Category Archives: vegan

Decluttering ordination plots in vegan part 2: orditorp()

Posted on January 13, 2013 by

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 →

Posted in Plotting, R, vegan | Tagged , , , | 4 Comments

Decluttering ordination plots in vegan part 1: ordilabel()

Posted on January 12, 2013 by

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 , , , , | 1 Comment

Quantitative palaeolimnology: my book chapters are finally out!

Posted on April 23, 2012 by

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 , ,

Customising vegan’s ordination plots

Posted on April 11, 2012 by

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 →

Posted in R, vegan | Tagged , , , | 45 Comments

Course: Analysing Palaeolimnological Data with R

Posted on April 8, 2012 by

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 →

Posted in Science, R, vegan, analogue, Palaeolimnology, Palaeoecology

permute: a package for generating restricted permutations

Posted on October 4, 2011 by

Multivariate ordination methods are commonly used in ecology to investigate patterns in species composition in space or time. Constrained ordination methods such as redundancy analysis (RDA) and canonical correspondence analysis (CCA) are effectively just multiple regressions, but we lack the … Continue reading →

Posted in permute, R, vegan | Tagged , , , | 4 Comments

What is ordisurf() doing…?

Posted on June 10, 2011 by

I’m writing this post for two reasons: i) someone searched on Google for the term “what is ordisurf doing” and ended up on my blog, and ii) because I have been on the receiving end of reviewers comments on a … Continue reading →

Posted in R, vegan | 6 Comments

Minor update to Vegan (1.17-10)

Posted on June 1, 2011 by

I overlooked blogging about this at the time, but Jari released a minor update to our Vegan package to fix a few issues following release of R 2.13-0. As far as the user is concerned, this mainly affects capscale(). metaMDSrotate(), … Continue reading →

Posted in R, vegan

New version of vegan released to CRAN (1.17-9)

Posted on April 1, 2011 by

Yesterday Jari packaged up the latest release in the current stable branch of the vegan package. Version 1.17-9 of vegan is now on CRAN as a source tarball with binaries for MS Windows and MacOS X to follow soon. New … Continue reading →

Posted in R, vegan

Why I love open source!

Posted on December 3, 2010 by

Today I had a great reminder of why I love open source software and why I spend a bit of my time contributing R code to several packages. In the vegan package, I had included some code to do an … Continue reading →

Posted in R, vegan