MCEM.phylo: MCEM routine for parameters inference under...

In franciscorichter/dmea02: Diversification and Macro-Evolution Analysis

Description

We performs...

Usage

MCEM.phylo(tree, init_par, cutTime = 10, printpar = TRUE, impsam = FALSE, parallel = F, ips = 20, n_trees = 50)

Arguments

tree
init_par
cutTime
printpar
impsam
parallel
ips
n_trees

Author(s)

F. Richter M.

References

[1] Flexible modelling framework for species assemblages in XXX

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (tree, init_par, cutTime = 10, printpar = TRUE, impsam = FALSE,
    parallel = F, ips = 20, n_trees = 50)
{
    print("MCEM computations initiated. This might take a while.")
    TIME = proc.time()
    n_pars = length(init_par)
    pars = init_par
    Pars = matrix(nrow = (1000), ncol = n_pars)
    i = 1
    qt = 0
    q = vector(mode = "numeric", length = 1000)
    Pars[i, ] = pars
    while (get.time(TIME, mode = "min") < cutTime) {
        time = proc.time()
        if (printpar) {
            print(paste("iteration #", i, ":"))
            print(pars)
            print(paste("previous iteration took", qt, "secs"))
        }
        p = proc.time()
        trees <- sim.srt(tree = tree, pars = pars, n_trees = n_trees,
            parallel = parallel)
        pars = mle.st(trees, impsam = impsam)
        Pars[(i + 1), ] = pars
        qt = get.time(time)
        q[i] = qt
        i = i + 1
        if (i%%ips == 0) {
            n_trees = n_trees + 100
        }
    }
    Pars = Pars[1:i, ]
    q = q[1:i]
    return(list(pars = Pars, times = q))
  }

franciscorichter/dmea02 documentation built on March 21, 2020, 3:46 a.m.