R/uniformMCMCTree.R

In PuttickMacroevolution/MCMCtreeR: Prepare MCMCtree Analyses and Plot Bayesian Divergence Time Analyses Estimates on Trees

# uniformMCMCtree - internal function

uniformMCMCtree <- function(xRange=c(0.1, 4), tL, tU, minProb, maxProb) {
    
    omega <- ((1 - maxProb) * tL) / (minProb * (tU - tL))
    omegaTwo <- (1 - maxProb) / (minProb * (tU - tL))
    xx <- seq(xRange[1], xRange[2], by=0.001)
    numero <- c()
    rc <- 1
    for(x in xx) {
        time <- x
        if(time <= tL) numero[rc] <- minProb * (omega / tL) * (time / tL)^(omega-1)
        if(tL < time && time <= tU) numero[rc] <- (1 - maxProb) / (tU - tL)
        if(time > tU) numero[rc] <- minProb * omegaTwo * exp(-omegaTwo * (time - tU))
        rc <- rc + 1
    }
    time <- xx ; density <- numero
    return(cbind(time, density))
}