R/HistDist-03-10-13.R

In gamlss: Generalized Additive Models for Location Scale and Shape

#---------------------------------------------------------------------------------------
# 2-12-2011 MS: the gamlssML() is tried first before using gamlss(). This should be faster
# gamlss() is used if gamlssML() failed.
# MS+CA Saturday, April 22, 2006 
# last 11-07-07 :... is taken out from barplot 
# last 12-2-10 : ammend to cope with the right frequency for ZIP ans ZAP type distributions
histDist <- function(y, 
                  family = NO, 
                    freq = NULL,
                 density = FALSE,
                   nbins = 10,
                    xlim = NULL, 
                    ylim = NULL,
                    main = NULL,
                    xlab = NULL, 
                    ylab = NULL, 
                    data = NULL,
                col.hist = "gray",
             border.hist = "blue",
                 fg.hist = rainbow(12)[9],
                 line.wd = 2,
                 line.ty = c(1,2), 
                line.col = c(2,3),
                col.main = "blue4", 
                 col.lab = "blue4", 
                col.axis = "blue",
                      ... )
{
             FA <- as.gamlss.family(family)    
          fname <- FA$family[1]
           dfun <- paste("d",fname,sep="")
           lpar <- length(FA$parameters)
       typeDist <- FA$type
    #if (!is.null(data)) {attach(data); on.exit(detach(data))}
         subsY <- substitute(y)
         if (!is.null(data))
         {
           y <- get(deparse(substitute(y)), envir=as.environment(data))
           if ( deparse(substitute(freq))!="NULL") freq <-  get(deparse(substitute(freq)), envir=as.environment(data))
         }
        #    y <- if (!is.null(data)) get(deparse(substitute(y)), envir=as.environment(data)) else y
        #  freq <- if (!is.null(data)&&is.null(freq)) get(deparse(substitute(freq)), envir=as.environment(data)) else freq  
  switch(typeDist, 
     "Continuous"=
           {
         extra <- (max(y,na.rm = TRUE)-min(y, na.rm = TRUE))/5
          xmin <- if (is.null(xlim))  min(y,na.rm = TRUE)-extra else xlim[1]
          xmax <- if (is.null(xlim))  max(y,na.rm = TRUE)+extra else xlim[2]
           # for the possitive distributions start from 0.001  
           if (!FA$y.valid(xmin)) xmin <- 0.001
           if (!FA$y.valid(xmax)) xmax <-0.999 # for the beta      y
                x1 <- seq(xmin,xmax,length=101)
           },
      "Discrete" =
           {
            if (fname %in% .gamlss.bi.list)# if binomial
              {
               if (NCOL(y) == 1) 
                 {
                #  if (is.factor(y))   
                   x1 <- c(0,1)
                   bd <- rep(1, 2)
                  # y1 <- y 
                 }
                else                 
                 {
                 if (any(abs(y - round(y)) > 0.001)) {warning("non-integer counts in a binomial GAMLSS!")}
                 bd <- y[, 1] + y[, 2]
                 y1 <- y[, 1]
                 if (any(y1 < 0 | y1 > bd)) stop("y values must be 0 <= y <= N")
               xmin <- if (is.null(xlim[1]))  
                           {if (all(bd==bd[1])) min(y1, na.rm = TRUE) else 0 }
                       else xlim[1]    
               xmax <- if (is.null(xlim)) 
                           {if (all(bd==bd[1])) max(bd ,na.rm = TRUE) else 1 }
                       else xlim[2]
                 x1 <- seq(xmin,xmax,by=1)
                 }
              }
            else
              { # if other discrete
          xmin <- if (is.null(xlim))  min(y,na.rm = TRUE) else xlim[1]
          xmax <- if (is.null(xlim))  max(y,na.rm = TRUE) else xlim[2]
            x1 <- seq(xmin,xmax,by=1)     
              }
           },
      "Mixed"=
           {
              stop("Mixed distributions are not implemented yet")
           })          
# fit the model  
if (is.null(freq)) 
            {  # no frequencies
                 # if (is.null(data)) 
                    {
                      mod <- try(gamlssML(y,family=fname), silent=TRUE)
                            if (any(class(mod)%in%"try-error")) 
                                { # if gamlssML fails use gamlss
                                  mod <-  try( gamlss(y~1, family=fname,  ...))
