Blog Archives

Summarising multivariate palaeoenvironmental data

January 9, 2014
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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 dominant gradients from multivariate palaeoecological data....

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Decluttering ordination plots part 4: orditkplot()

December 31, 2013
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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...

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Summarising multivariate palaeoenvironmental data

December 28, 2013
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Summarising multivariate palaeoenvironmental data

Ordination methods that yield orthogonal axes of variation are often used to summarise the multivariate data obtained from sediment cores. Usually the first or, less often, the first few ordination axes are taken as directions of change or the main patterns of variance in the multivariate data. There is an oft-overlooked issue with this approach that has the potential...

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New version of permute on CRAN

December 17, 2013
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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...

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New version of analogue on CRAN

December 14, 2013
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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...

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Time series plots in R

October 23, 2013
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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 show...

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Using Arial in R figures destined for PLOS ONE

September 9, 2013
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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...

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Decluttering ordination plots part 3: ordipointlabel()

June 27, 2013
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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().

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Decluttering ordination plots in vegan part 2: orditorp()

January 13, 2013
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Decluttering ordination plots in vegan part 2: orditorp()

In the earlier post in this series I looked at the ordilabel() function to help tidy up ordination biplots in vegan. An alternative function vegan provides is orditorp(), the last four letters abbreviating the words text or points. That is a pretty good description of what orditorp() does; it...

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Decluttering ordination plots in vegan part 1: ordilabel()

January 12, 2013
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Decluttering ordination plots in vegan part 1: ordilabel()

In an earlier post I showed how to customise ordination diagrams produced by our vegan package for R through use of colours and plotting symbols. In a series of short posts I want to cover some of the options available in vegan that can be used to help in producing better, clearer,...

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