gridsearch_burninthining_multiple: gridsearch_burninthining_multiple
In isci1102/ERPM:

View source: R/functions_burninthining.R

1	gridsearch_burninthining_multiple(partitions, presence.tables, theta, nodes, effects, objects, num.steps, neighborhoods, sizes.allowed, sizes.simulated, max.thining, parallel = F, cpus = 1)

`partitions`	Observed partitions.
`presence.tables`	Presenc of nodes.
`theta`	Innitial parameters.
`nodes`	Data frame of nodes.
`effects`	Effects or sufficient statistics. A list with a vector "names" and a vector "objects".
`objects`	Objects used for statistics calculation. A list with a vector "name" and a vector "object".
`num.steps`	Number of samples wanted.
`neighborhoods`	List of probability vectors (probability actors swap, probability merge/division, probability single actor move).
`sizes.allowed`	Vector of group sizes allowed in sampling (now, it only works for vectors like size_min:size_max).
`sizes.simulated`	Vector of group sizes allowed in the Markov chain but not necessraily sampled (now, it only works for vectors like size_min:size_max).
`max.thining`	Where to stop adding thining.
`parallel`	To run different neighborhoods in parallel. Default = False
`cpus`	Default = 1

##---- 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 (partitions, presence.tables, theta, nodes, effects,
    objects, num.steps, neighborhoods, sizes.allowed, sizes.simulated,
    max.thining, parallel = F, cpus = 1)
{
    if (parallel) {
        n <- ceiling(length(neighborhoods)/cpus)
        subindexes <- list()
        for (c in 1:cpus) {
            start <- (c - 1) * n + 1
            end <- c * n
            if (c == cpus)
                end <- length(neighborhoods)
            subindexes[[c]] <- start:end
        }
        sfExport("partitions", "presence.tables", "theta", "nodes",
            "effects", "objects", "num.steps", "neighborhoods",
            "sizes.allowed", "sizes.simulated", "max.thining",
            "subindexes")
        res <- sfLapply(1:cpus, fun = function(k) {
            subres <- list()
            for (i in 1:length(subindexes[[k]])) {
                index <- subindexes[[k]][i]
                subneighborhood <- neighborhoods[[index]]
                subres[[i]] <- simulate_burninthining_multiple(partitions,
                  presence.tables, theta, nodes, effects, objects,
                  num.steps, subneighborhood, sizes.allowed,
                  sizes.simulated, max.thining)
            }
            return(subres)
        })
        allsimulations <- list()
        for (c in 1:cpus) allsimulations <- append(allsimulations,
            res[[c]])
    }
    else {
        allsimulations <- list()
        for (i in 1:length(neighborhoods)) {
            allsimulations[[i]] <- simulate_burninthining_multiple(partitions,
                presence.tables, theta, nodes, effects, objects,
                num.steps, neighborhoods[[i]], sizes.allowed,
                sizes.simulated, max.thining)
        }
    }
    p1 <- c()
    p2 <- c()
    p3 <- c()
    reach0.4 <- c()
    firstthining0.4 <- c()
    reach0.5 <- c()
    firstthining0.5 <- c()
    finalmaxautocor <- c()
    for (i in 1:length(neighborhoods)) {
        p1 <- c(p1, neighborhoods[[i]][1])
        p2 <- c(p2, neighborhoods[[i]][2])
        p3 <- c(p3, neighborhoods[[i]][3])
        allmaxautocors <- apply(allsimulations[[i]]$autocorrelations.smoothed,
            1, FUN = max)
        finalmaxautocor <- c(finalmaxautocor, allmaxautocors[max.thining])
        reach0.4 <- c(reach0.4, sum(allmaxautocors <= 0.4, na.rm = T))
        reach0.5 <- c(reach0.5, sum(allmaxautocors <= 0.5, na.rm = T))
        if (length(which(allmaxautocors <= 0.4)) > 0) {
            firstthining0.4 <- c(firstthining0.4, min(which(allmaxautocors <=
                0.4)))
        }
        else {
            firstthining0.4 <- c(firstthining0.4, -1)
        }
        if (length(which(allmaxautocors <= 0.5)) > 0) {
            firstthining0.5 <- c(firstthining0.5, min(which(allmaxautocors <=
                0.5)))
        }
        else {
            firstthining0.5 <- c(firstthining0.5, -1)
        }
    }
    results.search <- data.frame(p_swap = p1, p_mergediv = p2,
        p_single = p3, final_max_autocorr = finalmaxautocor,
        reach_autocorr0.4 = reach0.4, first_thining_autocorr0.4 = firstthining0.4,
        reach_autocorr0.5 = reach0.5, first_thining_autocorr0.5 = firstthining0.5)
    return(list(results.search = results.search, all.simulations = allsimulations))
  }