A list of stuff for my student to look at before getting down to some Sage development

+James Campbell will be working with me this Summer on a project aimed at developing game theoretical stuff in to +Sage Mathematical Software System. James just emailed me asking for a list of stuff he could/should read up on before he starts. I thought more knowledgeable people than me might be able to contribute so I've lazily copied my email to him here: 

------------ email ------------

Code:

- git

- github (do +Daniele Procida's tutorial: https://dont-be-afraid-to-commit.readthedocs.org/en/latest/)

- sage development (tickets, documentation etc... This is something I don't know much about myself so read about it on the Safe site and watch videos on youtube there are a bunch of them)

- cython (http://cython.org/ - watch this intro to Sage lecture by +William Stein: https://www.youtube.com/watch?v=fI4NlMfGHC0 that's the first lecture in a class he's currently giving you also could watch the rest)

- C (to help with cython - you don't necessarily need to be an expert I think)

- markdown (https://www.youtube.com/watch?v=6A5EpqqDOdk)

- Test driven development: (watch all this and you will know what I mean: https://www.youtube.com/playlist?list=PL5859017B018F03F4)

- ssh and *nix (so that you're comfortable to jump on to one of my machines if necessary - depending on time we might also get you to tweak the Cardiff server)

- matplotlib (the python library that Sage uses to plot stuff, good to know it from a python pov so as to be able to get Sage to make it do what we want - we might or might not use this)

- How Sage plots graphs (graph theory graphs like I used for this: http://goo.gl/KHGYk7 - we might or might not need this)

Game Theory:

- Matching games (http://www.vincent-knight.com/teaching/gametheory/matchinggames/)

- Cooperative game theory (http://www.vincent-knight.com/teaching/gametheory/cooperativegames/)

We'll talk about this but 1 of the above (easy to code: 30 minutes of work) will be a gentle appetiser to the 'piece de resistance': normal form games,

- Normal form games (first 6 chapters of http://www.vincent-knight.com/teaching/gametheory/)

- The lrs algorithm (there is an implementation of this written in c that we either want to re-write to get working in Sage so you'll need to understand it or get Sage to talk to it / use it, I know Sage kind of has this as an optional library but I'm not entirely sure how to 'get at it' http://cgm.cs.mcgill.ca/~avis/C/lrs.html)

- Polytopes, you want to be comfortable-ish with the vocabulary around polytopes to be able to understand the lrs algorithm a bit. 

Books:

- In general I'd say don't spend much money on Python books. Like most OSS stuff there's an awesome amount of stuff online. Take a look at: http://pythonbooks.revolunet.com/ (a list of free Python books). There are various exceptions to this rule though.

- With regards to Sage I don't think you need a book for this project (as it's about building stuff for Sage so mainly reading about the development process and watching youtube videos is the way to go), I have a kindle copy of http://goo.gl/q9s9da, it's not bad but really everything is online. If you haven't already take a look at http://sagemath.org/help.html and join the relevant discussion groups on there.

- With regards to Game Theory there's a reading list on my website (all that follow are linked to on there). Webb's book is a gentle introduction, Algorithmic Game Theory is great and more about what you will be looking at. Finally there's a newish book by Maschler which looks really nice but I've not had time to work through it yet. In general my course site should suffice (reading/working through those books could take you years) with regards to what you need to know for game theory and I am certainly not asking you to spend money on a book. If there's a book (GT or code) that you really think would be useful let's talk.

------------

James is a pretty good coder with a good knowledge of a git based workflow already as his first year project (during which he actually learnt to code) has led his group to develop: http://thefightclub.herokuapp.com/ which is also on github (if you've made your way this far, please click on that and waste a minute or 2 of your life).

If there's anything missing from this list please add it to the comments :)

I'm looking forward to this project.

Installing and using Sage just got even easier.

+Sage Mathematical Software System just moved to git!

This is awesome news for a variety of reasons. First of all it's great for development (you can take a look at the github repo here: https://github.com/sagemath/sage. There's a good talk about the git workflow for development by +Volker Braun here: http://www.youtube.com/watch?v=0tejiKN5ctY.

The other great reason why this is awesome is that it just got really easy to use and install Sage.

Here's a short video demonstrating everything I've done below:

If you're familiar with git then you know this but if you're not then you can simply open up a terminal on anything *nix (linux/Mac OS) and type the following:

$ cd ~
$ git clone git://github.com/sagemath/sage.git 

This basically goes to the git repository on github and clones it to a folder called sage in your home directory (if you don't have git installed you'll have to do that first).

