Publications by Gavin L. Simpson
gratia 0.9.0
I am pleased to announce the release of gratia 0.9.0. This release has been over a year in the making and provides many new features as well as a more consistent user experience. Unfortunately, I have had to make a lot of breaking changes; nothing too egregious, but most user-facing functions are affected. This release represents a solid base to mo...
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What is ordisurf() doing…?
I’m writing this post for two reasons: i) someone searched on Google for the term ‘what is ordisurf doing’ and ended up on my blog, and ii) because I have been on the receiving end of reviewers comments on a paper I co-authored where they didn’t know what ordisurf() was doing either! It is hardly surprising that people who don’t know R ...
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Global warming since 1995 ‘now significant’
Updated: 17 July 2011 Yesterday (June 11, 2011) the BBC reported on comments by Prof. Phil Jones, of the Climatic Research Unit (CRU), University of East Anglia (UEA), that the warming experienced by the planet since 1995 was statistically significant. That the trend in the recent data was now significant when last year it was not, was attribut...
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Embedding a time series with time delay in R — Part II
Some months ago, I posted a function that extended the base R function embed() to allow for time delay embedding. Today, David Gonzales alerted me to an inconsistency between embed() and Embed(). The example David used was R> (x <- seq(1,20,3)) [1] 1 4 7 10 13 16 19 R> embed(x, 4) [,1] [,2] [,3] [,4] [1,] 10 7 4 1 [2,] 13 ...
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AGU Fall Meeting Day 2
One of the problems of trying to blog a conference when you are going to session talks and socialising in the evening is keeping up to date with your blogging. Day 2 was a little slower in regard to talks and I was able to pick to some degree. Sarah Hobbie gave a nice presentation on decomposition processes in soils and how reactive nitrogen af...
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Customising vegan’s ordination plots
As a developer on the vegan package for R, one of the most FAQs is how to customise ordination diagrams, usually to colour the sample points according to an external grouping variable. Now, just because we get asked how to do this a lot is not really a reflection on the quality of the plot() methods available in vegan. Ordination diagrams are di...
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What’s wrong with LOESS for palaeo data?
Locally weighted scatterplot smoothing (LOWESS) or local regression (LOESS) is widely used to highlight “signal” in variables from stratigraphic sequences. It is a user-friendly way of fitting a local model that derives its form from the data themselves rather than having to be specified a priori by the user. There are generally two things th...
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Decluttering ordination plots part 3: ordipointlabel()
Previously in this series I looked at first the ordilabel() and then orditorp() functions in the vegan package as means to improve labelling in ordination plots. In this the third in the series I take a look at ordipointlabel(). Numerical optimisation algorithms take a problem, such as the optimal placement of labels on an ordination plot, and f...
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Using Arial in R figures destined for PLOS ONE
Despite the refreshing change that the journal PLOS ONE represents in terms of open access and an refreshing change to the stupidity that is quality/novelty selection by the two or three people that review a paper, it’s submission requirements are far less progressive. Yes they make you jump through a lot of hoops getting your figures and table...
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Time series plots in R
I recently coauthored a couple of papers on trends in environmental data (Curtis & Simpson in press; Monteith et al. in press), which we estimated using GAMs. Both papers included plots like the one shown below wherein we show the estimated trend and associated point-wise 95% confidence interval, plus some other markings. The coloured sections sh...
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