R/GammaEntropy.R

In entropart: Entropy Partitioning to Measure Diversity

GammaEntropy <-
function(MC, q = 1, Correction = "Best", Tree = NULL, Normalize = TRUE, Z = NULL, PhyloDetails = FALSE, CheckArguments = TRUE) 
{
  if (CheckArguments) 
    CheckentropartArguments()
  
  if (!is.null(Tree)) {
    # Method <- "HCDT"
    if (is.IntValues(MC$Ns) | Correction=="None") {
      # Integer abundances or no correction: just estimate.
      Entropy <- bcPhyloEntropy(MC$Ns, q, Tree, Normalize, Correction, CheckArguments=FALSE)
    } else {
      # Use the fallback estimation. Calculate sample coverage in each slice of the tree.
      SampleCoverage <- PhyloApply(Tree, Coverage, rowSums(MC$Nsi), CheckArguments=FALSE)$Cuts
      # Only in this case (to be used only by DivPart), return the Phylovalue object instead of its $Total
      PhyloDetails = TRUE
      # $Corrections will be necessary to calculate alpha entropy
      Entropy <- bcPhyloEntropy(MC$Ns, q, Tree, Normalize, Correction, SampleCoverage=SampleCoverage, CheckArguments=FALSE)
    }
  } else {
    if (!is.null(Z)) {
      # Method <- "Similarity-based"
      if (is.IntValues(MC$Ns) | Correction=="None") {
        # Integer abundances or no correction: just estimate.
        Entropy <- bcHqz(MC$Ns, q, Z, Correction, CheckArguments=FALSE)
      } else {
        # Use the fallback estimation
        SampleCoverage <- Coverage(rowSums(MC$Nsi), CheckArguments=FALSE)
        Entropy <- bcHqz(MC$Ns, q, Z, Correction, SampleCoverage=SampleCoverage, CheckArguments=FALSE)
      }
    } else {
      # Method <- "HCDT"
      if (is.IntValues(MC$Ns) | Correction=="None") {
        # Integer abundances or no correction: just estimate.
        Entropy <- bcTsallis(MC$Ns, q, Correction, CheckArguments=FALSE)
      } else {
        # Use the fallback estimation
        SampleCoverage <- Coverage(rowSums(MC$Nsi), CheckArguments=FALSE)
        Entropy <- bcTsallis(MC$Ns, q, Correction, SampleCoverage=SampleCoverage, CheckArguments=FALSE)
      }
    }
  }
  
  # Return either the whole Phylovalue object or just the Total
  if (is.PhyloValue(Entropy) & !PhyloDetails) {
    return(Entropy$Total)
  } else {
    return(Entropy)
  }
}