Publications by ucfagls
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 t...
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Processing sample labels using regular expressions in R
I am often found in possession of palaeo core data where the sample identifiers contain a core code or label plus the sample depth. Often these are things generated by colleagues who have used other software where for one reason or another they don’t want to store the depth information as a separate numeric variable. I also generate such data s...
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A new version of analogue for a new year
Yesterday I rolled up a new version (0.10-0) of analogue, my R package for analysing palaeoecological data. It is now available from CRAN. There were lots of incremental changes to Stratiplot() to improve the quality of the stratigraphic diagrams produced and fix several annoying bugs. Also the definition of the standard error of MAT reconstructi...
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Monotonic deshrinking in weighted averaging models
Weighted averaging regression and calibration is the most widely used method for developing a palaeolimnological transfer function. Such models are used to reconstruct properties of the past lake environment such as pH, total phosphorus, and water temperature with, it has to be said, varying degrees of success and usefulness. In simple weighted a...
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Shading regions under a curve
Over on the Clastic Detritus blog, Brian Romans posted a nice introduction to plotting in R. At the end of his post, Brian mentioned he would like to colour in areas under the data curve corresponding to particular ranges of grain sizes. The comment area on a blog isn’t really amenable to giving a full answer to the problem posed so I gave a fe...
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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, less cluttered ordination diagrams. First up we have ordilabel()....
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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 draws sample or species labels using text where there ...
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