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Mathematics 4MB3/6MB3 at McMaster University


There are several software packages that you must have on your laptop for this course.

Learning R

There will a very brief introduction to R in class. You are strongly encouraged to use DataCamp to learn R more systematically. Math 4MB is registered with DataCamp so, during the course, you are free to explore all their instructional resources without having to pay a fee. If you are unfamiliar with R, the best way to start is probably by taking 4 hours to work through DataCamp’s Introduction to R.

A note about running workstation software remotely for Math & Stats graduate students

If you don’t have the above applications installed on your laptop or home computer, you can connect to your desktop linux workstation and run them remotely. This is much easier if you have a Mac or linux computer, but it can still be done for Windows computers. See Running Server and Workstation Applications Remotely on the Math & Stats Computing Resources web site.

XPPAUT for numerical analysis of dynamical systems

XPPAUT is a powerful program for exploration and bifurcation analysis of dynamical systems. It is already installed on all of the linux workstations in the math department (which you can login to remotely , as well as from the console). More importantly, it is open-source free software, which can be downloaded and installed on any computer.

There are many online resources available for XPPAUT:

See Using XPPAUT on a Mac for help with installing and using XPPAUT under OS X.

Note that XPPAUT does not incorporate the latest version of AUTO, which continues to be developed on its own. However, AUTO is much harder to use directly than via XPPAUT. If you do want to use AUTO directly then you can find the latest version to download via the main AUTO web page.

XPPAUT has limited graphical capabilities, but it is always possible to save output data to a file and use R to create professional graphics.

Installation & Configuration Notes for XPP


Mac OS X

Testing your installation of XPPAUT

After installing XPPAUT, you should be able to explore the SIR model using [[Media:SIR.ode|this XPPAUT sample .ode file]]. To get started put SIR.ode in the folder where you want to work and (assuming you’re working from the command line) type

  xppaut SIR.ode

then click the phaseflow button and hit RETURN. You should then see a sensible phase portrait. If you’re not working from the command line then start XPPAUT and load SIR.ode.


R is an open-source programming language that you can download and install on any computer (it is installed already on all the grad student workstations in the math department). Installing R gives you the language interpreter and a simple interactive shell.

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.


The standard system for mathematical typesetting. You must use it for your assignments, final project and presentations.

There are several distributions of TeX but TeXLive has the advantage of having both Windows and OS X versions and including good TeX/LaTeX editors (TeX is a typesetting program and does not itself include an editor).

Installation & Configuration Notes for LaTeX




Emacs is a very powerful editor and can be used for - among other things - R, LaTeX. The learning curve is a little bit steep, but the payoff comes in efficiency. Use is optional but encouraged.

Installation & Configuration Notes for Emacs



Aquamacs ( is a good graphical version of Emacs for OS X, but you can just also run the command emacs from a Terminal or XQuartz window.

Spell-checkers and word counters that understand LaTeX

There are a number of spell-checkers that understand LaTeX, for example:

The unix wc command can be used to count words in a plain text file. To use it, you first need to remove the TeX macros from your file. You can then pipe the output into wc. For example, from the terminal window on a Mac you can type

  detex filename | wc

where you need to insert the filename of the file in question.

If you have a Mac, the texcount command is much more helpful than the above. The command line syntax is

  texcount filename

after which helpful information is spewed on your screen.

Tools for online collaboration on documents and code



Main page for this course