TreEvo-package | R Documentation |
A package for applying Approximate Bayesian Computation to estimating parameters of trait evolution in comparative analyses.
Package: | TreEvo |
Type: | Package |
Version: | 0.3.3 |
Date: | 2012-07-02 |
License: | GPL |
Brian O'Meara, Barb L. Banbury, David W. Bapst
Maintainer: David Bapst <dwbapst@gmail.com>
# example analysis, using data simulated with TreEvo
set.seed(1)
# let's simulate some data, and then try to infer the parameters using ABC
# get a 20-taxon coalescent tree
tree <- rcoal(20)
# get realistic edge lengths
tree$edge.length <- tree$edge.length*20
genRateExample <- c(0.01)
ancStateExample <- c(10)
#Simple Brownian motion
simCharExample <- doSimulation(
phy = tree,
intrinsicFn = brownianIntrinsic,
extrinsicFn = nullExtrinsic,
startingValues = ancStateExample, #root state
intrinsicValues = genRateExample,
extrinsicValues = c(0),
generation.time = 100000
)
# NOTE: the example analyses below sample too few particles,
# over too few steps, with too few starting simulations
# - all for the sake of examples that reasonably test the functions
# Please set these values to more realistic levels for your analyses!
resultsBMExample <- doRun_prc(
phy = tree,
traits = simCharExample,
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,
nRuns = 2,
nStepsPRC = 3,
numParticles = 20,
nInitialSimsPerParam = 10,
jobName = "examplerun_prc",
stopRule = FALSE,
multicore = FALSE,
coreLimit = 1
)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.