test_that("methodsPLS works", {
set.seed(1)
simPhyExample <- rcoal(5)
simPhyExample$edge.length <- simPhyExample$edge.length * 20
nSimulations <- 6
#expect_warning(
simDataParallel <- parallelSimulateWithPriors(
nrepSim = nSimulations,
multicore = FALSE,
coreLimit = 1,
phy = simPhyExample,
intrinsicFn = brownianIntrinsic,
extrinsicFn = nullExtrinsic,
startingPriorsFns = "normal",
startingPriorsValues = list(c(mean(simCharExample[, 1]), sd(simCharExample[, 1]))),
intrinsicPriorsFns = c("exponential"),
intrinsicPriorsValues = list(10),
extrinsicPriorsFns = c("fixed"),
extrinsicPriorsValues = list(0),
generation.time = 300000,
checkpointFile = NULL,
checkpointFreq = 24,
verbose = FALSE,
freevector = NULL,
taxonDF = NULL
#,niter.brown = 25,
#niter.lambda = 25,
#niter.delta = 25,
#niter.OU = 25,
#niter.white = 25
)
#)
nParFree <- sum(attr(simDataParallel, "freevector"))
trueFreeValuesMat <- simDataParallel[, 1:nParFree]
summaryValuesMat <- simDataParallel[, -1:-nParFree]
expect_warning(
PLSmodel <- returnPLSModel(
trueFreeValuesMatrix = trueFreeValuesMat,
summaryValuesMatrix = summaryValuesMat,
validation = "CV",
scale = TRUE,
variance.cutoff = 95,
segments = nSimulations)
)
expect_silent(
PLSTransform(
summaryValuesMatrix = summaryValuesMat,
pls.model = PLSmodel
)
)
})
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