R/output.Ico.R

In MicroWeaR/MicroWeaR: Tool to Examine and Score Microwear Scars in a Semi-Automatic Way

#' output.Ico
#'
#' Print a summary statistics table reporting the number of pits and scratches (and the size of any sub-category).
#' @param big_matrix matrix: a matrix with stored coordinates (4) of the sampled marks (coordinates 1 and 2 for the lenght; coordinates 3 and 4 for the width)
#' @param Type character: a character vector
#' @param cross_paral matrix: output of the cross.parallel function
#' @param w.area output of Warea.Ico
#' @return output_1 numeric: matrix with sampled marks count and classification
#' @author Antonio Profico, Flavia Strani, Pasquale Raia, Daniel DeMiguel
#' @examples
#' \dontrun{
#' # A. brevirostris case-study
#' #load sampled scars
#' data("A_br_sam")
#' #load working area
#' data("A_br_war")
#' class<-autom_class(A_br_sam,A_br_war$image)
#' criss_cross<-cross.parallel(A_br_sam,A_br_war$image,class$Type)
#' output.Ico(A_br_sam,class$Type,criss_cross,A_br_war)
#' # C. elaphus eostephanoceros case-study
#' #load sampled scars
#' data("C_el_sam")
#' #load working area
#' data("C_el_war")
#' class<-autom_class(C_el_sam,C_el_war$image)
#' criss_cross<-cross.parallel(C_el_sam,C_el_war$image,class$Type)
#' output.Ico(C_el_sam,class$Type,criss_cross,C_el_war)
#' }
#' @export

 output.Ico<-function(big_matrix,Type,cross_paral,w.area){
  surf=((w.area$work_area[[3]]-w.area$work_area[[1]])^2)/10^6
  vett_1_temp<-NULL
  vett_2_temp<-NULL
  for(i in 1:length(big_matrix)){
    vett_1_temp[i]<-sqrt(sum(big_matrix[[i]][1,]-big_matrix[[i]][2,])^2)
    vett_2_temp[i]<-sqrt(sum(big_matrix[[i]][3,]-big_matrix[[i]][4,])^2)}

  vett_1<-vett_1_temp
  vett_2<-vett_2_temp
  vett_1[which(vett_2_temp>vett_1_temp)]=vett_2_temp[which(vett_2_temp>vett_1_temp)]
  vett_2[which(vett_2_temp>vett_1_temp)]=vett_1_temp[which(vett_2_temp>vett_1_temp)]
  output_1<-matrix(0,nrow=5,ncol=10)
  colnames(output_1)<-c("N.pits","N.sp","N.lp","N.scratches","N.fs","N.cs","N.Ps","N.Xs","%Ps","%Xs")
  rownames(output_1)<-c("Count","Mean_length","Sd_length","Mean_width","Sd_width")

  output_1[1,2]<-length(which(Type=="Sm.Pit"))
  output_1[2,2]<-mean(vett_1[(which(Type=="Sm.Pit"))])
  output_1[3,2]<-sd(vett_1[(which(Type=="Sm.Pit"))])
  output_1[4,2]<-mean(vett_2[(which(Type=="Sm.Pit"))])
  output_1[5,2]<-sd(vett_2[(which(Type=="Sm.Pit"))])

  output_1[1,3]<-length(which(Type=="Lg.Pit"))
  output_1[2,3]<-mean(vett_1[(which(Type=="Lg.Pit"))])
  output_1[3,3]<-sd(vett_1[(which(Type=="Lg.Pit"))])
  output_1[4,3]<-mean(vett_2[(which(Type=="Lg.Pit"))])
  output_1[5,3]<-sd(vett_2[(which(Type=="Lg.Pit"))])

  output_1[1,1]<-output_1[1,2]+output_1[1,3]
  output_1[2,1]<-mean(vett_1[which(Type%in% c("Lg.Pit","Sm.Pit"))])
  output_1[3,1]<-sd(vett_1[which(Type%in% c("Lg.Pit","Sm.Pit"))])
  output_1[4,1]<-mean(vett_2[which(Type%in% c("Lg.Pit","Sm.Pit"))])
  output_1[5,1]<-sd(vett_2[which(Type%in% c("Lg.Pit","Sm.Pit"))])

  output_1[1,5]<-length(which(Type=="Fi.Scr"))
  output_1[2,5]<-mean(vett_1[(which(Type=="Fi.Scr"))])
  output_1[3,5]<-sd(vett_1[(which(Type=="Fi.Scr"))])
  output_1[4,5]<-mean(vett_2[(which(Type=="Fi.Scr"))])
  output_1[5,5]<-sd(vett_2[(which(Type=="Fi.Scr"))])

  output_1[1,6]<-length(which(Type=="Co.Scr"))
  output_1[2,6]<-mean(vett_1[(which(Type=="Co.Scr"))])
  output_1[3,6]<-sd(vett_1[(which(Type=="Co.Scr"))])
  output_1[4,6]<-mean(vett_2[(which(Type=="Co.Scr"))])
  output_1[5,6]<-sd(vett_2[(which(Type=="Co.Scr"))])

  output_1[1,4]<-output_1[1,5]+output_1[1,6]
  output_1[2,4]<-mean(vett_1[which(Type%in% c("Fi.Scr","Co.Scr"))])
  output_1[3,4]<-sd(vett_1[which(Type%in% c("Fi.Scr","Co.Scr"))])
  output_1[4,4]<-mean(vett_2[which(Type%in% c("Fi.Scr","Co.Scr"))])
  output_1[5,4]<-sd(vett_2[which(Type%in% c("Fi.Scr","Co.Scr"))])

  if(is.null(cross_paral)==FALSE){
    output_1[1,7]<-length(which(cross_paral[,4]=="YES"))
    output_1[1,8]<-length(which(cross_paral[,3]=="YES"))###
  }

  if(is.null(cross_paral)==FALSE){
    output_1[1,9]<-round(length(unique(as.numeric(cross_paral[(which(cross_paral[,4]=="YES")),c(1,2)])))/
                          length(which(Type %in% c("Fi.Scr","Co.Scr"))),3)*100
    output_1[1,10]<-round(length(unique(as.numeric(cross_paral[(which(cross_paral[,3]=="YES")),c(1,2)])))/
                           length(which(Type %in% c("Fi.Scr","Co.Scr"))),3)*100

  }


  print(paste("number of","pits:",output_1[1,1]))
  print(paste("number of","small pits:",output_1[1,2]))
  print(paste("number of","large pits:",output_1[1,3]))
  print(paste("number of","scratches:",output_1[1,4]))
  print(paste("number of","fine scratches:",output_1[1,5]))
  print(paste("number of","coarse scratches:",output_1[1,6]))
  print(paste("percentage of pits =",round(output_1[1,1]/(output_1[1,1]+output_1[1,4])*100,1)))
  print(paste("percentage of scratches =",round(output_1[1,4]/(output_1[1,1]+output_1[1,4])*100,1)))
  print(paste("number of pits/mm2",output_1[1,1]/surf))
  print(paste("number of scratches/mm2",output_1[1,4]/surf))
  return(round(output_1,2))
}