R/summary.multipatt.r

In miquelcaceres/indicspecies: Relationship Between Species and Groups of Sites

summary.multipatt <- function (object, alpha = 0.05, minstat = NULL, At = NULL, Bt=NULL, indvalcomp=FALSE,...) {
  x <- object
  ncomb = ncol(x$str)
  ncolsign = ncol(x$sign)
  nsps = nrow(x$sign)
  cat("\n Multilevel pattern analysis")
  cat("\n ---------------------------\n")
  cat("\n Association function:", x$func)
  cat("\n Significance level (alpha):", alpha)
  if(!is.null(minstat)) cat("\n Minimum statistic value (minstat):", minstat)
  if(x$func=="IndVal" || x$func=="IndVal.g") {
    if(!is.null(At)) cat("\n Minimum positive predictive value (At):", At)
    if(!is.null(Bt)) cat("\n Minimum sensitivity (Bt):", Bt)
  }
  cat("\n\n Total number of species:", nsps)
  sel = !is.na(x$sign$p.value) & x$sign$p.value <= alpha
  if(!is.null(minstat)) sel = sel & (x$sign$stat >= minstat)
  if(!is.null(Bt) && !is.null(x$B)) {
    for(i in 1:nrow(x$sign)) sel[i] = sel[i] && (x$B[i,x$sign$index[i]]>=Bt)
  }
  if(!is.null(At) && !is.null(x$A)) {
    for(i in 1:nrow(x$sign)) sel[i] = sel[i] && (x$A[i,x$sign$index[i]]>=At)
  }
  a = x$sign[sel, ] #Selected matrix
  cat("\n Selected number of species:", nrow(a), "\n")
  cols = (ncolsign - 1):ncolsign
  
  #Collate indval components if required and possible
  if(indvalcomp && !is.null(x$B) && !is.null(x$A)) {
    As = numeric(nrow(x$sign))
    Bs = numeric(nrow(x$sign))
    for(i in 1:nrow(x$sign)) {
      As[i] = x$A[i,x$sign$index[i]]
      Bs[i] = x$B[i,x$sign$index[i]]
    }
    y = cbind(x$sign, As,Bs)
    cols = c(ncol(y)-1, ncol(y),cols)
    names(y) = c(names(x$sign),"A","B")
  }
  else y = x$sign
  
  
  #Show the number of species associated to each level
  for (k in 1:(ncolsign - 4)) {
    cat(" Number of species associated to", k, if(k==1) "group:" else "groups:", sum(rowSums(a[, 1:(ncolsign-3)]) == k), "\n")
  }
  
  cat("\n List of species associated to each combination: \n")
  
  #Show indicators for all combinations  
  for (i in 1:ncomb) {
    sel = x$sign$index == i & !is.na(x$sign$p.value) & x$sign$p.value <= alpha
    if(!is.null(minstat)) sel = sel & (x$sign$stat >= minstat)
    if(!is.null(Bt) && !is.null(x$B)) {
      for(j in 1:nrow(x$sign)) sel[j] = sel[j] && (x$B[j,x$sign$index[j]]>=Bt)
    }
    if(!is.null(At) && !is.null(x$A)) {
      for(j in 1:nrow(x$sign)) sel[j] = sel[j] && (x$A[j,x$sign$index[j]]>=At)
    }
    m = y[sel, ]
    if (nrow(m) > 0) {
      cat("\n Group", colnames(x$comb)[i], " #sps. ", nrow(m), "\n")
      m = m[order(m$stat, decreasing = TRUE), cols]
      printCoefmat(m, signif.stars = TRUE, signif.legend = FALSE, 
                   digits = 4, P.values = TRUE, has.Pvalue = TRUE)
    }
  }
  Signif <- symnum(x$sign$p.value, corr = FALSE, na = FALSE, 
                   cutpoints = c(0, 0.001, 0.01, 0.05, 0.1, 1), symbols = c("***", "**", "*", ".", " "))
  cat("---\nSignif. codes: ", attr(Signif, "legend"), "\n")
}