#################
# cd C:\Users\notDave\Desktop\remoteWorkplace && powershell -Command "(New-Object Net.WebClient).DownloadFile('https://raw.githubusercontent.com/bomeara/treevo/vignette_third_try/vignettes/.constructing_treevo_vignette.R','constructVignette.R')" && R CMD BATCH --no-save --no-restore constructVignette.R
#####################################################
# cd C:\Users\notDave\Desktop\remoteWorkplace && R CMD BATCH --no-save --no-restore treevo_ABC_vignette.R
################
## ------------------------------------------------------------------------
# Control Box
devtools::install_github("bomeara/treevo",ref="vignette_third_try")
setwd("C:/Users/notDave/Desktop/remoteWorkplace")
multicore<-TRUE
coreLimit<-6
nStepsPRC<-3
numParticles<-100
nInitialSimsPerParam <- 100
nRuns<-3
generation.time<-10000
## ----echo=FALSE----------------------------------------------------------
library(paleotree)
data(RaiaCopesRule)
set.seed(444)
## ------------------------------------------------------------------------
#plot(ladderize(ammoniteTreeRaia));axisPhylo()
## ------------------------------------------------------------------------
tree<-multi2di(ammoniteTreeRaia)
tree<-addTermBranchLength(tree,0.01)
#plot(ladderize(tree));axisPhylo()
## ---- echo=FALSE, fig.show='hold'----------------------------------------
#plotTraitgram(tree=tree, trait=sutureComplexity,
# conf.int=FALSE, main="Ammonite Suture Complexity")
#plotTraitgram(tree=tree, trait=shellSize,
# conf.int=FALSE, main="Ammonite Shell Diameter")
## ------------------------------------------------------------------------
library(TreEvo)
# character data for doRun must be in matrix form
# with rows labeled with taxon names
charData<-matrix(sutureComplexity,ncol=1)
rownames(charData)<-names(sutureComplexity)
save.image(file="treevo_vignette_workspace.Rdata")
## ------------------------------------------------------------------------
# typical Brownian Motion
resultsBM<-doRun_prc(
phy = tree,
traits = charData,
intrinsicFn=brownianIntrinsic,
extrinsicFn=nullExtrinsic,
startingPriorsFns="normal",
startingPriorsValues=matrix(c(mean(charData[,1]), sd(charData[,1]))),
intrinsicPriorsFns=c("exponential"),
intrinsicPriorsValues=matrix(c(10, 10), nrow=2, byrow=FALSE),
extrinsicPriorsFns=c("fixed"),
extrinsicPriorsValues=matrix(c(0, 0), nrow=2, byrow=FALSE),
generation.time=generation.time,
nInitialSimsPerParam = nInitialSimsPerParam,
nRuns=nRuns,
nStepsPRC=nStepsPRC,
numParticles=numParticles,
jobName="typicalBMrun",
stopRule=FALSE,
multicore=multicore,
coreLimit=coreLimit,
verboseParticles=TRUE
)
save.image(file="treevo_vignette_workspace.Rdata")
## ------------------------------------------------------------------------
resultsBound<-doRun_prc(
phy = tree,
traits = charData,
intrinsicFn=boundaryMinIntrinsic,
extrinsicFn=nullExtrinsic,
startingPriorsFns="normal",
startingPriorsValues=matrix(c(mean(charData[,1]), sd(charData[,1]))),
intrinsicPriorsFns=c("exponential","normal"),
intrinsicPriorsValues=matrix(c(10, 10, -10, 1), nrow=2, byrow=FALSE),
extrinsicPriorsFns=c("fixed"),
extrinsicPriorsValues=matrix(c(0, 0), nrow=2, byrow=FALSE),
generation.time=generation.time,
nInitialSimsPerParam = nInitialSimsPerParam,
nRuns=nRuns,
nStepsPRC=nStepsPRC,
numParticles=numParticles,
jobName="BMwithBoundRun",
stopRule=FALSE,
multicore=multicore,
coreLimit=coreLimit,
verboseParticles=FALSE
)
save.image(file="treevo_vignette_workspace.Rdata")
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