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From the Bottom of the Heap by Gavin L. Simpson is, unless otherwise expressly stated, licensed under a Creative Commons Attribution 3.0 Unported License.
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Author Archives: ucfagls
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 … Continue reading
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 … Continue reading
Posted in Plotting, R, vegan
Tagged Biplot, graphics, ordination, PCA, principal components
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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 … Continue reading
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 … Continue reading
Posted in analogue, Palaeoecology, Palaeolimnology, R
Tagged deshrinking, Statistics, transfer function, weighted averaging
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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 … Continue reading
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 … Continue reading
Posted in Palaeoecology, Palaeolimnology, R
Tagged data processing, regular expression, sediment core
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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 … Continue reading
Posted in Palaeoecology, Palaeolimnology, R, Science, Time series
Tagged autocorrelation, cross-validation, GCV, LOESS, overfitting
4 Comments
Sometimes I am lost for words…
Following on from yesterday’s momentous announcements from UK Government and RCUK on opening up access to research outputs funded by the British tax payer, John Wiley & Sons Inc. have announced the Geoscience Data Journal in partnership with the Royal Meteorological Society, … Continue reading
Posted in OpenAccess, Science
Tagged CC BY, geoscience data, John Wiley & Sons, Open Access, RCUK, Research Council UK, Royal Meteorological Society, UK Government, Wiley
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Quantitative palaeolimnology: my book chapters are finally out!
Today I received confirmation that the delayed fifth volume in the Developments in Palaeoenvironmental Research series has been published. The book is titled Data Handling and Numerical methods, though it covers more of the latter and, IMHO, is far more interesting than … Continue reading
Posted in analogue, Palaeoecology, Palaeolimnology, R, Science, vegan
Tagged Numerical analysis, Palaeolimnology, Statistics
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Customising vegan’s ordination plots
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 … Continue reading
