Nothing
## -----------------------------------------------------------------------------
Pedigree <- data.frame(
Indiv= c("Iffes", "Peter", "Anna-Lena", "Kevin", "Horst"),
Sire = c("Kevin", "Kevin", NA, 0, "Horst"),
Dam = c("Chantalle", "Angelika", "Chantalle", "", NA),
Breed= c("Angler", "Angler", "Angler", "Holstein", "Angler"),
Born = c(2015, 2016, 2011, 2010, 2015)
)
Pedigree
## -----------------------------------------------------------------------------
library("optiSel")
Pedig <- prePed(Pedigree)
## -----------------------------------------------------------------------------
Pedig[,-1]
## ----warning=FALSE------------------------------------------------------------
sPed <- subPed(Pedig, keep = c("Chantalle","Angelika"), prevGen = 2, succGen = 1)
pedplot(sPed, label = c("Indiv", "Born", "Breed"), cex = 0.55)
## ----results="hide"-----------------------------------------------------------
data("PedigWithErrors")
data("Phen")
Pedig <- prePed(PedigWithErrors)
## -----------------------------------------------------------------------------
compl <- completeness(Pedig, keep=Phen$Indiv, by="Indiv")
head(compl)
## ----warning=FALSE------------------------------------------------------------
compl <- completeness(Pedig, keep=Phen$Indiv, by="Sex")
library("ggplot2")
ggplot(compl, aes(x=Generation, y=Completeness, col=Sex)) + geom_line()
## -----------------------------------------------------------------------------
Summary <- summary(Pedig, keep.only=Phen$Indiv)
head(Summary[Summary$equiGen>3.0, -1])
## -----------------------------------------------------------------------------
Animal <- pedInbreeding(Pedig)
mean(Animal$Inbr[Animal$Indiv %in% Phen$Indiv])
## -----------------------------------------------------------------------------
pKin <- pedIBD(Pedig, keep.only=Phen$Indiv)
isMale <- Pedig$Sex=="male" & (Pedig$Indiv %in% Phen$Indiv[Phen$BV>1.0])
males <- Pedig$Indiv[isMale & summary(Pedig)$equiGen>5]
pKin[males, "276000812750188", drop=FALSE]
## ----results="hide"-----------------------------------------------------------
Pedig <- prePed(PedigWithErrors, thisBreed="Hinterwaelder", lastNative=1970)
## -----------------------------------------------------------------------------
cont <- pedBreedComp(Pedig, thisBreed="Hinterwaelder")
Pedig$NC <- cont$native
head(cont[rev(Phen$Indiv), 2:6])
## ----results="hide"-----------------------------------------------------------
pKinatN <- pedIBDatN(Pedig, thisBreed="Hinterwaelder", keep.only=Phen$Indiv)
## -----------------------------------------------------------------------------
pKinatN$of <- pKinatN$Q1/pKinatN$Q2
pKinatN$of["276000891862786","276000812497659"]
## -----------------------------------------------------------------------------
Pedig[c("276000891862786", "276000812497659"),c("Born","NC")]
## -----------------------------------------------------------------------------
pKinatN$mean
## -----------------------------------------------------------------------------
subKin <- pKin[Phen$Indiv, Phen$Indiv]
subNatKin <- pKinatN$of[Phen$Indiv, Phen$Indiv]
diag(subKin) <- NA
diag(subNatKin) <- NA
cor(c(subKin), c(subNatKin), use="complete.obs")
## -----------------------------------------------------------------------------
1 - mean(pKin[Phen$Indiv, Phen$Indiv])
## -----------------------------------------------------------------------------
pKinatN$mean
## -----------------------------------------------------------------------------
1 - pKinatN$mean
## -----------------------------------------------------------------------------
pKinatN <- pedIBDatN(Pedig, thisBreed="Hinterwaelder", keep.only=Phen$Indiv, nGen=6)
## -----------------------------------------------------------------------------
attributes(pKinatN)$nativeNe
## -----------------------------------------------------------------------------
id <- Summary$Indiv[Summary$equiGen>=4 & Summary$Indiv %in% Phen$Indiv]
g <- Summary[id, "equiGen"]
N <- length(g)
n <- (matrix(g, N, N, byrow=TRUE) + matrix(g, N, N, byrow=FALSE))/2
deltaC <- 1 - (1-pKin[id,id])^(1/n)
Ne <- 1/(2*mean(deltaC))
Ne
## ----results="hide"-----------------------------------------------------------
data("PedigWithErrors")
Pedig <- prePed(PedigWithErrors, thisBreed="Hinterwaelder", lastNative=1970)
set.seed(0)
keep <- sampleIndiv(Pedig[Pedig$Breed=="Hinterwaelder",], from="Born", each=50)
cand <- candes(phen = Pedig[keep,],
pKin = pedIBD(Pedig, keep.only=keep),
pKinatN= pedIBDatN(Pedig, thisBreed="Hinterwaelder", keep.only=keep),
quiet=TRUE, reduce.data=FALSE)
## ----fig.show='hold'----------------------------------------------------------
sy <- summary(cand, tlim=c(1970, 2000), histNe=150, base=1800, df=4)
ggplot(sy, aes(x=t, y=Ne)) + geom_line() + ylim(c(0,100))
ggplot(sy, aes(x=t, y=NGE)) + geom_line() + ylim(c(0,7))
## ----fig.width = 5, fig.height = 3--------------------------------------------
use <- Pedig$Breed=="Hinterwaelder" & Pedig$Born %in% (1950:1995)
cont <- pedBreedComp(Pedig, thisBreed="Hinterwaelder")
contByYear <- conttac(cont, cohort=Pedig$Born, use=use, mincont = 0.01)
ggplot(contByYear, aes(x=Year, y=Contribution, fill=Breed)) + geom_area(color="black")
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