boxcoxTransformation: Box-Cox Transformation for Simulation Summary Values

In bomeara/treevo: Using ABC to Understand Trait Evolution

Box-Cox Transformation for Simulation Summary Values

Description

boxcoxTransformation Box-Cox transforms summary values from a single simulation, while boxcoxTransformationMatrix Box-Cox transforms summary values from multiple simulations. The output of boxcoxTransformationMatrix needs to be provided as input for boxcoxTransformation.

Usage

boxcoxTransformation(summaryValuesVector, boxcoxAddition, boxcoxLambda)

boxcoxTransformationMatrix(summaryValuesMatrix)

Arguments

summaryValuesVector	Vector of summary statistics from a single simulation
boxcoxAddition	Vector of boxcox additions from boxcoxTransformationMatrix
boxcoxLambda	Vector of boxcox lambda values from boxcoxTransformationMatrix
summaryValuesMatrix	Matrix of summary statistics from simulations

Value

boxcoxTransformation returns a vector of Box-Cox transformed summary statistics from a single observation. boxcoxTransformationMatrix returns a matrix of Box-Cox transformed summary statistics with the same dimensions as summaryValuesMatrix.

Author(s)

Brian O'Meara and Barb Banbury

Examples

set.seed(1)
data(simRunExample)

# example simulation

simDataParallel <- parallelSimulateWithPriors(
  nrepSim = 5, 
  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"))

# separate the simulation results: 
  # 'true' generating parameter values from the summary values
summaryValuesMat <- simDataParallel[, -1:-nParFree]

boxTranMat <- boxcoxTransformationMatrix(
  summaryValuesMatrix = summaryValuesMat
  )
boxTranMat

boxcoxTransformation(
  summaryValuesVector = summaryValuesMat[, 1], 
  boxcoxAddition = boxTranMat$boxcoxAddition, 
  boxcoxLambda = boxTranMat$boxcoxLambda
  )

bomeara/treevo documentation built on Aug. 19, 2023, 6:52 p.m.