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Monthly Archives: June 2015
Basics of LaTeX and BibTeX for students in mathematical biology/epidemiology
Most journals in the field of mathematical epidemiology/biology require that you submit manuscripts in LaTeX format.
LaTeX is a word processing language, in which you create a document that contains directives to the latex compiler to produce a final document. LaTeX provides many capabilities not available in Word; perhaps most important to mathematicians, LaTeX enables typesetting of complex equations that would be difficult, if not impossible in Word.
In addition, LaTeX has a reference management package called BibTeX that easily enables citation of references within your document.
In this module, we will discuss some simple examples of document formatting in LaTeX, and describe how to include figures and tables in the document, and cite references.
Good work habits towards being a more effective researcher
Over the years I have developed some habits as I work that help to make me more efficient as a researcher. Of students that I’ve seen struggle in their doctoral studies, they are always lacking several of the habits in this list. Of students who excel, they have all (or nearly all of these habits) either because they were mentored in them, or somehow figured it out themselves.
In assigned homework, students will be expected to conform to good coding and plotting practices, and to submit an annotated bibliography in bibtex format if literature searches are required.
Many of these habits overlap with the list of good work habits in jobs in the private sector. Start using these practices now, and reap many benefits as you go along 🙂
MTBI 2015 summer lectures
[In these modules, students will become familiar with basic concepts that will enable them to fit the parameters of a mathematical model, such that the model gives a good description of a data set. Sources of data useful to mathematical epidemiology will be discussed, including online sources of data, and how to extract data sources from the literature using programs like DataThief.
Goodness-of-fit statistics will be discussed, as will computational methods for finding model parameters that optimize the goodness-of-fit statistic. In particular, in the examples we will focus on fitting the parameters of compartmental models of disease dynamics to epidemic data.
In passing along the way, we will discuss how to do literature searches, how to build an annotated bibliography in bibtex, how to come up with a solid research question, how to organize your work, and how to write a good research paper (essentially, many of the skills needed to excel at research!)]
Part I
- Good work habits, and requirements for homework
- Difference between mathematical and statistical modeling
- Where to find sources of data: finding free online data
- Literature searches with Google Scholar
- Where to find sources of data: extracting data from graphs in publications
- Basics of LaTeX and BibTeX
- Simple compartmental modelling in R