R/EE_function.R

In GabrielNakamura/Dimensionality_package: Package to compute dimensionality, alpha and beta measures of biodiversity

#' Evenness of Eigenvalues for diversity metrics (EE)
#'
#' @param matrix.M A matrix containing diversity metrics values (columns) for each sample (lines)
#' @param scale Logical. If TRUE (default) the diversity metrics are scaled to 0 mean and variance of 1 (standardization)
#' @param method Character, the method used to perform the scaling of diversity metrics.
#'     Default is "standardize".
#' @param evenness Character, the method used to calculate the Evenness of Eigenvalues.
#'     Default is "Camargo". Other options are "Pielou" or "both"
#'
#' @return A scalar (if used "Camargo" or "Pielou") or a numeric vector of length 2
#'     if "both" in evenness argument.
#'
#' @export
#'

EvennessEigen <- function(matrix.M,
                           scale = TRUE,
                           method = "standardize",
                           evenness = "Camargo"){

    if(is.matrix(matrix.M) == FALSE){
        matrix.M<- as.matrix(matrix.M)
        if(ncol(matrix.M)<3){
            stop("\n matrix M must be at least 3 components of diversity\n")
        }
        if(nrow(matrix.M)<3){
            stop("\n Matrix M must be at least 3 communities\n")
        }
    }
    matrix.M.stand <- vegan::decostand(x = matrix.M, method = method, MARGIN = 2)[1:nrow(matrix.M),]
    if(scale==TRUE){
        eingen.obs.stand <- (summary(stats::prcomp(x = matrix.M.stand, scale. = FALSE))$sdev)^2
        eveness.obs.camargo<- camargo.eveness(n_spec= as.vector(eingen.obs.stand))
        eveness.obs.pielou<- pielou.evenness(x = eingen.obs.stand)
        both_evenness<- list(Camargo= eveness.obs.camargo, Pielou= eveness.obs.pielou)
        if(evenness=="Camargo"){
            return(eveness.obs.camargo)
        }
        if(evenness=="Pielou") {
            return(eveness.obs.pielou)
        }
        if(evenness=="both"){
            return(both_evenness)
        }
    }
    if(scale==FALSE){
        eingen.obs<- (summary(stats::prcomp(x = matrix.M, scale. = FALSE))$sdev)^2
        eveness.obs.camargo<- camargo.eveness(n_spec= as.vector(eingen.obs))
        eveness.obs.pielou<- pielou.evenness(x = eingen.obs)
        both_evenness<- list(Camargo= eveness.obs.camargo, Pielou= eveness.obs.pielou)
        if(evenness=="Camargo"){
            return(eveness.obs.camargo)
        }
        if(evenness=="Pielou") {
            return(eveness.obs.pielou)
        }
        if(evenness=="both"){
            return(both_evenness)
        }
    }
}