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#' Test Against Random Networks
#' @description Performs significance tests for global measures
#' of semantic networks against the global measures of equivalent
#' size (and density) random networks
#'
#' @param ... Matrices or data frames.
#' Semantic networks to be compared against random networks
#'
#' @param iter Numeric.
#' Number of iterations in bootstrap.
#' Defaults to \code{1000}
#'
#' @param cores Number of computer processing cores to use for bootstrapping samples.
#' Defaults to \emph{n} - 1 total number of cores.
#' Set to any number between 1 and maximum amount of cores on your computer
#'
#' @return Returns a matrix containing p-values
#' for the network measures of the input networks against
#' the distribution of equivalent random networks. The last
#' two columns contain the mean (\code{"M.rand"}) and
#' standard deviation (\code{"SD.rand"}) of the network measures
#' for the random network distribution
#'
#' @examples
#' # Get openness data
#' one <- open.clean[which(open.group == "Low"),]
#' two <- open.clean[which(open.group == "High"),]
#'
#' \donttest{# Compute networks
#' net.one <- CN(one)
#' net.two <- CN(two)
#'
#' # Perform random networks test
#' randnet.test(net.one, net.two, iter = 100, cores = 2)
#' }
#'
#' @references
#' Viger, F., & Latapy, M. (2016).
#' Efficient and simple generation of random simple connected graphs with prescribed degree sequence.
#' \emph{Journal of Complex Networks}, \emph{4}, 15-37.
#'
#' @author Alexander Christensen <alexpaulchristensen@gmail.com>
#'
#' @importFrom stats pnorm
#'
#' @export
# Random network test----
# Updated 05.12.2020
randnet.test <- function (..., iter, cores)
{
#Missing arguments
if(missing(cores))
{cores <- parallel::detectCores() - 1
}else{cores <- cores}
if(missing(iter))
{iter <- 1000
}else{iter <- iter}
#Get names of networks
name <- as.character(substitute(list(...)))
name <- name[-which(name=="list")]
#Create list of input
listdata <- list(...)
#Initialize data list
data.list <- vector("list", length = length(name))
for(i in 1:length(name))
for(j in 1:iter)
{data.list[[i]][[j]] <- listdata[[i]]}
#Initialize random networks list
rand.list <- vector("list", length = length(name))
names(rand.list) <- name
#Message for begin random networks
message("Generating random networks...\n", appendLF = FALSE)
#Parallel processing
cl <- parallel::makeCluster(cores)
#Export variables
parallel::clusterExport(cl, varlist = c("data.list", "rand.list"),
envir = environment())
#Compute random networks
for(i in 1:length(data.list))
{rand.list[[i]] <- pbapply::pblapply(
X = data.list[[i]], FUN = function(X){
randnet(nodes = ncol(X), edges = floor(sum(X) / 2))
}, cl = cl)
}
#Stop parallel processing
parallel::stopCluster(cl)
#Message for begin of network measures
message("Computing network measures...\n", appendLF = FALSE)
#Initialize network measures list
net.meas <- vector("list", length = length(name))
names(net.meas) <- name
#Parallel processing
cl <- parallel::makeCluster(cores)
#Export variables
parallel::clusterExport(cl, varlist = c("net.meas"),
envir = environment())
#Compute network measures
for(i in 1:length(data.list))
{net.meas[[i]] <- pbapply::pbsapply(X = rand.list[[i]], FUN = semnetmeas, cl = cl)}
#Stop parallel processing
parallel::stopCluster(cl)
#Initialize result list
res <- vector("list", length = length(name))
names(res) <- name
#Compute significance tests
for(i in 1:length(data.list))
{
sig.mat <- matrix(0, nrow = 3, ncol = 3)
row.names(sig.mat) <- c("ASPL","CC","Q")
colnames(sig.mat) <- c(paste(name[i], "(p-value)"), "M.rand", "SD.rand")
#Insert random means and sds
sig.mat[,"M.rand"] <- round(rowMeans(net.meas[[i]]),4)
sig.mat[,"SD.rand"] <- round(apply(net.meas[[i]],1,sd),4)
#Compute semantic network measures for network
meas <- semnetmeas(listdata[[i]])
##ASPL
z.aspl <- (meas["ASPL"] - sig.mat["ASPL","M.rand"]) / sig.mat["ASPL","SD.rand"]
sig.mat["ASPL",paste(name[i], "(p-value)")] <- round(2 * pnorm(-abs(z.aspl)), 4)
##CC
z.cc <- (meas["CC"] - sig.mat["CC","M.rand"]) / sig.mat["CC","SD.rand"]
sig.mat["CC",paste(name[i], "(p-value)")] <- round(2 * pnorm(-abs(z.cc)), 4)
##Q
z.q <- (meas["Q"] - sig.mat["Q","M.rand"]) / sig.mat["Q","SD.rand"]
sig.mat["Q",paste(name[i], "(p-value)")] <- round(2 * pnorm(-abs(z.q)), 4)
#Insert results
res[[i]] <- sig.mat
}
return(res)
}
#----
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