library(data.table)
library(AGHmatrix)

#### pedigree ####
pedigreeOrg = fread("c:/Users/Student/Downloads/pedigree(4).csv")

uSireId = unique(pedigreeOrg$V2)
uDamId = unique(pedigreeOrg$V3)
uCowId = unique(pedigreeOrg$V1)

orginalId = c(uSireId, uDamId, uCowId)
orginalId = as.data.table(orginalId)
colnames(orginalId) = "orginalId"

orginalId = merge(orginalId, pedigreeOrg, by.x = "orginalId", 
                                          by.y = "V1", all.x = TRUE)

orginalId$V2[is.na(orginalId$V2)] = 0
orginalId$V3[is.na(orginalId$V3)] = 0
orginalId$V4[is.na(orginalId$V4)] = 0
orginalId$V5[is.na(orginalId$V5)] = 0

setorder(orginalId, V4)

orginalId$newId = 1:nrow(orginalId)
newId = orginalId[, c(1, 6)]
colnames(newId) = c("V2", "newSireId")

orginalId = merge(orginalId, newId, by = "V2", all.x = TRUE)
orginalId$newSireId[is.na(orginalId$newSireId)] = 0

colnames(newId) = c("V3", "newDamId")

orginalId = merge(orginalId, newId, by = "V3", all.x = TRUE)
orginalId$newDamId[is.na(orginalId$newDamId)] = 0

orginalId = orginalId[, c(3, 2, 1, 4, 5, 6, 7, 8)]
setorder(orginalId, newId)

A = Amatrix(orginalId[, c(6, 7, 8)])

#### phenotypes ####

data = fread("c:/Users/Student/Downloads/laktacje(1).csv")
firstInsemination = data[, .(firstIns = min(inseminationDate)),
                                                        by = cowId]
lastInsemination = data[, .(lastIns = max(inseminationDate)),
                                                        by = cowId]

IFL = merge(firstInsem	ination, lastInsemination, by = "cowId",
															 all.x = TRUE)
IFL$phenotype = IFL$lastIns - IFL$firstIns	
IFL = IFL[, -c(2, 3)]

IFL = merge(IFL, orginalId[, c(1, 6)], by.x = "cowId", 
                                       by.y = "orginalId", all.x = TRUE)

setorder(IFL, newId) 

#### fixed effects ####
breed = model.matrix(~ as.factor(orginalId$V5[321:499]) - 1)
birthYear = model.matrix(~ as.factor(orginalId$V4[321:499]) - 1)

X = cbind(breed, birthYear)

#### Z matrix ####
Z = matrix(0, nrow(IFL), nrow(A))
I = diag(nrow(IFL))
Z[1:179, 321:499] = I