Trying out Sublime Text 3

I've been a huge fan of TextWrangler for years. I use it for all of my coding (including with R), for taking notes during meetings, for taking notes on articles, and more. It's my most frequently used application. But, I'm ready for a change and am going to give Sublime Text 3 a try. It seems very powerful, relatively light, and incredibly extensible. 

I recently installed Sublime Text 3, added Package Control, and installed some R packages to try out. I'll give it a try for the next three weeks and see what I think. It might be time to say farewell to TextWrangler.

Recurrence Quantification Analysis

This page has some wonderful resources for recurrence analysis. One particularly useful resource on this site is the listing of software options for conducting recurrence analysis. After a fair amount of searching, I couldn't find an R package that computed the metrics from a recurrence quantification analysis. The tseriesChaos package provides a function for producing recurrence plots; but, I didn't see anything for quantifying these plots.

After digging through the different software options listed on this site, I tried out and really like the Commandline Recurrence Plots script offered by Norbert Marwan himself.

The script was very easy to setup on my Mac and, by using Rscript it was easy to combine with R code to (a) draw specific chunks of data for different individuals in my dataset; (b) compute and output the recurrence quantification metrics; (c) output the recurrence plot dataset for creating the actual plot; and, (d) producing the plot and creating a dataset of metrics.

I'll clean up, comment, and post the code that I used as soon as I can come up for air.

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