After some time brewing on my machines, I’m happy to have released a new version of my permute package for R. This release took quite a while to polish and get right as there was a lot of back-and-forth between vegan and permute as I tried to get the ... [Read more...]

It has been almost a year since the last release of the analogue package. At lot has happened in the intervening period and although I’ve been busy with a new job in a new country and coding on several other R packages, activity on analogue has also progressed a ... [Read more...]

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. ... [Read more...]

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 ... [Read more...]

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(). [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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. [Read more...]

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(). [Read more...]

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 ... [Read more...]

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 ... [Read more...]