lib

type AnalysisMaps interface {
	GetICDCode(did int) string
	// contains filtered or unexported methods
}

type Cohort struct {
	AgeGroup, Sex, Region, NofPatients, NofDiagnoses int
	DCtr                                             []int        //counts nr of patients per DID
	DPatients                                        [][]*Patient //contains a list of patients per DID
	Patients                                         []*Patient   //the patients in this cohort
}

type Diagnosis struct {
	PID, DID int
	Date     DiagnosisDate
	Icd10    Icd10Entry
}

type DiagnosisDate struct {
	Year, Month, Day int
}

type Experiment struct {
	NofAgeGroups, NofRegions, Level, NofDiagnosisCodes int
	DxDRR                                              [][]float64        // per disease pair, relative risk score (RR)
	DxDPatients                                        [][][]*Patient     // per disease pair, all patients diagnosed
	DPatients                                          [][]*Patient       // per disease, all patients diagnosed
	Cohorts                                            []*Cohort          // cohorts in the experiment
	Name                                               string             // Name of the experiment, for printing
	Icd10Map                                           map[int]Icd10Entry // maps diagnosis ID to Icd10Entry
	Trajectories                                       []*Trajectory      // a list of computed trajectories
	Pairs                                              []*Pair            // a list of all selected pairs that are used to compute trajectories
	IdMap                                              map[int]string     // maps the analysis DID to the original diagnostic ID used in the input data
	MCtr, FCtr                                         int                // counters for counting nr of males,females,patients
}

type ExperimentParams struct {
	// required parameters
	Name             string
	PatientInfo      string // path to the file with patient information (ID, gender," + birthyear, etc)
	DiagnosisInfo    string // path to the file with diagnosis information (ID,descriptor, hierarchy, etc)
	PatientDiagnoses string // path to the file with patient diagnoses.
	OutputPath       string // path where output files are written to.

	// optional parameters
	NofAgeGroups         int
	Lvl                  int
	MaxYears             float64
	MinYears             float64
	MinPatients          int
	MaxTrajectoryLength  int
	MinTrajectoryLength  int
	ICD9ToICD10File      string
	Cluster              bool
	ClusterGranularities string
	Iter                 int
	RR                   float64
	SaveRR               string
	LoadRR               string
	PFilters             string
	TFilters             string
	TumorInfo            string
	TreatmentInfo        string
	NrOfThreads          int
}

type Icd10Entry struct {
	Name       string    // medical Name for a DID in ICD10 encoding
	Categories [6]string // the names of the ICD10 encoding higher and lower in the hierarchy.
	Level      int       // the ICD10 hierarchy Level of this Name.
}

type Pair struct {
	First, Second int
}

type Patient struct {
	PID       int            // analysis ID
	PIDString string         // ID from TriNetX
	YOB       int            // year of birth
	CohortAge int            // age range a patient belongs to
	Sex       int            // 0 = male, 1 = female
	Diagnoses []*Diagnosis   // list of patient's diagnoses, sorted by date <, unique diagnosis per date
	EOIDate   *DiagnosisDate // Event of interest date, e.g. day of cancer diagnosis
	DeathDate *DiagnosisDate // Date of death
	Region    int            // Region where the patient lives
}

type PatientFilter func(patient *Patient) bool

type PatientMap struct {
	PIDStringMap map[string]int   // maps patient string id onto an int PID
	Ctr          int              // total nr of patients parsed, also used for creating PIDs
	PIDMap       map[int]*Patient // maps PID onto a patient object that contain YOB, sex, age group, etc
	// optional info for logging
	MaleCtr   int
	FemaleCtr int
}

type Trajectory struct {
	Diagnoses      []int            // A list of diagnosis codes that represent the trajectory
	PatientNumbers []int            // A list with nr of patients for each transition in the trajectory
	Patients       [][]*Patient     // A list of patients with the given trajectory
	TrajMap        map[*Patient]int // Maps patient IDs onto a diagnosis index for trajectory tracking
	ID             int              // An analysis id
	Cluster        int              // A cluster ID to which this trajectory is assigned to
}

type TrajectoryFilter func(t *Trajectory) bool

type TreatmentInfo struct {
	RCDate   *DiagnosisDate //Date of radical cystectomy
	MVACDate *DiagnosisDate //Date of MVAC chemotherapy
	IVTDate  *DiagnosisDate //Date of intravesical therapy
}

type TumorInfo struct {
	TStage, NStage, MStage, Stage string
	Date                          DiagnosisDate
}