R/div.param.invasion.obs.R

In VirtualCom: Assembling virtual plant communities

div.param.invasion.obs <- function(ispSite, iphy, ifun, imyinva) {
    # Check the number of simulated communites, and adjust the intput format
    Ncom <- nrow(ispSite)
    if (Ncom == 1) {
        ispSite <- rbind(ispSite, ispSite)
        row.names(ispSite) <- c(1, 2)
    }
    
    # Run the calculations
    phyloRes <- MDNC_MDNN_Invasive_new(samp = ispSite, dis = iphy, inva = imyinva)
    funRes <- MDNC_MDNN_Invasive_new(samp = ispSite, dis = ifun, inva = imyinva)
    
    iobs <- sapply(imyinva, function(x) {
        tm <- cbind(sapply(names(phyloRes), function(y) unlist(phyloRes[[y]][x])), sapply(names(funRes), function(y) unlist(funRes[[y]][x])))
        rownames(tm) <- 1:nrow(ispSite)
        colnames(tm) <- c(paste("phy_", names(phyloRes), sep = ""), paste("fun_", names(phyloRes), sep = ""))
        tm
    }, simplify = F, USE.NAMES = T)
    # Check the number of simulated communites, and adjust the output format
    if (Ncom == 1) {
        for (i in 1:length(iobs)) {
            iobs[[1]] <- iobs[[1]][1, ]
        }
    }
    return(iobs)
}