R Code Examples

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Below is a listing of my R Code. For each entry, I have provided a description, the source code, an example, and if applicable, sample output. The source code and example can be copy and pasted directly into R. To be efficient with space, I collapsed all sections except Description.

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encodeVideo.R (Windows only)

• Description

  This code simplifies the creation of a video in R. It saves a series of images and then invokes the shell to feed the images to a video encoder. It requires the video encoder mencoder. For more, read about it here

• Source Code

  
  # ---------------------------
  # File: encodeVideo.R
  # Author: Shaun Lysen
  # Description: This file takes in a plotting function forLoopPlotFnc and a vector
  # of values iterVals to iterate over in the plotting function.
  
  
  encodeVideo <- function(forLoopPlotFnc, iterVals, play=TRUE, fps=25, numDigitsFileNm=4,
        encodePath="C:\\\"Program Files\"\\eRightSoft\\SUPER\\mencoder\\mencoder.exe",
        playPath="C:\\\"Program Files\"\\eRightSoft\\SUPER\\mencoder\\mplayer.exe") {
  # This function creates a video output for a plotting function.
  # The two main arguments are forLoopPlotFnc, which is a function that creates a
  # plot, and iterVals which is a vector of values to iterate over for the plot.
  # For example, if we were graphing a scatterplot for various correlations, with
  # the forLoopPlotFnc taking in the correlation as its argument, then iterVals
  # will be a vector of all correlations to graph.
  # play is a flag to say whether to play the video after it's finished.
  # fps gives the number of frames per second for the video.
  # !! IMPORTANT !! the encodePath and playPath give the location of the mencoder.exe
  # and mplayer.exe files.  mencoder is required to encode the file.
  # Currently this is just for mpeg4, though mencoder allows many other video formats.
  # The code creates jpgs, merges them into a video and then cleans up after itself.
    
    shell("mkdir videoEncodeFolder")
    setwd("./videoEncodeFolder")
  
    for(i in 1:length(iterVals)) {
      jpeg(paste(getNumberFileName(i, numDigitsFileNm), ".jpg", sep=""))
      forLoopPlotFnc(iterVals[i])
      dev.off()
    }
    
    shell(paste(encodePath, " mf://*.jpg -mf fps=", fps, ":type=jpg -ovc lavc -lavcopts vcodec=mpeg4 -o output.avi 1> nul 2>&1", sep=""))
    shell("move output.avi ..")
    shell("del *.jpg")
    setwd("..")
    shell("rmdir videoEncodeFolder")
  
    if(play) {
      shell(paste(playPath, "output.avi 1> nul 2>%1"))
    }
  
  }
  
  getNumberFileName <- function(number, numDigits=4) {
  # This function creates a string with leading 0s for file names.
  # This is important because otherwise pic2.jpg comes after pic11.jpg alphabetically.
  # If we enforce 4 digits, these become pic0002.jpg and pic0011.jpg and they are
  # sorted properly.
    if(number > 10^(numDigits))
      stop("Not enough Digits for file name")
    if(number <= 0)
      stop("File number must be positive")
    number <- as.integer(number)
  
    numNonZero <- as.integer(log10(number))
    numZero <- numDigits - numNonZero - 1  
    
    fileNumString <- paste(c(rep("0", numZero), number), sep="", collapse="")
  
    return(fileNumString)
  }
  

• Example

  
  # Set up the initial data
  datax <- rnorm(100)
  dataz <- resid(lm(rnorm(100)~datax))
  datax <- (datax-mean(datax))/sd(datax)
  dataz <- (dataz - mean(dataz))/sd(dataz)
  
  plotxycor <- function(corr) {
  # Plotting function for the for loop
    r <- corr
  
    xlim <- c(-3.5,3.5)
    ylim <- c(-3.5,3.5)
    slope <- 2*(r>=0) - 1
    x <- datax
    y <- r*datax+sqrt(1-r^2)*dataz
  
    plot(x, y, xlim=xlim, ylim=ylim, pch=19, cex=1, col="blue",
         main=paste("r = ", round(r, 4), "\n"))
    abline(lm(y~x), col="red", lwd=2)
    lines(1.5*ellipsePoints(r), col="black", lwd=3, lty=2)
    abline(0, slope, col="green3", lwd=3)
    
  }
  
  ellipsePoints <- function(r, npts=500) {
  # This function adds the ellipse to the plot depending on the given correlation
    pts <- 1:npts/npts*2*pi
    xEll <- sqrt((1+r))*cos(pts)
    yEll <- sqrt((1-r))*sin(pts)
    ellTmp <- cbind(xEll, yEll)
    secAxis <- c(1, -1) 
    coorMat <- cbind(c(1,1), secAxis)
  
    return(ellTmp %*% coorMat)
  }
  
  source("encodeVideo.R")
  corrIter <- c(0:100, 99:-100, -99:0)/100
  
  encodeVideo(plotxycor, corrIter)
  

• Output

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