context("Extraction of results from spatial splines model")
########################
data(m1)
dat <- as.data.frame(m1)
fixed.fml <- phe_X ~ sex
n.obs <- nrow(dat)
n.fixed <- length(attr(terms(fixed.fml), 'term.labels'))
nlevels.fixed <- nlevels(dat$sex)
n.knots <- c(4, 3)
n.splines <- prod(n.knots + 2)
# Use a different number of knots for rows and columns
res <- try(
suppressMessages(
remlf90(fixed = fixed.fml,
spatial = list(model = 'splines',
coord = coordinates(m1),
n.knots = n.knots),
data = dat,
method = 'em')
)
)
test_that("The splines model runs with EM-REML without errors", {
expect_that(!inherits(res, "try-error"), is_true())
})
test_that("coef() gets a named vector of coefficients", {
expect_is(coef(res), 'numeric')
expect_equal(length(coef(res)), nlevels.fixed + n.splines)
expect_named(coef(res))
})
test_that("ExtractAIC() gets one number", {
expect_is(extractAIC(res), 'numeric')
expect_equal(length(extractAIC(res)), 1)
})
test_that("fitted() gets a vector of length N", {
expect_is(fitted(res), 'numeric')
expect_equal(length(fitted(res)), n.obs)
})
test_that("fixef() gets a named list of numeric vectors with estimated values and s.e.", {
x <- fixef(res)
expect_is(x, 'breedR_estimates')
expect_named(x)
expect_equal(length(x), n.fixed)
for (f in x) {
expect_is(f, 'numeric')
expect_false(is.null(fse <- attr(f, 'se')))
expect_is(fse, 'numeric')
expect_equal(length(fse), length(f))
}
})
test_that("get_pedigree() returns NULL", {
expect_null(get_pedigree(res))
})
test_that("logLik() gets an object of class logLik", {
expect_is(logLik(res), 'logLik')
})
test_that("model.frame() gets an Nx2 data.frame with a 'terms' attribute", {
x <- model.frame(res)
expect_is(x, 'data.frame')
expect_is(terms(x), 'terms')
expect_equal(dim(x), c(n.obs, n.fixed + 1))
})
test_that("model.matrix() gets a named list of fixed and random incidence matrices", {
x <- model.matrix(res)
expect_is(x, 'list')
expect_named(x, names(res$effects))
expect_equal(dim(x$sex), c(n.obs, nlevels.fixed))
expect_is(x$spatial, 'sparseMatrix')
expect_equal(dim(x$spatial), c(n.obs, n.splines))
})
test_that("nobs() gets the number of observations", {
expect_equal(nobs(res), n.obs)
})
test_that("plot(, type = *) returns ggplot objects", {
expect_is(plot(res, type = 'phenotype'), 'ggplot')
expect_is(plot(res, type = 'fitted'), 'ggplot')
expect_is(plot(res, type = 'spatial'), 'ggplot')
expect_is(plot(res, type = 'fullspatial'), 'ggplot')
expect_is(plot(res, type = 'residuals'), 'ggplot')
})
test_that("print() shows some basic information", {
## Not very informative currently...
expect_output(print(res), 'Data')
})
test_that("ranef() gets a ranef.breedR object with random effect BLUPs and their s.e.", {
x <- ranef(res)
expect_is(x, 'ranef.breedR')
expect_equal(length(x), 1)
expect_named(x, c('spatial'))
expect_is(x$spatial, 'numeric')
expect_equal(length(x$spatial), n.splines)
expect_false(is.null(xse <- attr(x$spatial, 'se')))
expect_is(xse, 'numeric')
expect_equal(length(xse), n.splines)
})
test_that("residuals() gets a vector of length N", {
rsd <- residuals(res)
expect_is(rsd, 'numeric')
expect_equal(length(rsd), n.obs)
})
test_that("summary() shows summary information", {
expect_output(print(summary(res)), 'Variance components')
expect_output(print(summary(res)), 'knots:')
})
test_that("vcov() gets the covariance matrix of the spatial component of the observations", {
x <- vcov(res)
expect_is(x, 'Matrix')
expect_equal(dim(x), rep(n.obs, 2))
})
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.