## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/"
)

## ----eval=FALSE, include=TRUE-------------------------------------------------
# dip <- sim.ind.simple(mvec = 0.5, cover = 100,
#                       s.size = 5000, sampled = TRUE)
# tri <- sim.ind.simple(mvec = c(0.33, 0.67), cover = 100,
#                       s.size = 5000, sampled = TRUE)
# 
# par(mfrow=c(1,2))
# hist(dip[,2]/dip[,1], main = "Diploid", xlab = "Allele Frequency", xlim = c(0,1))
# hist(tri[,2]/tri[,1], main = "Triploid", xlab = "Allele Frequency", xlim = c(0,1))
# 

## ----echo=FALSE, out.width="125%", fig.align='center'-------------------------
knitr::include_graphics("../man/figures/SimpleSim.png",  dpi = 5000)

## ----eval=FALSE, include=TRUE-------------------------------------------------
# dip.adv <- sim.ind.BB(mvec = 0.5, svec = 0.1, avec = 1.0,
#                       error = 0.001, s.size = 5000,
#                       max.coverage = 100, min.coverage = 50, lambda = 75)
# tri.adv <- sim.ind.BB(mvec = c(0.33, 0.67), avec = c(0.5, 0.5), svec = c(0.01, 0.01),
#                       error = 0.001, s.size = 5000,
#                       max.coverage = 100, min.coverage = 50, lambda = 75)
# 
# par(mfrow=c(1,2))
# hist(dip.adv[,2]/dip.adv[,1], main = "Diploid - Advanced",
#      xlab = "Allele Frequency", xlim = c(0,1))
# hist(tri.adv[,2]/tri.adv[,1], main = "Triploid - Advanced",
#      xlab = "Allele Frequency", xlim = c(0,1))
# 

## ----echo=FALSE, out.width="125%", fig.align='center'-------------------------
knitr::include_graphics("../man/figures/AdvancedSimulation.png",  dpi = 5000)