Publications by Luis
R, Julia and the shiny new thing
My head exploded a while ago. Perhaps not my head but my brain was all mushy after working every day of March and first week of April; an explanation—as good as any—for the post hiatus. Back to the post title. It is not a mystery that for a while there have been some underlying unhappiness in the R world. Ross Ihaka and Duncan Temple Long ha...
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R, Julia and genome wide selection
— “You are a pussy” emailed my friend. — “Sensu cat?” I replied. — “No. Sensu chicken” blurbed my now ex-friend. What was this about? He read my post on R, Julia and the shiny new thing, which prompted him to assume that I was the proverbial old dog unwilling (or was it unable?) to learn new tricks. (Incidentally, with friends l...
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Late-April flotsam
It has been month and a half since I compiled a list of statistical/programming internet flotsam and jetsam. Via Lambda The Ultimate: Evaluating the Design of the R Language: Objects and Functions For Data Analysis (PDF). A very detailed evaluation of the design and performance of R. HT: Christophe Lalanne. If you are in statistical genetics and...
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Teaching code, production code, benchmarks and new languages
I’m a bit obsessive with words. May be I should have used learning in the title, rather than teaching code. Or perhaps remembering code. You know? Code where one actually has very clear idea of what is going on; for example, let’s say that we are calculating the average of a bunch of n numbers, we can have a loop that will add up each of them...
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Bivariate linear mixed models using ASReml-R with multiple cores
A while ago I wanted to run a quantitative genetic analysis where the performance of genotypes in each site was considered as a different trait. If you think about it, with 70 sites and thousands of genotypes one is trying to fit a 70×70 additive genetic covariance matrix, which requires 70*69/2 = 2,415 covariance components. Besides requiring h...
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R’s increasing popularity. Should we care?
Some people will say ‘you have to learn R if you want to get a job doing statistics/data science’. I say bullshit, you have to learn statistics and learn to work in a variety of languages if you want to be any good, beyond getting a job today coding in R. R4stats has a recent post discussing the increasing popularity of R against other statis...
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End of May flotsam
The end is near! At least the semester is coming to an end, so students have crazy expectations like getting marks back for assignments, and administrators want to see exam scripts. Sigh! What has been happening meanwhile in Quantum Forest? Tom cracked me up with “…my data is so fucking patchy. I’m zipoissoning the place up like a motherfu...
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Review: “Forest Analytics with R: an introduction”
Forestry is the province of variability. From a spatial point of view this variability ranges from within-tree variation (e.g. modeling wood properties) to billions of trees growing in millions of hectares (e.g. forest inventory). From a temporal point of view we can deal with daily variation in a physiological model to many decades in an empiric...
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Split-plot 1: How does a linear mixed model look like?
I like statistics and I struggle with statistics. Often times I get frustrated when I don’t understand and I really struggled to make sense of Krushke’s Bayesian analysis of a split-plot, particularly because ‘it didn’t look like’ a split-plot to me. Additionally, I have made a few posts discussing linear mixed models using several diff...
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Split-plot 2: let’s throw in some spatial effects
Disappeared for a while collecting frequent flyer points. In the process I ‘discovered’ that I live in the middle of nowhere, as it took me 36 hours to reach my conference destination (Estoril, Portugal) through Christchurch, Sydney, Bangkok, Dubai, Madrid and Lisbon. Where was I? Showing how split-plots look like under the bonnet (hood for y...
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