R Graphics Parameters -- Rows and Columns

For some reason I always forget the code for setting R's graphics parameters. And, I always need this same line. So, now I shan't forget it.

quartz(type="pdf",file="figure_NUM.pdf")
par(mfrow=c(3,2), cex=1, mar=c(2,2,2,2))
dev.off()

Convert CD tracks to mp3 using ffmpeg

Just a small chunk of code to convert CD tracks (aiff) to mp3 files:

#!/bin/bash
for i in {1..12}
do
  ffmpeg -i ${i}.aiff -f mp3 -acodec libmp3lame -ab 192000 -ar 44100 ${i}.mp3
done

Using color in R graphics

I'm sticking this here because I always forget the simple ways to specify and manipulate color in R graphics:

Earl Glynn put together a very useful presentation, which covers a range of topics on using color in R graphics.

Ruby code to parse and combine text files

I use this ruby code to parse several tab-delimitted text files that contain individual raters' perceptions of a target (in this case a video). The rater id is embedded in the filename. The target video number is also embedded in the filename.

#! /usr/bin/env ruby

out = Dir.glob('*.txt')

# open the file to write to and add the column headers
columns = "group\trater\tmin\tengage\tprepare\tdiverge\tconverge\texecute\tcentralize\tattentive\ttone\tactivation\n" 
File.open("./all_ratings.txt", 'w') { |f| f.write(columns) }

out.each do |filename|
  rater = filename.split('.')[0].split('_')[0]
  group = filename.split('.')[0].split('_')[1]  
 
  # Assign a number for the rater
  case rater.downcase
    when "rater1"
      rater_id = 1
    when "rater2"
      rater_id = 2
    when "rater3"
      rater_id = 3
    when "rater4"
      rater_id = 4
    end
    puts "rater: " + rater + "(#{rater_id})" + " group: " + group

    # Open the file
    f = File.open(filename, "r").read
 
    # Split by lines - This will make sure that the end of line from Mac Classic is \n
    str = f.gsub!(/\r\n?/, "\n").split("\n")
 
    # Identify the line number that starts the data entry for this file by finding a specific expression in the text of the file
 
    linenum = 0
    exp = "- Low marked by sluggishness"
    line = str[linenum]
    puts line
    until line.include?(exp)    
      line = str[linenum] 
      linenum += 1
    end
 
    linenum.upto(linenum+30) do |currentline|
      min = (currentline-linenum)+1
      # add the rater_id and the group_id to the line
      line = group.to_s + "\t" + rater_id.to_s + "\t" + str[currentline] + "\n"
      File.open("./all_ratings.txt", 'a') { |f| f.write(line) }
    end
end

Copy files from incrementally-numbered drives

This code moves through drives (attached via USB) that are numbered incrementally and copies the files on the drives to the local hard disk. I'm using this to more quickly pull the data off of a number of Affectiva Q-Sensors, which I connect to my computer with a USB hub.

#!/bin/bash
for i in {1..20}
do
  # Create the directory
  mkdir "./sensor_data/${i}"
  # Check to see if the volume is mounted
  drive="Q${i}"
  if mount|grep $drive;
  then
    echo "${drive} is mounted"
    # move the files over to the directory
    cp -r /Volumes/${drive}/ ./sensor_data/${i}/
  else
    echo "${drive} is NOT mounted"
  fi
done

Create a filled line graph with R

I used the code below to create a presentation-quality graph of data on how individual's activation level (measured as electrodermal activity) changes over time during a group-based task. (Click on the image to enlarge.)

quartz(width=16,height=8,type="pdf",file="indiv_eda_z.pdf",dpi=600)
par(xpd=TRUE)
par(family="Tahoma", bg="white", mar=c(3,3,3,3), mgp=c(1,1,1))

ylim <- c(-1.5, 1.5)
xlim <- c(-540, 2700)
x <- aggsub$task_time
y <- aggsub$eda_z
ylo <- rep(min(y), length(y))
plot(x,y, type="n", ylim=ylim, axes=FALSE, ylab="Electrodermal Activity", xlab="Time (in minutes)", xlim=xlim, col="dark green")

xpos <- seq(-540, 2700, 180)
lab <- seq(-9, 45, 3)
axis(1, at=xpos, labels=lab, cex =1.5, lwd=.5, lty=3, tck=1, col="dark gray", pos=-1.5, col.axis="dark gray")

ypos <- seq(-1.5, 1.5, .5)
axis(2, at=ypos , labels=ypos, cex =1.5, las=2, tck=1, lwd=.5, lty=3, col="dark gray", pos=-540, col.axis="dark gray")

zerox <- -540:2700
zeroy <- rep(0, length(zerox))
lines(zerox, zeroy, lty=1, lwd=2, col="red")


lines(x,y, lwd=2.5,col="dark green")
xx <- c(x, rev(x))
yy <- c(ylo, rev(y))   
polygon(xx, yy, col="light green", border=FALSE)

sessionstart <- min(x)
taskstart <- 0
taskend <- 1800
recordend <- 1920
sessionend <- max(x)

polygon(c(sessionstart, sessionstart, taskstart, taskstart), c(1.5, min(y), min(y), 1.5), col="#0015FF25", border=FALSE)
text(-270, 1.25, "Pre-Task Survey", col="dark blue")


