Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
echo = TRUE,
collapse = TRUE,
comment = "#>",
dpi = 300,
fig.align = "center")
## ----eval = FALSE-------------------------------------------------------------
# install.packages("pedsuite")
## ----eval = FALSE-------------------------------------------------------------
# # install.packages("devtools")
# devtools::install_github("magnusdv/pedsuite")
## -----------------------------------------------------------------------------
library(pedsuite)
## ----fc-ped1, fig.height = 3.5, fig.width = 3.5, out.width = "40%"------------
x = cousinPed(1, child = TRUE)
plot(x)
## ----fc-ped2, fig.height = 3.5, fig.width = 3.5, out.width = "40%"------------
x = swapSex(x, ids = 3)
plot(x,
hatched = 9,
carrier = 7:8,
fill = list(pink = 1),
textAnnot = list(inside = c("1" = "?")))
## -----------------------------------------------------------------------------
inbreeding(x, ids = 9)
## -----------------------------------------------------------------------------
library(ibdsim2)
## -----------------------------------------------------------------------------
sims = ibdsim(x, N = 200, seed = 123)
## -----------------------------------------------------------------------------
fr = realisedInbreeding(sims, id = 9)
## -----------------------------------------------------------------------------
head(fr$perSimulation)
## ----fr-hist, echo = -1, out.width = "80%", fig.height = 3, fig.width = 7-----
op <- par(mar = c(4.1, 4.1, 1, 1))
hist(fr$perSimulation$fReal, xlim = c(0, 0.15), breaks = 16, xlab = "f_R", main = NULL)
# Expected value
abline(v = 1/16, col = 2)
## ----echo = F-----------------------------------------------------------------
# Just for CRAN
par(op)
## -----------------------------------------------------------------------------
y = markerSim(x, N = 500, alleles = c("A", "B"))
## -----------------------------------------------------------------------------
y
## ----check-pairwise, results="hide", fig.height = 5, fig.width = 5, out.width = "60%"----
checkPairwise(y)
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