multicell

type Body struct {
	Genome   Genome
	Cells    []Cell // Array of cells of different types
	PErr     float64
	NDevStep int
}

type CPDArray []ElemsCPD

type Cell struct {
	Id       int
	E        Vec     // Env + noise
	F        Vec     // Epigenetic markers
	G        Vec     // Gene expression
	H        Vec     // Higher order complexes
	P, Pvar  Vec     // moving average and variance of P (P is already EMA)
	PErr     float64 // ||e - p||_1
	NDevStep int     // Developmental path length

}

type CoreTensor3 []elem_tensor3

type Cue = Vec //Environment cue is a special kind of vector

type Cues = []Cue //Cue array object

type Dmat = []Vec

type ElemsCPD struct {
	SVal float64
	Axes []Vec
}

type Genome struct {
	E Spmat //Environment cue effect on epigenome
	F Spmat //Regulatory effect of epigenetic markers on gene expression
	G Spmat //Regulatory effect of gene expression on epigenetic markers
	H Spmat //Contribution of gene expression on higher order complexes
	J Spmat //Interaction between higher order complexes
	P Spmat //Resulting expressed phenotype
}

type Indiv struct {
	Id         int
	DadId      int
	MomId      int
	Bodies     []Body  //IAncEnv, INovEnv (see above const.)
	Fit        float64 //Fitness with cues
	WagFit     float64 //Wagner relative fitness
	Plasticity float64 //Observed Plasticity
	Dp1e1      float64 // ||p(e1) - e1||
	Dp0e0      float64 // ||p(e0) - e0||
	Dp1e0      float64 // ||p(e1) - e0||
	Dp0e1      float64 // ||p(e0) - e1||
}

type PopStats struct {
	PEDot      float64 // (delta P, delta E) dot product
	PErr1      float64 // <|| p(e1) - e1 ||> (Nov)
	PErr0      float64 // <|| p(e0) - e0 ||> (Anc)
	PED10      float64 // <|| p(e1) - e0 ||> (Nov-Anc)
	PED01      float64 // <|| p(e0) - e1 ||> (Anc-Nov)
	WagFit     float64
	Fitness    float64
	Plasticity float64
	Div        float64
	NDevStep   float64
}

type Population struct {
	Params  Settings
	Gen     int
	NovEnvs Cues //Novel Environment
	AncEnvs Cues // Ancestral Environment
	Indivs  []Indiv
}

type Settings struct {
	MaxPop     int // Maximum number of individuals in population
	MaxDevStep int // Maximum steps for development.
	NGenes     int
	NEnv       int
	NSel       int
	NCells     int     // Number of cell types
	WithCue    bool    // With cue?
	FLayer     bool    // f present?
	HLayer     bool    // h present?
	JLayer     bool    //  J present?
	Pfback     bool    // P feedback to E layer
	SDNoise    float64 // probability (or stdev) of environmental noise
	MutRate    float64 // mutation rate
	TauF       float64
	TauG       float64
	TauH       float64
	DensityE   float64
	DensityF   float64
	DensityG   float64
	DensityH   float64
	DensityJ   float64
	DensityP   float64
}

type Spmat struct {
	Ncol int                 // number of columns
	Mat  [](map[int]float64) // Sparse matrix is an array of maps.
}

type Tensor3 []Dmat

type Vec = []float64 //Vector is a slice