# NOT RUN {
# Load the data, compute the sampling fraction rho
data(conifers)
totalConiferSpecies <- 630
sampledConiferSpecies <- conifers$Nnode+1
rho <- sampledConiferSpecies / totalConiferSpecies
# Run a tess analysis
tess.analysis(tree = conifers,
initialSpeciationRate=c(1.0),
initialExtinctionRate=c(0.5),
empiricalHyperPriors = FALSE,
numExpectedRateChanges = 2,
numExpectedMassExtinctions = 2,
samplingProbability = rho,
MAX_ITERATIONS = 200,
BURNIN = 100,
dir = "./run_1")
tess.analysis(tree = conifers,
initialSpeciationRate=c(1.0),
initialExtinctionRate=c(0.5),
empiricalHyperPriors = FALSE,
numExpectedRateChanges = 2,
numExpectedMassExtinctions = 2,
samplingProbability = rho,
MAX_ITERATIONS = 200,
BURNIN = 100,
dir = "./run_2")
# Process the output
coniferOutput_1 <- tess.process.output(dir="./run_1",
numExpectedRateChanges=2,
numExpectedMassExtinctions=2)
coniferOutput_2 <- tess.process.output(dir="./run_2",
numExpectedRateChanges=2,
numExpectedMassExtinctions=2)
# Plot the output
outputs <- list(coniferOutput_1,coniferOutput_2)
tess.plot.multichain.diagnostics(outputs)
# }
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