Publications by ibartomeus
Running motivation #An R amusement
Henry John-Alder told me once that in a marathon, twice as runners cross the line at 2h 59m than at 3h 00m. He pointed out that this anomaly in the distribution of finishers per minute (roughly normal shaped) is due to motivation. I believe that. I am not physically stronger than my friend Lluismo, in fact we are pretty even, but some times one o...
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is.invasive( )
Celebrating that I am contributing to the R-bloggers.com blog aggregator I am going to post a very simple function to check which species (both plants and animals) are considered “invaders” somewhere in the world. Basically the function asks that to the Global Invasive Species Database (GISD). I coded this because a friend of mine aks me pre...
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Who are the pollinators? (with R plot)
I’ve been dreaming on writing a manuscript about who are the pollinators for a while, but it looks I’m not going to have the time soon, so here is an early draft of what the main figure should look like: It’s surprisingly difficult to gather quantitative information on which animals are the main pollinators, and on which aspects of pol...
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Pollination effectiveness landscape
I want to show you a pollination landscape, but this is not a pollinator landscape with flowers and nesting sites, but a plot showing two components of pollination. Quantity and quality. A recent paper by Pedro Jordano (see here for other work on seed dispersal landscapes) inspired me to plot my data that way, which I think is just awesome. I am...
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Happy biRthday
Today is my birthday. It’s also the birthday of a close friend. What an incredible coincidence! Or wait, may be is just expected. One more time R comes into our help, because it has a built-in function to answer our question. Which is the probability of two coincident anniversaries among a group of 17 people? (yes we have a mailing list, so I ...
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Software carpentry
I would never call myself a programmer, but as an ecologists I manage moderately big and complicated datasets, and that require to interact with my computer to get the most of them. I self-taught most of the things I need to do and more or less I succeeded on managing my data (MySQL), write simple functions to analyze it (R) or use other people f...
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Science at the speed of ligth
May be is not going that fast, but at the speed of R at least. And R is pretty quick. This has pros and cons. I think that understanding the drawbacks is key to maximize the good things of speed, so here are a few examples. I have a really awful excel file with a dozen sheets calculating simple diversity indexes and network parameters from my dis...
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Quick and dirty notes on General Linear Mix Models
My datasets tend to have random factors. I try to stick to general models whenever I can to avoid dealing with both random factors and complex error distributions (not always possible). I am compiling some notes here to avoid visiting the same R-forums every time I work in a new project. Those are some notes to self, but may be they are useful to ...
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About Data
I recently did a workshop about data with PhD students. That was great to order my thoughts and put together a lot of good resources. All material used (with lots of links) is available in GitHub: https://github.com/ibartomeus/Data. Topics range from hardcore R code to read, clean and transform data, to discussions about data sharing and reprodu...
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On Functional Diversity metrics
Summary: FD is getting very popular, so I figured that would be good to post not only the code (mostly borrowed) I am using: https://github.com/ibartomeus/fundiv, but also what I learnt of it. This posts assume you have read about FD calculation a bit. I’ve been working with functional diversity (FD) for a couple of years now, and some papers ...
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