tests/testthat/test_genetic_functions.R

In lukembrowne/sgsR: Spatial genetic structure analyses in R

library(sgsR)
context("Genetic functions")
#
# test_that("Allele frequencies", {
#   expect_equal(calcAlleleFreqPop(c(0,1,2), c(1,2,3), Nallele = 4),
#                c(1/6, 2/6, 2/6, 1/6 ))
#   expect_equal(calcAlleleFreqCppInd(0,1, Nallele = 2),
#                c(1/2, 1/2))
#   expect_equal(calcAlleleFreqCppInd(-999,1, Nallele = 3),
#                c(-999,0,0)) ## Handling missing data
#   expect_equal(calcAlleleFreqCppInd(1,-999, Nallele = 3),
#                c(-999,0,0)) ## Handling missing data
# })
#
#
# ref_gen <- matrix(rep(1/3, 6), nrow = 2, byrow = TRUE)
# alfreq1 <- matrix(c(1/2, 1/2, 0, 1/2, 1/2, 0), nrow = 2, byrow = TRUE)
# alfreq2 <- matrix(c(1/2, 1/2, 0, -999, 1/2, 0), nrow = 2, byrow = TRUE)
# Nloci = 2
# Nallele = 3
# Ngenecopies = 4
#
# test_that("Fij coefficient", {
#   expect_equal(calcFijPairwiseCpp(ref_gen, alfreq1, alfreq2,
#                                   Nloci, Nallele, Ngenecopies), -999)



# })
#
#