# test_vc.R
# Time-stamp: <23 Apr 2019 15:05:49 c:/x/rpack/lucid/tests/testthat/test_vc.R>
require(lucid)
data(Rail, package="nlme")
# ----------------------------------------------------------------------------
test_that("default", {
expect_error(vc(1))
})
test_that("nlme", {
require(nlme)
m1n <- lme(travel~1, random=~1|Rail, data=Rail)
expect_equal(
vc(m1n),
structure(list(effect =
structure(1:2,
.Label = c("(Intercept)", "Residual"),
class = "factor"),
variance = c(615.31, 16.17),
stddev = c(24.81, 4.02)),
.Names = c("effect", "variance", "stddev"),
row.names = c(NA, -2L), class = c("vc.lme", "data.frame")),
tolerance=1e-1)
# print method
print(vc(m1n))
})
# ----------------------------------------------------------------------------
test_that("lmer", {
require("lme4")
m1l <- lmer(travel~1 + (1|Rail), data=Rail)
expect_equal(
vc(m1l),
structure(list(grp = c("Rail", "Residual"),
var1 = c("(Intercept)", NA),
var2 = c(NA_character_, NA_character_),
vcov = c(615.32, 16.17),
sdcor = c(24.81, 4.02)),
row.names = c(NA, -2L),
class = c("vc.lmerMod", "data.frame")),
tolerance=1e-1)
# print method
print(vc(m1l))
})
# ----------------------------------------------------------------------------
test_that("glmer", {
require("lme4")
m1g <- glmer(travel~1 + (1|Rail), data=Rail, family=gaussian(link="log"))
expect_equal(
vc(m1g),
structure(list(grp = c("Rail", "Residual"),
var1 = c("(Intercept)", NA),
var2 = c(NA_character_, NA_character_),
vcov = c(1.64, 11.11),
sdcor = c(1.28, 3.33)),
.Names = c("grp", "var1", "var2", "vcov", "sdcor"),
row.names = c(NA, -2L), class = c("vc.lmerMod", "data.frame")),
tolerance=1e-1)
# print
print(vc(m1g))
})
# ----------------------------------------------------------------------------
test_that("asreml", {
if(require("asreml")){
m1a <- asreml(travel~1, random=~Rail, data=Rail)
expect_equal(
vc(m1a),
structure(list(effect = structure(1:2, .Label = c("Rail", "units!R"),
class = "factor"),
component = c(615.74, 16.18),
std.error = c(391.58, 6.61),
z.ratio = c(1.57, 2.45),
bound=c("P", "P"),
`%ch` = c(0.2, 0)),
class = c("vc.asreml", "data.frame"),
row.names = c(NA, -2L)),
tolerance=1e-1)
# print method
print(vc(m1a))
}})
# ----------------------------------------------------------------------------
test_that("mmer",{
require("sommer")
m1s <- mmer(travel~1, random = ~ Rail, data=Rail)
expect_equal(
vc(m1s),
structure(list(effect = c("Rail.travel-travel", "units.travel-travel"),
VarComp = c(615.26, 16.17),
VarCompSE = c(392.28, 6.60),
Zratio = c(1.57, 2.45),
Constraint = c("Positive", "Positive")),
row.names = c(NA, -2L),
class = c("vc.mmer", "data.frame")),
tolerance=1e-1)
# print
print(vc(m1s))
})
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