                                }
                    }
             }
            else
             { # with frequencies
                     {
                       mod <- try(gamlssML(y, weights=freq, family=fname, ...), silent=TRUE)
                            if (any(class(mod)%in%"try-error")) 
                                { # if gamlssML fails use gamlss
                                  mod <-  try( gamlss(y~1, weights=freq, family=fname,  ...))
                                }
                     }
             } 
mod$call$family <- eval(as.expression(fname)) 
if (mod$method=="BFGS"||mod$method=="nlminb") 
        {
        mod$call$formula <-  subsY
        }   
else  
        {
        mod$call$formula[[2]] <-  subsY
        }   
if (!is.null(data)) mod$call$data <- substitute(data)
           # get the pdf
switch(lpar, 
    "1" =  {
      newcall <- if ((fname %in% .gamlss.bi.list)) 
                    call(dfun,x1, mu = fitted(mod)[1], bd=bd[1] )
                  else   call(dfun,x1, mu = fitted(mod)[1])
           },
    "2" =  {
      newcall <- if ((fname %in% .gamlss.bi.list))
                  {  
      call(dfun,x1, mu = fitted(mod)[1],sigma = fitted(mod,"sigma")[1], bd=bd[1])
                  }  
                  else                            
                  {
      call(dfun,x1, mu = fitted(mod)[1], sigma = fitted(mod,"sigma")[1])  
                  }
                 },
    "3" = {      
      newcall <- if ((fname %in% .gamlss.bi.list))
                  {  
      call(dfun,x1, mu = fitted(mod)[1],sigma = fitted(mod,"sigma")[1],
                                  nu = fitted(mod,"nu")[1], bd=bd[1])
                  }  
                 else 
                  {
                    call(dfun,x1, mu = fitted(mod)[1], 
                                  sigma = fitted(mod,"sigma")[1], 
                                     nu = fitted(mod,"nu")[1])
                  }
                 },
    "4" =  {
      newcall <- if ((fname %in% .gamlss.bi.list))
                  {  
      call(dfun,x1, mu = fitted(mod)[1],
              sigma = fitted(mod,"sigma")[1],
                 nu = fitted(mod,"nu")[1],
                tau = fitted(mod,"tau")[1],
                  bd = bd[1])

                   }  
                 else    
                  {
        call(dfun, x1, mu = fitted(mod)[1], 
                    sigma = fitted(mod,"sigma")[1],
                       nu = fitted(mod,"nu")[1],
                      tau = fitted(mod,"tau")[1])
                         } 
                })
switch(typeDist,  
    "Continuous"=  
              { 
                y1 <- eval(newcall)
                xlim <- c(xmin,xmax)
#===================================================================
#MIKIS functions in version of histDist (incl. the discrete case) 
#truehist(y, xlim = mm, main=main, ...)   #MIKIS OLD function
#lines(x1,y1, col="blue3") #MIKIS OLD function
           #===================================================================
#Poppy's Function -  Date: Friday 21, 2006 at 13:46
#main1 <- paste("Histogram of y-variable and ", sep = "") #main <- paste("Histogram of y and a fitted (GAMLSS family), ", family," distribution to y", sep = "")
#main2 <- paste("the fitted ", FA$family[2]," distribution to y-variable", sep = "") #main <- paste("Histogram of y and a fitted (GAMLSS family), ", family," distribution to y", sep = "")
# main <- c(main1, main2) 
        main <-  if (is.null(main))  
                      paste("The ", deparse(subsY), " and the fitted ", FA$family[1]," distribution", sep = "")
                 else main
if (!is.null(freq)) y <- rep(y,freq) # in case frequencies are used
                 xlab <- if (is.null(xlab)) deparse(subsY) else xlab
                 ylab <- if (is.null(ylab)) paste("f()") else ylab
           truehist(y, xlim = xlim, ylim = ylim, xlab=xlab, ylab=ylab, nbins=nbins,
                main = main, col=col.hist,  lty=3, 
                border= border.hist, fg=fg.hist, col.main = col.main, 
                col.lab = col.lab, col.axis = col.axis)
#Poppy's Function
            lines(x1, y1, col = line.col[1], lwd=line.wd, lty=line.ty[1], 
                  fg = gray(0.7))
if (density==TRUE) 
                 { dens <- density(y)
                  lines(dens$x, dens$y, col=line.col[2], lwd=line.wd, lty=line.ty[2]) 
                 }
#===================================================================
