Blog Archives

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 … Continue reading →

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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 … Continue reading →

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Shading regions under a curve

January 11, 2013
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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 →

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Monotonic deshrinking in weighted averaging models

January 5, 2013
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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 … Continue reading →

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A new version of analogue for a new year

January 4, 2013
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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 →

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Processing sample labels using regular expressions in R

August 15, 2012
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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 … Continue reading →

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What’s wrong with LOESS for palaeo data?

July 24, 2012
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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 →

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Quantitative palaeolimnology: my book chapters are finally out!

April 23, 2012
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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 →

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Customising vegan’s ordination plots

April 11, 2012
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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 →

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Course: Analysing Palaeolimnological Data with R

April 8, 2012
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Course: Analysing Palaeolimnological Data with R

Update: As of 18 April 2012 the course is now fully subscribed. Should you wish to be placed on a waiting list please contact Steve Juggins. Analysing Palaeolimnological Data with R 16th — 20th August 2012, University Marine Biological Station … Continue reading →

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