R/dynRB_Pn.R

In dynRB: Dynamic Range Boxes

dynRB_Pn <-
function(A=A,steps=201,correlogram=FALSE, row_col = c(2, 2)){
  steps0<-steps
  names(A)[1]<-"Species"
  dims<-ncol(A)-1
  
  if(dims==1){
    
    insects<-levels(factor(A$Species))
    G<-expand.grid(insects,insects)
    names(G)[1:2]<-c("V1","V2")
    for(i in 1:dims){
      G<-cbind(G,data.frame(x=0))
      names(G)[i+2]<-names(A)[i+1]
    }
    plot_data_overlap<-list()
    plot_alpha_grid<-list()
    names_data_V1<-c()
    names_data_V2<-c()
    for(i in 1:nrow(G)){
      S1<-subset(A,A$Species==G$V1[i])[,2:(dims+1)]
      S2<-subset(A,A$Species==G$V2[i])[,2:(dims+1)]
      SH<-A[,2:(dims+1)]
      names_data_V1<-c(names_data_V1,as.character(G$V1[i]))
      names_data_V2<-c(names_data_V2,as.character(G$V2[i]))
      
      EE<-.portionAinB_coordinates_full_dim1(S1,S2,steps=steps0)
      G[i,3:(dims+2)]<-EE$integral_coord
      plot_data_overlap[[i]]<-rbind(EE$integral_coord, EE$plot_data_overlap)
      plot_alpha_grid[[i]]<-EE$alpha_grid
      print(i)
    }
    print(G)
    r<-list(names_data_V1=names_data_V1, names_data_V2=names_data_V2, plot_data_overlap=plot_data_overlap, plot_alpha_grid=plot_alpha_grid, result=G)
    invisible(r)
    
  }else{
    
    insects<-levels(factor(A$Species))
    if(correlogram==TRUE){
      par(mfrow=row_col)
      G<-expand.grid(insects)
      h<-1
      k<-1
      for(i in 1:length(insects)){
        S1<-subset(A,A$Species==G$Var1[i])[,2:(dims+1)]
        M<-cor(S1,use="pairwise.complete.obs")
        corrplot(M, method="color",   
                 type="upper", order="hclust", addCoef.col = "black", 
                 tl.col="black", tl.srt=45,
                 sig.level = 0.01, insig = "blank", diag=FALSE, mai = c("",as.character(G$Var1[i])),mar = c(0,2,0,0))
        if(k/h==row_col[1]*row_col[2]){
          title("Correlogram for each species", outer = T)
          h<-h+1
          readline(prompt = "Press <Enter> to continue...")}
        k<-k+1
      }
      title("Correlogram for each species", outer = T)
    }
    G<-expand.grid(insects,insects)
    names(G)[1:2]<-c("V1","V2")
    for(i in 1:dims){
      G<-cbind(G,data.frame(x=0))
      names(G)[i+2]<-names(A)[i+1]
    }
    plot_data_overlap<-list()
    plot_alpha_grid<-list()
    names_data_V1<-c()
    names_data_V2<-c()
    for(i in 1:nrow(G)){
      S1<-subset(A,A$Species==G$V1[i])[,2:(dims+1)]
      S2<-subset(A,A$Species==G$V2[i])[,2:(dims+1)]
      SH<-A[,2:(dims+1)]
      names_data_V1<-c(names_data_V1,as.character(G$V1[i]))
      names_data_V2<-c(names_data_V2,as.character(G$V2[i]))
      
      EE<-.portionAinB_coordinates_full(S1,S2,steps=steps0)
      G[i,3:(dims+2)]<-EE$integral_coord
      plot_data_overlap[[i]]<-rbind(EE$integral_coord, EE$plot_data_overlap)
      plot_alpha_grid[[i]]<-EE$alpha_grid
      print(i)
    }
    print(G)
    r<-list(names_data_V1=names_data_V1, names_data_V2=names_data_V2, plot_data_overlap=plot_data_overlap, plot_alpha_grid=plot_alpha_grid, result=G)
    invisible(r)
    
  }
  
}