Category: teaching (Page 12 of 17)

Odd ratios for the different levels of stomach inflammation.

GM-fed pigs, chance and how research works

2013-06-21 / Luis

Following my post on GM-fed pigs I received several comments, mostly through Twitter. Some people liked having access to an alternative analysis, while others replied with typical anti-GM slogans, completely ignoring that I was posting about the technical side of the paper. This post is not for the slogan crowd (who clearly are not interested in understanding), but for people that would like to know more about how one would evaluate claims from a scientific article. While I refer to the pig paper, most issues apply to any paper that uses statistics.

In general, researchers want to isolate the effect of the treatments under study (diets in this case) from any other extraneous influence. We want control over the experimental conditions, so we can separate the effects of interest from all other issues that could create differences between our experimental units (pigs in this case). What could create ‘noise’ in our results? Animals could have different genetic backgrounds (for example with different parents), they could be exposed to different environmental conditions, they could be treated differently (more kindly or harshly), etc.

Subsetting data

2013-05-07 / Luis

At School we use R across many courses, because students are supposed to use statistics under a variety of contexts. Imagine their disappointment when they pass stats and discovered that R and statistics haven’t gone away!

When students start working with real data sets one of their first stumbling blocks is subsetting data. We have data sets and either they are required to deal with different subsets or there is data cleaning to do. For some reason, many students struggle with what should be a simple task.
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Learning to code in R

2013-04-26 / Luis

It used to be that the one of the first decisions to make when learning to program was between compiled (e.g. C or FORTRAN) and interpreted (e.g. Python) languages. In my opinion these days one would have to be a masochist to learn with a compiled language: the extra compilation time and obscure errors are a killer when learning.

Today the decision would be between using a generic interpreted language (e.g. Python) and an interpreted domain specific language (DSL) like R, MATLAB, etc. While some people prefer generic languages, I’d argue that immediate feedback and easy accomplishment of useful tasks are a great thing when one is learning something for the first time. Continue reading

Gratuitous picture: building blocks for research (Photo: Luis, click to enlarge).

Matrix Algebra Useful for Statistics

2012-12-17 / Luis

I was having a conversation with an acquaintance about courses that were particularly useful in our work. My forestry degree involved completing 50 compulsory + 10 elective^† courses; if I had to choose courses that were influential and/or really useful they would be Operations Research, Economic Evaluation of Projects, Ecology, 3 Calculus and 2 Algebras. Subsequently my PhD was almost entirely research based but I sort of did Matrix Algebra: Dorian lent me his copy of Searle’s Matrix Algebra Useful for Statistics and passed me a pile of assignments that Shayle Searle used to give in his course in Cornell. I completed the assignments on my own pace and then sat a crazy take-home exam for 24 hours.

More sense of random effects

2012-11-17 / Luis

I can’t exactly remember how I arrived to Making sense of random effects, a good post in the Distributed Ecology blog (go over there and read it). Incidentally, my working theory is that I follow Scott Chamberlain (@recology_), who follows Karthik Ram ?(@_inundata) who mentioned Edmund Hart’s (@DistribEcology) post. I liked the discussion, but I thought one could add to the explanation to make it a bit clearer.

The idea is that there are 9 individuals, assessed five times each—once under each of five different levels for a treatment—so we need to include individual as a random effect; after all, it is our experimental unit. The code to generate the data, plot it and fit the model is available in the post, but I redid data generation to make it a bit more R-ish and, dare I say, a tad more elegant: Continue reading