Reddit reviews Modeling Infectious Diseases in Humans and Animals

I didn't look at the code because I don't know perl, but I can offer some advice for the future. I work at a research group that collaborates with local and international governments on modelling various epidemics as a mathematician. I'm not bragging but letting you know my credentials and experience.


I mainly use MATLAB. Why? Everything is extremely well documented and well developed. The user interface is simple and the language is not so complicated either. There is also a very big, welcoming community which is extremely important. Don't know how to do something in MATLAB? Chances are someone has asked it and someone has answered it, now you don't have to spend hours developing your own solution or, in some cases, never coming up with a solution. It is true it may not be the fastest, but you don't necessarily always want the fastest programming language there is. There is always a trade off and MATLAB excels in other areas where other programming languages don't for this kind of thing. Also, pretty much everyone at the group uses MATLAB.


Use R for data visualization. This is a must. MATLAB has pretty subpar data visualization. Not many programming languages do and I really doubt perl does. From my experience in working with health scientists, doctors and government administrators, they seem to like what R produces the best and this was recommended to me by my supervisor. R is not too hard to learn, in fact I learned in one night how to transfer my output from MATLAB to R and then produce some pretty beautiful graphs.


If you're still learning and would like to learn more, check out Modeling Infectious Diseases in Humans and Animals link. Chapter 2 should be the main chapter for you and try to reproduce results.