Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
set.seed(997)
## ----setup--------------------------------------------------------------------
library(hwep)
## -----------------------------------------------------------------------------
drbounds(ploidy = 4)
drbounds(ploidy = 6)
drbounds(ploidy = 8)
drbounds(ploidy = 10)
drbounds(ploidy = 12)
## -----------------------------------------------------------------------------
dgamete(x = 0:2, alpha = 0.1, G = 3, ploidy = 4)
## -----------------------------------------------------------------------------
gsegmat(alpha = 0.1, ploidy = 4)
## -----------------------------------------------------------------------------
gsegmat(alpha = 0.1, ploidy = 4)[3, 2]
## -----------------------------------------------------------------------------
gsegmat_symb(ploidy = 4)
## -----------------------------------------------------------------------------
sega <- zsegarray(alpha = 0.1, ploidy = 4)
sega
## -----------------------------------------------------------------------------
sega[4, 3, 5]
## -----------------------------------------------------------------------------
hout <- hwefreq(r = 0.1, alpha = 0.1, ploidy = 6)
round(hout, digits = 5)
## -----------------------------------------------------------------------------
freqnext(freq = c(0.9, 0, 0, 0, 0.1), alpha = 0.1)
## -----------------------------------------------------------------------------
hwefreq(r = 0.1, alpha = 0.1, niter = 1, ploidy = 4)
## -----------------------------------------------------------------------------
library(future)
availableCores()
plan(multisession, workers = 2)
## -----------------------------------------------------------------------------
geno_freq <- hwefreq(r = 0.5, alpha = 0.1, ploidy = 6)
nmat <- t(rmultinom(n = 1000, size = 100, prob = geno_freq))
head(nmat)
## -----------------------------------------------------------------------------
uout <- hwefit(nmat = nmat, type = "ustat")
## -----------------------------------------------------------------------------
mean(uout$alpha1)
## -----------------------------------------------------------------------------
hist(uout$alpha1)
## -----------------------------------------------------------------------------
hist(uout$p_hwe, breaks = 10, xlab = "P-values", main = "")
qqplot(x = ppoints(length(uout$p_hwe)),
y = uout$p_hwe,
xlab = "Theoretical Quantiles",
ylab = "Empirical Quantiles",
main = "QQ-plot")
abline(0, 1, lty = 2, col = 2)
## -----------------------------------------------------------------------------
qqpvalue(pvals = uout$p_hwe, method = "base")
## -----------------------------------------------------------------------------
plan("sequential")
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