R/filterCoefData.R

In jebyrnes/multifunc: Analysis of Ecological Drivers on Ecosystem Multifunctionality

#' @title filterCoefData
#' @title filterCoefData
#'
#' @description
#' \code{filterCoefData} filters contributions of species
#' to function by sign.
#'
#' @details Takes a matrix of functions and coefficients
#' for species and filters out
#' only the sign of contributions desired.  Typically used by other functions in the package.
#'
#' @author Jarrett Byrnes.
#' @param coefData Matrix of functions and coefficients for which species affect them from \code{getRedundancy}.
#' @param type Are the kinds of effects we're looking at "positive", "negative" or "all".
#'
#' @export
#' @return Returns a filtered matrix.
#'
#' @examples
#' data(all_biodepth)
#' allVars <- qw(biomassY3, root3, N.g.m2, light3, N.Soil, wood3, cotton3)
#'
#' germany <- subset(all_biodepth, all_biodepth$location == "Germany")
#'
#' vars <- whichVars(germany, allVars)
#' species <- relevantSp(germany, 26:ncol(germany))
#'
#' # re-normalize N.Soil so that everything is on the same
#' # sign-scale (e.g. the maximum level of a function is
#' # the "best" function)
#' germany$N.Soil <- -1 * germany$N.Soil + max(germany$N.Soil, na.rm = TRUE)
#'
#' res.list <- lapply(vars, function(x) sAICfun(x, species, germany))
#' names(res.list) <- vars
#'
#' coefs <- getRedundancy(vars, species, germany, output = "coef")
#' stdCoefs <- stdEffects(coefs, germany, vars, species)
#'
#' filterCoefData(stdCoefs)
#'
#'
#' #########
#' # filterCoefData takes a matrix of coefficients
#' # and filters it so that only the positive, negative, or both contributions
#' # are present
#' #########
filterCoefData <- function(coefData, type = "positive") {
  # format the data properly given the type of analysis being done
  neg <- which(coefData < 0, arr.ind = TRUE)
  pos <- which(coefData > 0, arr.ind = TRUE)

  if (type == "positive") apply(neg, 1, function(x) coefData[x[1], x[2]] <<- 0) # ugh, using apply and <<- because nothing else worked
  if (type == "negative") {
    apply(pos, 1, function(x) coefData[x[1], x[2]] <<- 0)
  }
  #  if(type=="all") apply(neg, 1, function(x) coefData[x[1], x[2]]<<-1)

  coefData
}