#polygon(c(taskstart, taskstart, taskend, taskend), c(1.5, min(y), min(y), 1.5), col="#EAFF0025", border=FALSE)
text(900, 1.25, "Group Members Work to Develop Recruitment Video", col="dark green")


polygon(c(taskend, taskend, recordend, recordend), c(1.5, min(y), min(y), 1.5), col="#FA050535", border=FALSE)
text(recordend-(recordend-taskend)/2, 1.25, "Record\nVideo", col="red")


polygon(c(recordend, recordend, sessionend, sessionend), c(1.5, min(y), min(y), 1.5), col="#0015FF25", border=FALSE)
text(sessionend-(sessionend-recordend)/2, 1.25, "Post-Task Survey", col="dark blue")

dev.off()

Create animated graphs with R

I collected some longitudinal data on how group members' electrodermal activity changes over the course of a group task. Displaying the data in motion was helpful for emphasizing a few points, which I won't re-hash here. The size of the bubbles in the graph below correspond to the average amount of variation within groups in the sample.

Click on the GIF file below to see the result, which uses the animation package in R to create a moving graph.

 # Record this as a movie  
 ymin <- -1.5  
 ymax <- 1.5  
 xmin <- -7  
 xmax <- 45  
 aggsub <- agg[agg$min1 >= (xmin+2) & agg$min1 <=xmax,]  
 sessionstart <- xmin  
 taskstart <- 0  
 taskend <- 30  
 recordend <- 32  
 sessionend <- xmax  
 saveMovie({  
   for (i in (xmin+2):xmax) {  
     x <- aggsub[aggsub$min1 >= xmin & aggsub$min1 <=i, c("min1")]  
     y <- aggsub[aggsub$min1 >= xmin & aggsub$min1 <=i, c("eda_z")]  
     r <- aggsub[aggsub$min1 >= xmin & aggsub$min1 <=i, c("eda_z_sd")]          
     plot(x,y,ylim = c(-1.5,1.5), xlim=c(xmin,xmax),ylab="Electrodermal Activity", xlab="Time", axes=FALSE, type="n")  
     xpos <- seq(xmin, xmax, 3)  
     lab <- seq(xmin, xmax, 3)  
     axis(1, at=xpos, labels=lab, cex =1.5, lwd=.5, lty=3, tck=1, col="dark gray", pos=ymin, col.axis="dark gray")  
     ypos <- seq(ymin, ymax, .5)  
     axis(2, at=ypos , labels=ypos, cex =1.5, las=2, tck=1, lwd=.5, lty=3, col="dark gray", pos=xmin, col.axis="dark gray")  
     zerox <- xmin:xmax  
     zeroy <- rep(0, length(zerox))  
     lines(zerox, zeroy, lty=1, lwd=2, col="red")  
     polygon(c(sessionstart, sessionstart, taskstart, taskstart), c(ymax, ymin, ymin, ymax), col="#0015FF25", border=FALSE)  
     text(taskstart-(taskstart-xmin)/2, 1.35, "Pre-Task Survey", col="dark blue")  
     if(i >= taskstart) {  
       #polygon(c(taskstart, taskstart, taskend, taskend), c(1.5, min(y), min(y), 1.5), col="#EAFF0025", border=FALSE)  
       text(taskend-(taskend-taskstart)/2, 1.35, "Group Members Work to Develop Recruitment Video", col="dark green")  
     }  
     if(i >=taskend) {  
       polygon(c(taskend, taskend, recordend, recordend), c(ymax, ymin, ymin, ymax), col="#FA050535", border=FALSE)  
       text(recordend-(recordend-taskend)/2, 1.35, "Record\nVideo", col="red")  
     }  
     if(i >=recordend) {          
       polygon(c(recordend, recordend, sessionend, sessionend), c(ymax, ymin, ymin, ymax), col="#0015FF25", border=FALSE)  
       text(sessionend-(sessionend-recordend)/2, 1.35, "Post-Task Survey", col="dark blue")  
     }  
     symbols(x, y, circles=r, inches=.5, fg="white", bg="dark blue", add=TRUE)    
     lines(x,y, lwd=1,col="light gray", lty=3)      
     }  
 }, interval=.25, moviename="eda_z_team_full.gif", loop=1, filename="eda_z_team_full", fileext="png", outdir=getwd(), width=1600, height=800)