      },
      "Discrete"=
      {  
    if (fname %in% .gamlss.bi.list) # if binomial 
     {                  
      if (all(bd==bd[1]))     # binary + equal bd
          { 
            y1 <- eval(newcall) # find the fitted values 
        tabley <- if (NCOL(y) == 1) table(y) else  table(y[,1])
           dft <- data.frame(tabley)# get the table  
          if (!is.null(freq)) dft[,2] <- freq # replace with frequency
            r <- barplot(dft[,2]/sum(dft[,2]), fg = fg.hist, col=col.hist, axis.lty=1, 
                          border= border.hist, col.axis = col.axis, col.main = col.main, 
                          col.lab = col.lab, ylim=ylim, xlim=xlim, ylab=ylab, 
                          xlab=xlab, main=main)
          yy1 <- y1[ x1%in%dft[[1]]] # this is to make sure that we have as many points as in the bar plot
                        lines(r, yy1, type='h', col = line.col[1],  lwd=line.wd, lty=line.ty[1])  
                        points(r, yy1,  col=line.col[1], pch=21, lwd=2) # extra points  
          }
      else  
          {
          xlim <- c(xmin, xmax)
          main <- paste("proportions of ", deparse(subsY), sepp = "")
          main <-  if (is.null(main))  paste("proportions of ", deparse(subsY), sepp = "")
                    else main
          xlab <- if (is.null(xlab)) deparse(subsY) else xlab
                      ylab <- if (is.null(ylab)) paste("f()") else ylab
                  truehist(y1/bd, xlim = xlim, xlab="proportions", ylab=ylab, ylim=ylim, 
                      nbins=nbins, col="gray", 
                      lty=3, border=border.hist, col.axis = col.axis,col.main = col.main, 
                      col.lab = col.lab, main=main, fg=fg.hist)#P
                      lines( fitted(mod), rep(1,length(fitted(mod))), type="h", 
                               col = line.col, lwd=line.wd,  lty=line.ty[1]  )
                      points(fitted(mod), rep(0, length(fitted(mod))), col = line.col, pch=25)
                      points(fitted(mod),rep(1,length(fitted(mod))),   col=line.col, pch=24)
        }
       }  
  else # count data
      {
            y1 <- eval(newcall) # find the fitted values 
            fy <- if (is.null(freq)) factor(y,levels=x1) else factor(rep(y,freq),levels=x1)
       notresy <- if (is.null(freq)) factor(y) else factor(rep(y,freq))# RR DS Friday, February 12, 2010 at 17:41
           dft <- data.frame(tabley<- xtabs(~fy))# get the table    
#===================================================================
#MIKIS functions in version of histDist (incl. the discrete case)
#r <- barplot(tabley/sum(tabley), col="lightblue",  ...)## rainbow(20))#rainbow(20
#yy1<- y1[ x1%in%dft[[1]]] # this is to make sure that we have as many points as in the bar plot
#lines(r,  yy1, type='h', col="red", lwd=3) # fitted lines 
#points(r, yy1,  col="red", pch=21, lwd=3) # extra points
#===================================================================
#Poppy's Function -  Date: Thursday 20, 2006 at 13:46
# main1 <- paste("Histogram of y-variable and ", sep = "") #main <- paste("Histogram of y and a fitted (GAMLSS family), ", family," distribution to y", sep = "")
# main2 <- paste("the fitted ", FA$family[2]," distribution to y-variable", sep = "") #main <- paste("Histogram of y and a fitted (GAMLSS family), ", family," distribution to y", sep = "")
#  main <- c(main1, main2)
          main <- if (is.null(main))  
                  paste("Barplot of the ", deparse(subsY), " and the fitted ", FA$family[2]," distribution", sep = "")
                  else main 
             r <-  barplot(tabley/ sum(xtabs(~notresy)),  # Friday, February 12, 2010 at 17:41
                                    fg =  fg.hist, col=col.hist, axis.lty=1, 
                                    border=border.hist, col.axis = col.axis,col.main = col.main, 
                                    col.lab = col.lab, main=main, ylim=ylim, ylab=ylab, xlab=xlab ) 
            yy1 <- y1[ x1%in%dft[[1]]] # this is to make sure that we have as many points as in the bar plot
                            lines(r, yy1, type='h', col = line.col[1], lwd=line.wd, 
                                   lty=line.ty[1])  
              points(r, yy1,  col=line.col[1], pch=21, lwd=2) # extra points  
                 }  
              },
        "Mixed"=
              {
              stop("Mixed distributions are not implemented yet")
              }) 
            mod
}