Once you've done that you need to 'make' sage:

$ cd ~/sage
$ make

This will take a little while (it goes and gets most of what you need so it's hard to say how long as it depends on your machine) but after that you'll have Sage on your machine. If you're still in the ~/sage directory you can simply type ./sage to start sage.

You'll want to add sage to your path so that you can use it from any directory. In this video I did this by using a bit of a trick but here's I'll do something simpler: create a symbolic link to the sage file in ~/sage directory and place that symbolic link in your path (in /usr/bin/local). To do that type this:

$ ln -s ~/sage/sage /usr/local/bin/sage

Now you can type sage anywhere and you'll get sage up and running.

What's really great about all this is that if and when updates/development happens you can just git pull to get all up to date changes. Based on the +Sage Mathematical Software System post on G+: here: it looks like you can already play around with the develop branch...

Awesome.

Of course if you want the easiest way to use Sage then simply grab an account on +The Sagemath Cloud. I gave a talk last week at the Cardiff Django/Python user group about it and  +William Stein was kind enough to drop in and take some questions: http://www.youtube.com/watch?v=OYVLoTL4xt8 (sound quality isn't always great because I move around a fair bit...)

Setting up bup as my backup system, making it act like a timemachine.

This is one of those: 'writing this post to make sure I remember how I've done this'.

+William Stein posted about bup which he is using to backup +The Sagemath Cloud (if you haven't seen that before make sure you go check it out, here's a video in which I describe it: http://goo.gl/5DtYQq).

bup is a piece of backup software based on git. Here's a talk by +Zoran Zaric explaining it:

The documentation isn't too great for bup, this is the blog post I found the most helpful on it: http://kacper.blog.redpill-linpro.com/archives/tag/bup

the ubuntu man pages are also pretty helpful.

Anyway, here's how I setup bup to work like apple's time machine.

Once bup is installed (super easy following readme instruction on Mac OSX and ubuntu). I run:

$ bup -d pathtochosenharddrive init

By default bup uses the ~/.bup directory for everthing. Using the -d flag tells bup to run whatever command (in the above instance: init)  in a chosen hard drive. If you're happy to backup to your ~ then ignore all instances of -d pathtochosenharddrive in the following. (Note you can also change $BUP_DIR to take care of this, and you'll also need to know the path to your given hard drive).

This initialises a git repository (you only need to do this once really).

I put the following in a script (backup.sh):

bup -d pathtochosenharddrive index -ux /directorytobackup
bup -d pathtochosenharddrive save -n backupname /directorytobackup

The first line indexes the files (the -ux flags are something to do with recursively going through the files: type man bup index to read more). The second line checks the index and then saves all files as required (giving them a name).

To setup this backup script to run every hour I write the following to a txt file (crontab.txt):

0 */1 * * * globalpathtobackupscript/backup.sh

To add this to the cron jobs:

$ crontab crontab.txt

If you type:

$ crontab -l

You should see the the contents of the crontab.txt file now added to the scheduled jobs. The first 0 implies that it'll run at the 0th minute, the */1 means every one hour (so you can easily change this), the other * mean 'every', day, month and day of the week.

The first time you run this it should take a fair while (especially if you're backing up your whole ~) but afterwards it shouldn't take too long at all.

To check what bup has done, run:

$ bup -d pathtochosenharddrive ls

That should return:

backupname/

and/or any other names of backups. If you want to see the actual backup snapshots:

$ bup -d pathtochosenharddrive ls backupname

which will return a list of timestamped snapshots.

This has been working pretty seamlessly for a week for me now and I'm probably going to set it up on my work Mac instead of timemachine.

A very brief and shallow analysis of the funniest jokes.

The Edinburgh Fringe Festival takes place every year and according to Wikipedia "is the world's largest arts festival, with the 2012 event spanning 25 days totalling over 2,695 shows from 47 countries in 279 venues". Every year at the festival there is a competition for the funniest one line joke. The winner for 2013 was this joke by Rob Auton:

"I hear a rumour that Cadbury is bringing out an oriental chocolate bar. Could be a Chinese Wispa"

You can see all the top 10s over the past year here:

• 2013
• 2012
• 2011
• 2010
• 2009

I've spent an hour or so this evening grabbing all the jokes and doing some very basic analysis of them in Python. The full github repo with all the code (and the data set) can be found here.

