R/samEx.R

In Waiguru254/Propcalc: Epidemiology Tabulation Analysis

#' Two Way Tabulation That Excluding the Missing values 
#' @name samEx
#' @param row The factors to be analysed
#' @param  column The groups to be considered 
#' @return  value
#' @export samEx
#' 

  samEx <- function(row, column, decimal=1, percent=c("col","row"), missing = TRUE,sort.group = c(decreasing, 
                                                                                                         "increasing"), cum.percent = !any(is.na(row)),las=0, main = "auto", xlab = "auto", 
                    ylab = "auto", col="auto",  ...) {
        tab <- table(row, column, deparse.level=1,dnn=list(deparse(substitute(row)),deparse(substitute(column)))) 
      # column percent
    cpercent <-tab
    for(i in 1:ncol(tab)) { cpercent[,i] <-paste("",format(round(tab[,i]/colSums(tab)[i]*100, digits=decimal),trim=TRUE),"", sep="")}
    cpercent <- rbind(cpercent, rep("100", ncol(tab)))
    col.1.1 <- cbind(format(c(tab[,1],sum(tab[,1])), trim=TRUE), cpercent[,1])
    for(i in 2:ncol(tab)){
      col.1.1 <- cbind(col.1.1, c(format(tab[,i], trim=TRUE), format(sum(tab[,i]), trim=TRUE)), cpercent[,i])
    }
    cpercent <- col.1.1
    cnames <- character(0)
    for(i in 1:ncol(tab) ){ cnames <- c(cnames, colnames(tab)[i], "%")}
    colnames(cpercent) <- cnames
    rownames(cpercent)[nrow(cpercent)] <- "Total"
    var1 <- deparse(substitute(row))
    if(length(var1)>1){
      string2 <- var1[length(var1)]	
    }else
      if(substring(search()[2],first=1,last=8)!="package:"){
        string2 <-  attr(get(search()[2]), "var.labels")[attr(get(search()[2]), "names")==deparse(substitute(row))]
        if(length(string2)==0){
          string2 <- deparse(substitute(row))
        }
        if(string2==""){
          string2 <- deparse(substitute(row))
        }
      }else{
        string2 <- deparse(substitute(row))
      }
    if(substring(search()[2],first=1,last=8)!="package:"){
      string4 <-  attr(get(search()[2]), "var.labels")[attr(get(search()[2]), "names")==deparse(substitute(column))]
      if(length(string4)==0){
        string4 <- deparse(substitute(column))
      }else{
        if(string4==""){
          string4 <- deparse(substitute(column))
        }
      }
    }else{
      string4 <- deparse(substitute(column))
    }
    
    suppressWarnings(if(percent=="col"){
      cat("Column percent", "\n")
      names(attr(cpercent,"dimnames")) <- c(string2, string4)
      print.table(cpercent, right=TRUE, print.gap=2)
      cat( "\n")})
    
    cpercent <- tab
    for(i in 1:ncol(tab)) {cpercent[,i] <- tab[,i]/colSums(tab)[i]*100}
    returns<- cpercent
  }