In MoisesExpositoAlonso/popgensim: Wright Fisher simulations: C++ implementation with interactive Shiny app visualization

---

title: "Lilelihood: observed fitness, selection and epistasis"

subtitle: "EQUATIONS"

author: "Moi Exposito-Alonso"

date: 'r Sys.Date()'

output: pdf_document: header-inclusdes: - \usepackage{amsmath} - \usepackage{caption} - \usepackage{subcaption} - \usepackage{graphicx} #html_document: default #header-includes: #- \setlength{\parindent}{4em} #- \setlength{\parskip}{0em}

---

$$P(AABB)_{out}= 0.2^2 \times (1/1) + 2 \times 0.2 \times 0.8 \times (1/16) + 0.8^2 \times (0/1) = 0.06$$

$$P(AABB){self}= 0.99 + 0.01 \times P(AABB){out} = 0.99006$$

# For one pop of N=100 with 2 genotypes of 2 loci
# With random mating in 1 genation homozyotes carrying an epistasis?

0.2^2 * (1/1) + 2 * 0.2 *0.8 * (1/16) + 0.8^2 * (0/1)

0.99 + 0.001 * ( 0.2^2 * (1/1) + 2 * 0.2 *0.8 * (1/16) + 0.8^2 * (0/1))

0.99+0.01


pABAB=0.2
pabab=0.8



ABAB = pABAB^2 + (pabab) * (1/16)
ABAB

ABAB = 0.99 + 0.001 * (pABAB^2 + pabab * (1/16) )
ABAB

ABAB

# 
# pAb=0.25
# paB=0.25
# pab=0.25
# 
# pAB*pAB + 2*pAb*paB *1/4
# 
# pAB*pAB + 2*pAb*paB *3/4 + 2*pab*paB*1/4 + 2*pab*pAb*1/4 + 2*pab*pAB*1/2
# 
# 
# pAB*pAB + 2*pAb*paB + 2*pab*paB + 2*pab*pAb + 2*pab*pAB +
# 
# expand.grid(vector('pAB','pAb','paB','pab'),c('pAB','pAb','paB','pab')  )
# 
# 1-(pab^2)
# 
# 0.98 + 0.02*(pAB*pAB + 0.02*pAb*paB *1/4)

MoisesExpositoAlonso/popgensim documentation built on May 7, 2019, 8:57 p.m.