tests/testthat/test-tajd.R

In deponent-verb/popgen.stats: Popgen summary statistics calculator

pacman::p_load("testthat","popgen.stats")

context("tajd Function Rcpp")

### Test for the Rcpp implementation of Tajima's D

test_that("tajd cpp computed correctly",{

  #test coefficients of tajd
  #a1f
  N=4
  expect_equal(a1f(N),1+1/2+1/3)

  #a2f
  test=1+1/2^2+1/3^2
  expect_equal(a2f(N),test)

  #b1f
  test=1/3*(N+1)/(N-1)
  expect_equal(b1f(N),test)

  #b2f
  test=2*(N^2+N+3)/(9*N*(N-1))
  expect_equal(b2f(N),test)

  #c function tests
  a1=3
  a2=4
  b1=2
  b2=5

  #c1f
  expect_equal(c1f(b1=b1,a1=a1),b1-(1/a1))

  #c2f
  test=b2-(N+2)/(a1*N)+a2/(a1*a1)
  expect_equal(c2f(a1=a1,a2=a2,N=N,b2=b2),test)

  ##e function test
  a1=3
  a2=6
  c1=4
  c2=7

  expect_equal(e1f(a1=a1,c1=c1),c1/a1)

  expect_equal(e2f(a1=a1,c2=c2,a2=a2),c2/(a1^2+a2))


})