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I ended the last post with some pretty plots of air temperature change within and between years in the Central England Temperature series. The elephant in the room1 at the end of that post was is the change in the within year (seasonal) effect over time statistically significant? This is ... [Read more...]

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In a series of irregular posts1 I’ve looked at how additive models can be used to fit non-linear models to time series. Up to now I’ve looked at models that included a single non-linear trend, as well as a model that included a within-year (or seasonal) part and ... [Read more...]

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Back in the mists of time, whilst programming early versions of Canoco, Cajo ter Braak decided to allow users to specify how species and site ordination scores were scaled relative to one another via a simple numeric coding system. This was fine for the DOS-based software that Canoco was at ... [Read more...]

At the risk of coming across as even more of a curmudgeonly old fart than people already think I am, I really do dislike the current vogue in R that is the pipe family of binary operators; e.g. %__%. Introduced by Hadley Wickham and popularised and advanced via the magrittr ... [Read more...]

On Twitter and elsewhere there has been much wailing and gnashing of teeth for some time over one particular aspect of the R ecosphere: CRAN. I’m not here to argue that everything is peachy — far from it in fact — but I am going to argue that the problems we ... [Read more...]

I was sent an email this week by a vegan user who wanted to draw rarefaction curves using rarecurve() but with different colours for each curve. The solution to this one is quite easy as rarecurve() has argument col so the user could supply the appropriate vector of colours to ... [Read more...]

In December I found myself helping one of our graduate students with a data problem; for one of their thesis chapters they needed a lot of hourly climate data for a handful of stations around Saksatchewan. All of this data was and is available for download from the Government of ... [Read more...]

It has been a long time coming. Vegan now has in-built, native ability to use restricted permutation designs when testing effects in constrained ordinations and in range of other methods. This new-found functionality comes courtesy of Jari (mainly) and my efforts to have vegan permutation routines use the permute package. ... [Read more...]

A couple of week’s ago I packaged up a new release of analogue, which is available from CRAN. Version 0.14-0 is a smaller update than the changes released in 0.12-0 and sees a continuation of the changes to dependencies to have packages in Imports rather than Depends. The main ... [Read more...]

Coenoclines are, according to the Oxford Dictionary of Ecology (Allaby 1998), “gradients of communities (e.g. in a transect from the summit to the base of a hill), reflecting the changing importance, frequency, or other appropriate measure of different species populations”. In much ecological research, and that of related fields, data ... [Read more...]

Last time out I looked at one of the complications of time series modelling with smoothers; you have a non-linear trend which may be statistically significant but it may not be increasing or decreasing everywhere. How do we identify where in the series the data are changing? In that post ... [Read more...]

In previous posts (here and here) I looked at how generalized additive models (GAMs) can be used to model non-linear trends in time series data. In my previous post I extended the modelling approach to deal with seasonal data where we model both the within year (seasonal) and between year (... [Read more...]

In previous posts I have looked at how generalized additive models (GAMs) can be used to model non-linear trends in time series data. At the time a number of readers commented that they were interested in modelling data that had more than just a trend component; how do you model ... [Read more...]

The horseshoe effect is a well known and discussed issue with principal component analysis (PCA) (e.g. Goodall 1954; Swan 1970; Noy-Meir & Austin 1970). Similar geometric artefacts also affect correspondence analysis (CA). In part 1 of this series I looked at the implications of these “artefacts” for the recovery of temporal or single dominant ... [Read more...]

Earlier in this series I looked at the ordilabel() and then the orditorp() functions, and most recently the ordipointlabel() function in the vegan package as means to improve labelling in ordination plots. In this, the fourth and final post in the series I take a look at orditkplot(). If you’... [Read more...]

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...]