Shorter jokes are better

The mean length of the jokes are 88 characters and 17 words. Taking a look at the distribution of the word counts we see that quite a large proportion of the jokes have between 10 and 15 words in them even though there are some jokes that are twice as long.

This does not necessarily imply anything but if we take a look at the rank of a joke against the number of words we see (a very slight) trend towards an affirmation of the fact that shorter jokes rank better:

Joking often does not necessarily help

There are certain comedians who has more than 1 joke in the list of top tens (this does not necessarily imply that they were joking at multiple festivals as some comedians had multiple jokes ni the top 10 of a given year). If we look at the mean and minimum (best) rank per number of jokes:

we see that a part from the 1 comedian who has four jokes there does not necessarily seem to be an advantage of joking often...

The words don't seem too important

One final bit of preanalysis done is to look at the words in each joke. Before removing the common words (I use the nltk python library which has a set of common words) the distribution is given below:

Once we remove the common words we get:

A part from the word 'FAT' which appears in 3 jokes I can't say I recognise any words that I'd normally associate with jokes so I don't suppose there's any particular words worth honing in to.

Conclusion

I can't say that I've found anything too amazing here but if anything the python file in the github repo contains the data from the past 5 years so if I (or anyone else) had time I'd take a closer look at some things...

On a technical note, pretty much everything above was done in pure matplotlib and the nltk library is very easy to use. This is all in the github repo...

Why and how: open education resources.

This is the fourth post in a series of posts reflecting on the teaching and learning in a recent course I've taught on SAS and R. This post will be quite different in nature to the previous posts which looked at students choices between SAS and/or R in their assessment:

• Individual course work
• Teaching presentations
• Class test

Here I would like to talk about how I deliver teaching materials (notes, exercises, videos etc) to my students.

All of the teaching materials for the course can be found here: drvinceknight.github.io/MAT013/.

How they got there and why I think it's a great place for them to be will be what I hope to discuss...

A Virtual Learning Environment that was not as good as alternatives.

At +Cardiff University we have a VLE provided that is automatically available to all our students that all lecturers are encouraged to use. So when I started teaching I diligently started using the service but it had various aspects that did not fit well with my workflow (having to upload files on every change, clunky interface that actually seemed optimised for IE and various other things). It was also awkward (at the time, I believe that this has been addressed now) for students to use the environment on smart phones etc...

As an alternative, I setup a very simple website using google sites and would use +Dropbox's public links to link pdfs and other resources for my students. An example of such a delivery is these basic Game Theoretical materials. This gave me great control, I no longer had to mess around with uploading versions of files, every change I made was immediately online and also as the site was pretty simple (links and pdfs) it was easily accessible to students on all platforms (I could also include some YouTube videos).

An immediate consequence of this approach is that my materials are all publicly available online.

To anyone, our students or not. The first thing I did was check with +Paul Harper: the director of the MSc course that I was only teaching on at the time that this was ok. We chatted about it a bit and were both happy to carry on. My main train of thought was that there are far better resources already available online so mine might as well be. (I've subsequently checked with our School's director of learning and teaching and there's no internal regulations against it which is nice to know about +Cardiff University)

There is a huge amount of talk about open access in research (I won't go in to that here) but less so to some extent in teaching. I did find this interesting newspaper article that ponders as to "Why don't more academics use open educational resources?". This offers a good general discussion about open education resources.

I would feel very very humbled if anyone chose to actually use my resources. I'm at the early part of my career and am still learning so I don't think that will happen anytime soon but there is another more important benefit to having my teaching stuff online for everyone.

I always post about any new courses I'm working on, on G+ and am grateful to get a fair bit of feedback from other academics around the world. This in itself gives me a certain level of confidence in front of my students who know that what I'm teaching them is verifiable by anyone in the world. I've often changed a couple of things based on feedback by other academics and I think that's brilliant.

To some extent my teaching resources are not just reviewed by a couple of peers in my university but also by anyone online who might be interested in them.

(It would be great if research worked this way too)

Through G+ (I've posted about how awesome a tool G+ is as an academic personal development tool) I learnt about git and github. If you don't know about git watch this video by +Zoë Blade is very helpful:

After a while I jumped in and starting using it. After a little longer while I found out that you can use github to host a website:

Using this I it is really easy to put together a very basic website that has all the teaching materials. The added benefit is that the materials are now all in a github repo which opens them up even more (using dbox, only the pdf files were in general in view) whereas now everything is (md, tex source files etc...) and theoretically if anyone wanted to they could pull etc...

