R/elgrin.R

In econetwork: Analyzing Ecological Networks

elgrin <- function(presence, metaweb, environmentvar, ncores=1){
    # symmetrizing the metaweb
    if("igraph" %in% class(metaweb)){
        metaweb <- as.matrix(as_adjacency_matrix(metaweb), type="both")
    } else{
        metaweb <- as.matrix(as_adjacency_matrix(graph_from_adjacency_matrix(metaweb, mode="undirected")))
    }
    metaweb <- metaweb*1.0 ## requiring numeric weights
    if(nrow(presence)!=nrow(metaweb))
        stop("inconsistent number of species between presence data and metaweb")
    environmentvar <- as.matrix(environmentvar)
    if(ncol(presence)!=nrow(environmentvar))
        stop("inconsistent number of locations between presence data and environmentvar data")
    environmentvar <- apply(environmentvar,2,function(v)(v-mean(v))/sd(v))
    ## warning("Be aware that environment variables are standardized before use")
    model <- elgrincore(presence, metaweb, environmentvar, ncores)
    return(model)
}

elgrinsim <- function(metaweb, environmentvar,
                      a, al, b, c, betaPres, betaAbs, compat,
                      ncores=1){
    if("igraph" %in% class(metaweb)){
        metaweb <- as.matrix(as_adjacency_matrix(metaweb))
    } else{
        metaweb <- as.matrix(metaweb)
    }
    metaweb <- metaweb*1.0 ## requiring numeric weights
    environmentvar <- as.matrix(environmentvar)
    environmentvar <- apply(environmentvar,2,function(v)(v-mean(v))/sd(v))
    ##warning("Be aware that environment variables are standardized before use")
    return(elgrinsimcore(metaweb, environmentvar, a, al, b, c, betaPres, betaAbs, compat, ncores))
}