Nothing
#devtools::test("dae")
context("canonical")
cat("#### Test for marginality algoritm using LRCCD\n")
test_that("LRCCD", {
skip_on_cran()
library(dae)
data("LRRCD.lay")
# All factor anatomy
LRRCD.canon <- designAnatomy(formulae = list(carts = ~ (Block*MainPosn)/BLane/Cart,
trts = ~ Line*Watering),
grandMean = TRUE, data = LRRCD.lay)
summary(LRRCD.canon)
testthat::expect_true(is.null(LRRCD.canon$aliasing))
testthat::expect_equal(LRRCD.canon$Q[[2]]$`BLane[Block:MainPosn]&Residual`, 71)
# Effect of removing `Block#MainPosn`
LRRCD.Posn.canon <- designAnatomy(formulae = list(carts = ~ (Block+MainPosn)/BLane/Cart,
trts = ~ Line*Watering),
grandMean = TRUE, data = LRRCD.lay)
summary(LRRCD.Posn.canon)
testthat::expect_true(is.null(LRRCD.Posn.canon$aliasing))
testthat::expect_equal(LRRCD.Posn.canon$Q[[2]]$`Block#MainPosn#BLane&Residual`, 89)
# Effect of using only a linear trend for MainPosn (Block:MainPosn:BLane defines a Mainunit)
LRRCD.xPosn.canon <- designAnatomy(formulae = list(carts = ~ Block/MainPosn:BLane/Cart,
trts = ~ xMainPosn + Line*Watering),
grandMean = TRUE, omit.projectors = "combined", data = LRRCD.lay)
summary(LRRCD.xPosn.canon, which.criteria = c("aeff", "eeff", "xeff", "ord", "dfor"))
testthat::expect_true(!is.null(LRRCD.xPosn.canon$aliasing))
testthat::expect_equal(nrow(LRRCD.xPosn.canon$aliasing), 2)
testthat::expect_equal(LRRCD.xPosn.canon$aliasing$Alias, c("xMainPosn", "## Information remaining"))
testthat::expect_true(all(abs(LRRCD.xPosn.canon$aliasing$aefficiency - c(0.2749455, 0.9923205)) < 1e-05))
testthat::expect_equal(LRRCD.xPosn.canon$Q[[2]]$`MainPosn:BLane[Block]&Residual`, 97)
# Covariate followed by factor interaction
print(p <- pstructure(formula = ~ xMainPosn + Line*Watering, data = LRRCD.lay,
aliasing.print = FALSE),
which = "aliasing", which.criteria = c("aeff", "eeff", "xeff", "ord"))
testthat::expect_true(!is.null(p$aliasing))
testthat::expect_equal(nrow(p$aliasing), 2)
testthat::expect_equal(p$aliasing$Alias, c("xMainPosn", "## Information remaining"))
testthat::expect_true(all(abs(p$aliasing$aefficiency - c(0.2749455, 0.9923205)) < 1e-05))
# Covariate followed by factor interaction - eigen orthogonalize
testthat::expect_warning(
print(p <- pstructure(formula = ~ xMainPosn + Line*Watering, data = LRRCD.lay,
aliasing.print = FALSE, orthogonalize = "eigen"),
which = "aliasing", which.criteria = c("aeff", "eeff", "xeff", "ord")))
testthat::expect_true(!is.null(p$aliasing))
testthat::expect_equal(nrow(p$aliasing), 1)
testthat::expect_equal(p$aliasing$Alias, "unknown")
testthat::expect_true(abs(p$aliasing$aefficiency - 0.2749455) < 1e-05)
# Factor interaction followed by a Covariate
print(p <- pstructure(formula = ~ Line*Watering + xMainPosn, data = LRRCD.lay,
aliasing.print = FALSE),
which = "aliasing", which.criteria = c("aeff", "eeff", "xeff", "ord"))
testthat::expect_true(!is.null(p$aliasing))
testthat::expect_equal(nrow(p$aliasing), 2)
testthat::expect_equal(p$aliasing$Alias, c("Line", "## Information remaining"))
testthat::expect_true(all(abs(p$aliasing$aefficiency - c(0.2749455, 0.7250545)) < 1e-05))
### Investigate a factor-covariate interaction
LRRCD.BlkxPosn.canon <- designAnatomy(formulae = list(carts = ~ Block/MainPosn:BLane/Cart,
trts = ~ Block*xMainPosn + Line*Watering),
grandMean = TRUE, omit.projectors = "combined", data = LRRCD.lay)
summary(LRRCD.BlkxPosn.canon, which.criteria = c("aeff", "eeff", "xeff", "ord", "dfor"))
testthat::expect_true(!is.null(LRRCD.BlkxPosn.canon$aliasing))
testthat::expect_equal(nrow(LRRCD.BlkxPosn.canon$aliasing), 3)
testthat::expect_equal(LRRCD.BlkxPosn.canon$aliasing$Alias,
c("xMainPosn", "Block[xMainPosn]", "## Information remaining"))
testthat::expect_equal(LRRCD.BlkxPosn.canon$aliasing$Source, rep("Line", 3))
testthat::expect_true(all(abs(LRRCD.BlkxPosn.canon$aliasing$aefficiency -
c(0.2749455, 0.3605941, 0.9698102)) < 1e-05))
# Factor-covariate and factor-factor interaction
print(p <- pstructure(~ Block*xMainPosn + Line*Watering, data = LRRCD.lay,
aliasing.print = FALSE),
which = "aliasing", which.criteria = c("aeff", "eeff", "xeff", "ord"))
testthat::expect_true(!is.null(p$aliasing))
testthat::expect_equal(nrow(p$aliasing), 3)
testthat::expect_equal(p$aliasing$Alias, c("xMainPosn", "Block[xMainPosn]", "## Information remaining"))
testthat::expect_equal(p$aliasing$Source, rep("Line", 3))
testthat::expect_true(all(abs(p$aliasing$aefficiency - c(0.2749455, 0.3605941, 0.9698102)) < 1e-05))
print(p <- pstructure(formula = ~ Block*xMainPosn + Line*Watering, data = LRRCD.lay,
aliasing.print = FALSE, grandMean = TRUE),
which = "aliasing", which.criteria = c("aeff", "eeff", "xeff", "ord"))
testthat::expect_true(!is.null(p$aliasing))
testthat::expect_equal(nrow(p$aliasing), 3)
testthat::expect_equal(p$aliasing$Alias, c("xMainPosn", "Block[xMainPosn]", "## Information remaining"))
testthat::expect_equal(p$aliasing$Source, rep("Line", 3))
testthat::expect_true(all(abs(p$aliasing$aefficiency - c(0.2749455, 0.3605941, 0.9698102)) < 1e-05))
})
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