I'm certainly not the first person to put teaching stuff up on github, (watching people like +Dana Ernst, +Theron Hitchman and various others do it is what made me jump in).

The github repo for my R and SAS course can be found here and here are some other teaching things I have up on github (with the corresponding webpage if I've gotten around to setting it up):

• A game theory course (still a work in progress): site
• A one day intro to OOP workshop: site
• A LaTeX course
• A outreach workshop introducing game theory to high school kids

To finish off here are the various reasons I have for putting my teaching stuff up on github:

• Openness:
  • my students know that this is viewable by everyone which hopefully gives the resources a level of confidence;
  • people on G+ and elsewhere are able to point out improvements and fixes (if and when they have time);
• Access: the sites are really simple (basic html with links) so they can be viewed on more or less anything;
• Ease of use: I don't have to struggle to use whatever system is being used. If it's an option I kind of refuse to use stuff that makes me less efficient (an example of this is our email system: I use gmail). At the moment the system I like is github + git.

I wrote a blog post (which is the most read thing I've ever written - online or offline - I think) showing how to combine various things like tikz, makefiles, +Sage Mathematical Software System etc to automate the process of creating a course site so I'll put a link to that here.

Invitation to play a game

So I've blogged about the two thirds of the average game quite a few times now. The latest pos that is kind of a summary of the other posts can be found here.

This post is however a bit different. I'm teaching a new game theory course next year and am busy preparing that. I'm planning on using various interactive games to help with my teaching. As a result I've been figuring out google's app engine so that I can host some of these games online.

The result of this is that I've put together an online open version of the two thirds of the average game that I'd really appreciate you taking the time to play.

The website is: twothirdsoftheaveragegame.appspot.com/ and it will take you 3 minutes to make a guess (you're welcome to guess a bunch of times, only your last guess will count).

Thanks to +Leanne Smith, +Zoe Prytherch, +Izabela Komenda, +Penny Holborn and +Angelico Fetta for testing it for me. Hopefully the bugs are all gone :)

I'll let this run for a week and pick the winner(s) on the 3rd of May at 1200 GMT. That's a week away. I would really aprpeciate you taking the time to play and can't offer much to the winners a part from being named (if you would like me to) in my blog post I write next week :)

So please do take the take to guess, more details about the game itself can be found at the site:

twothirdsoftheaveragegame.appspot.com/

All the code for the site can be found at this github repo.

Two thirds of the average game

The two thirds of the average game is a great way of introducing game theory to students.

I've used this game on outreach events with +Paul Harper, at conferences with +Louise Orpin (when describing my outreach activities with other academics) and also in my classroom. I've blogged about the results before:

• School kids
• Postgraduate students
• OR 54 conference delegates
• MSc students (Note that one point of this post is to show better graphs than the ones on those posts)

The definition of the game from the wiki page is given here:

"In game theory, Guess 2/3 of the average is a game where several people guess what 2/3 of the average of their guesses will be, and where the numbers are restricted to the real numbers between 0 and 100, inclusive. The winner is the one closest to the 2/3 average."

I run this game once without any instruction. I just explain the rules and let them fill in the form in front of them (contained in this repo).

I then bring up slides discussing how iterated elimination of weakly dominated strategies leaves the "rational" strategy to be that everyone guesses 0.

After this I invite the participants to have a second guess. In general the results are pretty cool as you see the initial shift towards equilibrium. The fact that the winning guess in the second play of the game is in fact not 0 gives an opportunity to discuss irrational behaviour and also what would happen if we played again (and again...).

I've run this game a couple of times now and here's the graph of the histogram showing the results for all guesses I've recorded.

You certainly see that the guesses move after rationalising the strategies. Funnily enough though no one has guessed 100 during the first guess but a couple of people have in the second guess. I assume this is either some students trying to tell me that I'm boring them, trying to help a colleague win or I'm perhaps not doing a great job of explaining things :)

Here's some graphs from the individual events that I've collected data for:

• A talk I gave during a high school revision week:

• An outreach event with the MSI:

• MSc students from the 2012-2013 cohort:

• Academics at a talk on outreach at OR54 (the OR society annual conference):

• The OR society student conference SCOR2012:

• Academic at a talk on outreach at YOR18 (The OR society conference for early career academics):

Despite the low number of participants in some of the events they all show a a similar expected trend: the second guesses are lower. Surprisingly on one occasion the second winning guess was actually 1! This is a very quick move towards the theoretical equilibrium.

