R/plot.clme.r

Defines functions plot.summary.clme plot.clme

Documented in plot.clme plot.summary.clme

#' S3 method to plot objects of class \code{clme}
#'
#' @description Generates a basic plot of estimated coefficients which are subject to constraints (\eqn{\theta_1}{theta_1} ). Lines indicate individual constraints (not global tests) and significance.
#' 
#' @inheritParams plot.summary.clme
#' 
#' @note
#' While it is possible to plot the output of a clme fit, this will only plot the fitted means.
#' To indicate significance, plotting must be performed on the summary of a clme fit. This method
#' will change the class so that plot.summary.clme will be called properly.
#' 
#' @seealso
#' \code{\link{CLME-package}}
#' \code{\link{clme}}
#' \code{\link{plot.summary.clme}}
#' 
#' @examples
#' \dontrun{
#'   set.seed( 42 )
#'   data( rat.blood )
#'   cons <- list(order = "simple", decreasing = FALSE, node = 1 )
#'   clme.out <- clme(mcv ~ time + temp + sex + (1|id), data = rat.blood , 
#'                    constraints = cons, seed = 42, nsim = 10)
#'   plot( clme.out )
#' }
#' 
#' @import graphics
#' @export
#' 
plot.clme <- function(x , ...){
  
  if( is.clme(x) ){
    class(x) <- "summary.clme"
  } else{
    stop("'x' is not of class clme")
  }
  
  x$p.value.ind <- rep( 1, length(x$ts.ind) )
  x$p.value     <- rep( 1, length(x$ts.glb) )
  
  # plot(x)
  
  plt_call  <- as.list( environment() )  
  dots      <- as.list(substitute(list(...)))[-1L]
  new_call  <- append( plt_call, dots )
  
  do.call( "plot" , new_call )
   
  
}



#' S3 method to plot objects of class \code{clme}
#'
#' @description Generates a basic plot of estimated coefficients which are subject to constraints (\eqn{\theta_1}{theta_1} ). Lines indicate individual constraints (not global tests) and significance.
#'
#' @param x  object of class 'clme' to be plotted.
#' @param alpha  significance level of the test.
#' @param legendx  character indicating placement of legend. See Details.
#' @param inset  inset distance(s) from the margins as a fraction of the plot region when legend is placed by keyword.
#' @param ci  plot individual confidence intervals. 
#' @param ylim  limits of the y axis.
#' @param cex  size of plotting symbols.
#' @param pch  plotting symbols.
#' @param bg  background (fill) color of the plotting symbols.
#' @param xlab  label of the x axis.
#' @param ylab  label of the y axis.
#' @param tree  logical to produce alternate graph for tree ordering. 
#' @param ...  additional plotting arguments. 
#'
#' @details 
#' All of the individual contrasts in the \code{constraints\$A} matrix are tested and plotted. 
#' The global test is not represented (unless it happens to coincide with an individual contrast). 
#' Only the elements of \eqn{\theta}{theta} which appear in any constraints (e.g. the elements of
#'  \eqn{\theta_{1}}{theta_1}) are plotted. Coefficients for the covariates are not plotted.
#' Solid lines denote no significant difference, while dashed lines denote statistical significance.
#'  Significance is determined by the individual p-value being less than or equal to the supplied 
#'  \eqn{\alpha}{alpha} threshold. By default a legend denoting the meaning of solid and dashed lines
#'   will be placed below the graph. Argument \code{legendx} may be set to a legend keyword (e.g. 
#'   \code{legend=''bottomright''}) to place it inside the graph at the specified location. Setting
#'    \code{legendx} to \code{FALSE} or to a non-supported keyword suppresses the legend.
#' Confidence intervals for the coefficients may be plotted. They are individual confidence intervals,
#'  and are computed using the covariance matrix of the unconstrained estimates of 
#'  \eqn{\theta_{1}}{theta_1}. These confidence intervals have higher coverage probability than the 
#'  nominal value, and as such may appear to be in conflict with the significance tests. Alternate
#'   forms of confidence intervals may be provided in future updates.#'
#' 
#' @seealso
#' \code{\link{CLME-package}}
#' \code{\link{clme}}
#' 
#' @examples
#' \dontrun{
#'   set.seed( 42 )
#'   data( rat.blood )
#'   cons <- list(order = "simple", decreasing = FALSE, node = 1 )
#'   clme.out <- clme(mcv ~ time + temp + sex + (1|id), data = rat.blood , 
#'                    constraints = cons, seed = 42, nsim = 10)
#'   clme.out2 <- summary( clme.out )
#'   plot( clme.out2 )
#' }
#' 
#' 
#' @import graphics
#' 
#' @export
#' 
plot.summary.clme <- 
  function(x , alpha=0.05 , legendx="below" , inset=0.01,
           ci=FALSE , ylim=NULL , cex=1.75 , pch=21 , bg="white" , 
           xlab = expression( paste( "Component of " , theta[1] ) ),
           ylab = expression( paste( "Estimated Value of " , theta[1] ) ) , 
           tree=NULL, ...){
  
