Nothing
###Wrapper function.
###Current version are not able to control the nlm function, which will be improved in the later versions.
BMControl <- function(print=FALSE, zStepSize=1, logPiTol=3, returnParam=FALSE,
CILevel=0.95,...)
{
if(zStepSize<0|logPiTol<0|CILevel>1|CILevel<0)
stop("Wrong Input !")
return(list(print=print,
zStepSize=zStepSize,
logPiTol=logPiTol,
logPiSubTol=logPiTol*2,
returnParam=returnParam,
CILevel=CILevel,
...))
}
BMAnimalTrack <- function(dataList, controlList=BMControl())
{
if(controlList$print) cat("Step 1. Estimating parameters.\n")
#Parameter estimation.
pest <- nlm(nllh.BB.Phi_XY, c(0, 0), logS2=TRUE,
gpsList=dataList$glist, print.level=as.numeric(controlList$print))
#In the log scale again. Obtain the Hessian
pestWh <- nlm(nllh.BB.Phi_XY, pest$est, hessian=TRUE, logS2=TRUE,
gpsList=dataList$glist, print.level=0)
if(controlList$print) cat("Step 2. Searching for the grid of numerical Integration. \n")
piMx <- zSearch(pestWh, dataList$glist,
controlList$zStepSize, controlList$logPiTol, controlList$logPiSubTol)
if(controlList$print) cat(nrow(piMx), "grid points are used. \n")
if(controlList$print) cat("Step 3. Bayesian Melding for bias correction and uncertainty characterization. \n")
fbRes <- postMar.BB.Eta(piMx, dataList$XMx, dataList$glist,
printK=controlList$print)
ciConst <- qnorm(1-(1-controlList$CILevel)/2)
fbRes <- cbind(fbRes, fbRes[,1]-ciConst*sqrt(fbRes[,2]), fbRes[,1]+ciConst*sqrt(fbRes[,2]))
colnames(fbRes[,3:4]) <- c("CI.lower", "CI.upper")
if (controlList$returnParam)
{
return(list(param=exp(pest$est), etaMar=fbRes))
}
else
return(fbRes)
}
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