These experiments have been done on a much wider scale and in a much more rigorous way than my humble "bits of fun" for example the coursera game theory MOOC collect a bunch of data on this game and there's also a pretty big experiment mentioned in this talk:

Having said that I can't recall if other experiments look at successive guesses following an explanation of rational behaviour...

Github repo

https://github.com/drvinceknight/two_thirds_of_the_average_game

I've put all the code used to analyse a game on github. It's a simple python file that can be pointed at a directory or a file and will produce the graph (using matplotlib) as well as spit out some other information. The data set for all these events (the first graph on this post) is also on there and if anyone would like to add to it please let me know :)

(There's also the handout that I use to get the student answers in the repo)

(If you found your way here because of interests in game theory this previous post of mine listing free OSS software for game theory might be of interest)

Using sed to make sure hyper links refer to the correct format of file when using pandoc

In a previous post (which is by far the most popular thing on this blog which is mainly due I believe to a kind retweet by +John Cook and SciPyTip) I describe the makefiles I use to write large documents containing Tikz diagrams and +Sage Mathematical Software System plots in multiple formats (pdf, html and docx) using markdown and pandoc.

This is a short follow up post to fix one minor thing. In the previous post if you created hyper links in your markdown file (say pointing to another markdown document, which for my purposes was multiple chapters in some teaching notes) then all the formats (pdf, html and docx) would all point to the same format.

Here's a slight modification of the pandocipy_given_file.py script (from the previous post) which will use sed to replace the .md to the relevant format in all links.

#!/usr/bin/env python
from sys import argv
from os import system

e = argv[1][:-3]
print e

system("sed 's/.md/.html/g' %s > tmp" % (e + ".md"))
system("pandoc -s tmp -N -o " + e + ".html --mathjax")
system("sed 's/.md/.docx/g' %s > tmp" % (e + ".md"))
system("pandoc tmp -o " + e + ".docx")
system("sed 's/.md/.pdf/g' %s > tmp" % (e + ".md"))
system("pandoc tmp -N -o " + e + ".pdf --latex-engine=xelatex")
system("rm tmp")

This script creates a temporary file (tmp- this is actually important to make sure that the makefile doesn't think that you're recurrently changing the md files) that sed makes sure has the correct format for each link and pandoc can use to get the required files. For example the sed 's/.md/.html/g' command will replace all instances of ".md" with ".html". If you're not familiar with sed it's a *nix program that allows you to do find and replace in files "easily" (it's still a bit of voodoo to me). The script can be used by simply typing:

python pandocipy_given_file.py file.md

(Which assumes that file.md has all links sending to other md files.)

I use this script in the makefile as I did in the previous post:

md = $(wildcard *.md)
htmls = $(md:%.md=%.html)

all: $(htmls)

%.html: %.md
    ./pandocipy_given_file.py $<
    ../Scripts/generate_website.py

The final line of that file is not relevant to this blog post but it just runs a python script that will generate the website for the course (which is still a work in progress!). That python script doesn't do anything fancy but it goes in to each Chapter document for example and reads the Chapter title which it uses to write the index.html file. All this allows me to modify a given md file and simply run make to update the website file.

If any of this is of interest the github repo is here.

Note that in this particular case the links being "format loyal" is mainly useful for the `html` files to the general audience. The loyal links in pdf and docx format are mainly useful to me as all the paths are relative to my setup. I'm posting this again so that I don't forget it but also in case it's useful to others (you can obviously use sed to replace other things).

Blog/YouTube Channel

I don't post to my blog very often yet I have started making a few more videos on my YouTube channel in one of three categories I guess:

- "Tech" (for want of a better name) how to's (or more exactly how I've figure out how to do stuff which might not be the best way...)
- "Education" (for want of a better name) stuff
- Research presentations

I've decided that I'll also throw those videos on here when I put them together (not too sure why, perhaps the best reason is "why not?"). To get started here are 3 past videos:

- Using GitHub to host a website:

- Simulating a Queue: Basic Discrete Event Simulation

- A game theoretical approach to the EMV ED interface