R/niche.overlap.R

In spaa: SPecies Association Analysis

niche.overlap <-
function(mat, method = c("levins","schoener","petraitis","pianka","czech","morisita") ){
    match.arg(method)
    mat <- na.omit(mat)
    result <- rep(NA, ncol(mat)*ncol(mat))
    dim(result) <- c(ncol(mat), ncol(mat))
    rownames(result) <- colnames(mat)
    colnames(result) <- colnames(mat)
    for(i in 1:(ncol(mat)-1)){
       for(j in (i+1):ncol(mat)){
          if(method == "levins"){
            result[j,i] <- niche.overlap.pair(mat[,i],mat[,j], method = "levins")
          }
            else {
                if(method == "schoener"){
                   result[j,i] <- niche.overlap.pair(mat[,i],mat[,j], method = "schoener")
                  } 
                 else{
                     if(method == "petraitis") {
                      result[j,i] <- niche.overlap.pair(mat[,i],mat[,j], method = "petraitis")
                      }
                      else{
                           if(method == "pianka"){
                              result[j,i] <- niche.overlap.pair(mat[,i],mat[,j], method = "pianka")
                            }
                            else{          
                                if(method == "czech"){       
                                    result[j,i] <- niche.overlap.pair(mat[,i],mat[,j], method = "czech")
                                  }
                                  else{          
                                    if(method == "morisita"){    
                                        result[j,i] <- niche.overlap.pair(mat[,i],mat[,j], method = "morisita")
                                       }                              
                                    }
                        
                               }
                           
                      }
                
                 }
            
            }
        
        }
    
    }
    as.dist(result)
}