Publications by Gavin L. Simpson
New version of analogue on CRAN
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 pace. As the version 0.12-0 of the package hits a CRAN mirror near you, I thought I...
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New version of permute on CRAN
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 latter working nicely for both useRs and developers, whilst Jari worked on using the new permut...
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Decluttering ordination plots part 4: orditkplot()
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’ve created ordination diagrams before or been followi...
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Summarising multivariate palaeoenvironmental data
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 domina...
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Modelling seasonal data with GAMs
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 data collected throughout the year over many years with a GAM? In th...
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Identifying periods of change in time series with GAMs
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 (trend) variation with separate smooth functions. One of t...
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Simultaneous confidence intervals for derivatives of splines in GAMs
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 I explained how we can use the first derivatives of the mod...
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Simulating species abundance data with coenocliner
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 on the...
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analogue 0.14-0 released
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 development of analogue now takes place on github and bugs and featu...
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Analysing a randomised complete block design with vegan
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. Jari also cooked up a st...
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