test_that("boxcoxTransformation works", {
set.seed(1)
simPhyExample <- rcoal(5)
simPhyExample$edge.length <- simPhyExample$edge.length * 20
#expect_warning(
simDataParallel <- parallelSimulateWithPriors(
nrepSim = 2,
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 = 100000,
checkpointFile = NULL,
checkpointFreq = 24,
verbose = FALSE,
freevector = NULL,
taxonDF = NULL
)
nParFree <- sum(attr(simDataParallel, "freevector"))
summaryValuesMat <- simDataParallel[, -1:-nParFree]
boxTranMat <- boxcoxTransformationMatrix(summaryValuesMatrix = summaryValuesMat)
result<-boxcoxTransformation(
summaryValuesVector = summaryValuesMat[,1],
boxcoxAddition = boxTranMat$boxcoxAddition,
boxcoxLambda = boxTranMat$boxcoxLambda
)
expect_is(result, "numeric")
})
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