context(strwrap("check full and low rank constructors have valid output using
admixed dataset"))
data("admixed")
svdXkinship <- svd(admixed$Xkinship)
number_nonzero_eigenvalues <- 20
fullrank_kinship <- try(new_fullrank_kinship(x = admixed$xtrain, y = admixed$ytrain,
kinship = admixed$kin_train),
silent = TRUE)
fullrank_K <- try(new_fullrank_K(x = admixed$xtrain, y = admixed$ytrain,
K = admixed$Xkinship),
silent = TRUE)
fullrank_UD <- try(new_fullrank_UD(x = admixed$xtrain, y = admixed$ytrain,
U = svdXkinship$u[,which(svdXkinship$d > 0), drop = FALSE],
D = svdXkinship$d[which(svdXkinship$d > 0)]),
silent = TRUE)
test_that("no error in full rank constructor functions", {
skip_on_cran()
expect_false(inherits(fullrank_kinship, "try-error"))
expect_false(inherits(fullrank_K, "try-error"))
expect_false(inherits(fullrank_UD, "try-error"))
expect_is(fullrank_kinship, class = "fullrank")
expect_is(fullrank_K, class = "fullrank")
expect_is(fullrank_UD, class = "fullrank")
# expect_equivalent(class(coef(fit_sim)), "dgCMatrix")
# expect_equal(dim(coef(fit_sim))[[1]], dim(fit_sim$design)[[2]] + 1)
# expect_equal(dim(coef(fit_sim))[[2]], sum(fit_sim$converged))
})
# kin <- gaston::GRM(gaston::as.bed.matrix(admixed$Xkinship), autosome.only = FALSE)
# need to have pacman::p_load(RSpectra)
lowrank_kinship <- try(new_lowrank_kinship(x = admixed$xtrain, y = admixed$ytrain,
kinship = admixed$kin_train,
n_nonzero_eigenvalues = number_nonzero_eigenvalues,
n_zero_eigenvalues = nrow(admixed$kin_train) - number_nonzero_eigenvalues),
silent = TRUE)
lowrank_K <- try(new_lowrank_K(x = admixed$xtrain, y = admixed$ytrain,
K = admixed$Xkinship,
n_nonzero_eigenvalues = number_nonzero_eigenvalues,
n_zero_eigenvalues = min(nrow(admixed$Xkinship),
ncol(admixed$Xkinship)) -
number_nonzero_eigenvalues),
silent = TRUE)
lowrank_UD <- try(new_lowrank_UD(x = admixed$xtrain, y = admixed$ytrain,
U = svdXkinship$u, D = svdXkinship$d,
n_nonzero_eigenvalues = length(svdXkinship$d),
n_zero_eigenvalues = 50),
silent = TRUE)
test_that("no error in low rank constructor functions", {
skip_on_cran()
expect_false(inherits(lowrank_kinship, "try-error"))
expect_false(inherits(lowrank_K, "try-error"))
expect_false(inherits(lowrank_UD, "try-error"))
expect_is(lowrank_kinship, class = "lowrank")
expect_is(lowrank_K, class = "lowrank")
expect_is(lowrank_UD, class = "lowrank")
# expect_equivalent(class(coef(fit_sim)), "dgCMatrix")
# expect_equal(dim(coef(fit_sim))[[1]], dim(fit_sim$design)[[2]] + 1)
# expect_equal(dim(coef(fit_sim))[[2]], sum(fit_sim$converged))
})
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