context("genetic_structure.R")
test_that("checking",{
loc1 <- c( locus( c(1,1) ),
locus( c(1,2) ),
locus( c(1,2) ),
locus( c(1,1) ),
locus( c(2,2) ),
locus( c(2,1) ),
locus( c(2,1) ),
locus( c(2,2) ) )
loc2 <- c( locus( c(1,1) ),
locus( c(1,2) ),
locus( c(1,2) ),
locus( c(1,2) ),
locus( c(2,2) ),
locus( c(2,1) ),
locus( c(2,3) ),
locus( c(2,3) ) )
pops <- rep( c("A","B"), each=2 )
df <- data.frame( Population=pops, TPI=loc1 )
gs <- genetic_structure( df )
expect_that( gs, is_a("data.frame") )
expect_that( dim(gs), is_equivalent_to(c(1,5) ) )
expect_that( names(gs), is_equivalent_to(c("Locus","Gst","Hs","Ht","P") ) )
df$PGM <- loc2
gs <- genetic_structure( df )
expect_that( gs, is_a("data.frame") )
expect_that( dim(gs), is_equivalent_to(c(3,5) ) )
expect_that( names(gs), is_equivalent_to(c("Locus","Gst","Hs","Ht","P") ) )
expect_that( gs$Locus, is_equivalent_to( c("TPI","PGM","Multilocus")))
expect_true( gs$Gst[1] < gs$Gst[2])
gs <- genetic_structure( df, pairwise=TRUE )
expect_that( gs, is_a("matrix") )
expect_that( dim(gs), is_equivalent_to( c(2,2)) )
expect_true( all( is.na(diag(gs))) )
expect_true( gs[1,2] == gs[2,1] )
})
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