  object <- x
  
  #if( !is.clme(object) ){ stop("Argument 'object' is not of class clme.") }
  class(object) <- "clme"


  theta <- fixef(object)
  A     <- object$constraints$A
  r     <- nrow(A)
  p1    <- max(A)
  
  all_pair <- object$all_pair
  
  if( ci ){ 
    ci.wd <- min( 1/p1 , 1/15 ) 
    CIs <- confint(object, level=(1-alpha))
  }
  
  if( legendx=="below" ){
    layout( rbind(1,2) , heights=c(7,1) )
  }
  
  theta1 <- object$theta[1:p1]
  
    # Pick some reasonable plot limits
    if( is.null(ylim) ){
      if( ci ){
        ylim <- c( min(CIs[1:p1,]) , max(CIs[1:p1,]))
      } else{
        if( min(theta1) < 0 ){ 
          ymin <- min(theta1)*1.05 
        } else{
          ymin <- min(theta1)/1.05
        }
        if( max(theta1) < 0 ){ 
          ymax <- max(theta1)/1.05
        } else{
          ymax <- max(theta1)*1.05
        }
        ylim <- c( ymin , ymax )
      }
    }
    
    if( is.null(tree) ){
      tree <- object$order$order == "simple.tree"      
    }
    
    
    ## PLOT FOR SIMPLE / UMBRELLA ORDERS
    if( !tree ){
      # The initial plot of the points
      plot( 1:p1 , theta1 , cex=cex , pch=pch , bg=bg ,
          ylim = ylim , xaxt='n' , xlab = xlab , ylab = ylab, ...)
      
      axis(side=1, at=1:p1, labels=names(theta1), ...)
  
      # Connect the contrasts with solid/dashed lines
      if( all_pair==FALSE  ){
        for( ii in 1:r){  
          idx <- A[ii,]
          if( object$p.value.ind[ii]  > alpha ){ lty <- 1 }
          if( object$p.value.ind[ii] <= alpha ){ lty <- 2 }
          points( idx , theta[idx] , lty=lty , lwd=2 , type="l")
        }
      }
  
      ## Add the CIs if necessary
      if( ci ){
        for( ii in 1:p1){
          points( c(ii,ii)  , c(CIs[ii,1], CIs[ii,2]) , type="l"  )
          points( c(ii-ci.wd, ii+ci.wd)  , c(CIs[ii,1], CIs[ii,1]) , type="l"  )
          points( c(ii-ci.wd, ii+ci.wd)  , c(CIs[ii,2], CIs[ii,2]) , type="l"  )        
        }    
      }
      
      # Replot the pointsso the circles are filled
      points( 1:p1 , theta[1:p1] , cex=cex , pch=pch , bg=bg )
    }
    
    if( tree ){
      ## PLOT FOR TREE ORDER
      plot(x=1, y=0, col=0, ylim=ylim, xlim=c(0.9,2.1), xlab="", ylab="Estimated Coefficient", xaxt="n")
      axis(side=1, at=c(1,1.78), labels=c("Control (Node)" , "Treatment") )
      node <- object$constraints$node
      
      legend( 0.86, theta1[node]+0.35, names(theta1)[node] ,cex=.8, bty='n' ) 
      
      for( ii in (1:p1)[-node] ){
          legend(   1.77    , theta1[ii]+0.15, names(theta1)[ii] ,cex=.8, bty='n' ) 
          points( c(1,1.78) , theta1[c(node,ii)] , col=1 , type="l" , lwd=2 , lty=(1 + 1*(object$p.value.ind[ii-1] < alpha)) )
          points( c(1,1.78) , theta1[c(node,ii)] , col=1 , cex=1.5 , pch=21 , bg="white" )        
      }
    }
    
    
  ## Put a legend on the plot if requested (if the p-values aren't all =1)  
  if( !identical( object$p.value.ind, rep(1, length(object$p.value.ind)) ) ){
    if( legendx=="below" ){
      safe.mar <- par( no.readonly=TRUE )$mar
      par(mar=c(0, 0, 0, 0) , ...)
      plot.new()
      legend('center','groups', c( paste("p >" , alpha, "  " ) , paste("p <" , alpha, "  " )),
             lty = c(1,2), col=1 , ncol=2 , bty ="o" , ...)
      
      par( mar=safe.mar )
    } else{
      leg.texts <- c("bottom", "bottomleft", "left", "topleft",
                    "top", "topright", "right", "bottomright", "center")
      if( legendx %in% leg.texts){
        legend( legendx , legend=c( paste("p >" , alpha, "  " ) , paste("p <" , alpha, "  " )), 
                lty = c(1,2), col=1 , ncol=1 , bty ="o" , inset=inset , ...)
      }
    }
  }
}
jelsema/CLME documentation built on May 25, 2018, 4:43 a.m.