};
Options const &d_options;
Status d_status = PRESENT;
StringVect const &d_labels;
Scenario d_scenario;
Costs d_costs;
Densities d_densities;
TumorInfo d_tumorInfo;
Tumor d_tumor;
Modalities d_modalities;
Screening d_screening;
int16_t d_roundDetected; // -1: no detection
// Analysis &d_analysis;
// Beir7 const &d_beir7;
// Incidence const &d_incidence;
//FBB double d_sumDeathAge = 0;
double d_naturalDeathAge = 0; // dying age w/o tumor
double d_deathAge = 0; // actual dying age
uint16_t d_nRounds; // from Screening::nRounds()
// when screening is used:
uint16_t d_firstRoundAge; // age of the first screening round
uint16_t d_round = 0; // currently used screening round
std::string d_roundInfo;
SizeVect d_nIntervals; // # interval cancer per round
SizeVect d_nTrueIntervals; // # interval cancer per round
// following a previously attended
// screening round
// initialized in resetcounters.cc
// SizeVect d_nRoundFP; // # of false-positives per round
// SizeVect d_nRoundFN; // # of false-negatives per round
// SizeVect d_nRoundTP; // # of true-positives per round
// SizeVect d_nRoundTN; // # of true-negatives per round
SizeVect d_nDetections;
double d_caseCost;
double d_biopCosts; // sum of biop costs per case
DoubleVect d_roundBiopCosts; // and per round
//FBB double d_totalCost;
DoubleVect d_roundCost; // sum of costs over all scr. rounds
// (org: screeningRoundCosts)
// randomly determined (breast cancer)
// bi-rad indices for the ages of the
// screening rounds, or table S3 indices
// for lung cancer.
Uint16Vect d_indices; // ('densities' in the original sources)
std::string d_timestamp;
void (*d_tnm)(std::ostream &out); // noTNM or fillTNM
ProbGroup::Vector const *d_groupVector; // breast- or lung cancer
// probGroup::Vector to use when
// constructing d_indices
static StringSet s_availableFiles;
static char const *s_status[];
public:
Loop(StringVect const &labels);
void iterate();
private:
double addBiopCosts(double costs);
bool betaFunction(uint16_t modalityNr);
void caseInit();
size_t cases() const; // #cases in womenLoop
Uint16Vect cptIndices() const; // cpt d_indices
static void fillTNM(std::ostream &out);
static void fillZeroes(std::ostream &out, size_t idx);
void genCases(size_t iter, size_t nCases);
FBB::CSVTable headerData(size_t iter) const;
FBB::CSVTable headerRounds(size_t iter) const;
//FBB FBB::CSVTable headerSensitivity() const;
bool intervalCancer();
void labels(std::ostream &out) const;
bool leaving(double screeningAge);
void maybeFalseNegative(ModBase *modBase, double screeningAge);
bool falseNegative(ModBase *modBase);
void tumorDetected(ModBase *modBase, double screeningAge);
bool falsePositive(ModBase *modBase, double screeningAge);
double naturalDeathAge();
static void noTNM(std::ostream &out);
static std::ofstream open(std::string const &fname);
static std::ofstream outStream(std::string const &fname, size_t idx);
void postScreen();
static std::string replaceDollar(std::string const &settingsFile,
size_t idx);
void resetCounters();
// # active modalities
void roundsNcols(FBB::CSVTable &tab) const;
void roundsColHdrs(FBB::CSVTable &tab) const;
void roundsMidLevelCols(FBB::CSVTable &tab) const;
void roundsBottomColNames(FBB::CSVTable &tab) const;
// returns the sensitivity for the
double sensitivity(ModBase *modBase) const; // current round 1.cc
bool left(Status status, double deathAge); // also logs the reason
void screen(double screeningAge);
void screening();
std::string showRound() const;
double treatmentCosts(double screeningAge) const; // .ih
// NOTE: in the orig. source density NRs are used: 1..4
// here density INDICES are usd: 0..3
// but when writing the data file (e.g., data-0.txt, original
// name e.g., women-test-i0.txt) a + 1 correction is
// currently applied
bool use(ModBase *modBase); // use this modality
void writeData(FBB::CSVTable &dataTable, size_t idx) const;
void writeParameters(size_t iter) const; // also opens the file
void writeRounds(FBB::CSVTable &roundTable) const;
//FBB void writeSensitivity(FBB::CSVTable &sensTable, size_t iter) const;
};
// OBSOLETE
// void characteristics(Status natural, Status tumor);
// void preTumorDeath(); // early natural death
// void preScreen();
void preSelfDetected(); // self detected tumor pre-screening
// covered by 'left(...)'
// void setStatus(Status status, double age); // only sets the d_ vars.
// void removeCase(double screeningAge, double selfDetectAge);
#endif
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