Articles by ucfagls

Shading regions under a curve

January 11, 2013 | ucfagls

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 → [Read more...]

Monotonic deshrinking in weighted averaging models

January 5, 2013 | ucfagls

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 → [Read more...]

A new version of analogue for a new year

January 4, 2013 | ucfagls

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 → [Read more...]

What’s wrong with LOESS for palaeo data?

July 24, 2012 | ucfagls

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 → [Read more...]

Customising vegan’s ordination plots

April 11, 2012 | ucfagls

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 | ucfagls

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 → [Read more...]

A better way of saving and loading objects in R

April 1, 2012 | ucfagls

Hadley Wickham (@hadleywickham) this week mentioned on Twitter his preference for saveRDS() over the more familiar save(). Being a new function to me, I thought I’d take a look… save() and load() will be familiar to many R users. They … Continue reading → [Read more...]

New version of analogue (0.8-0)

January 12, 2012 | ucfagls

Yesterday I pushed an update of my analogue package to CRAN. The new version is 0.8-0 and contains some new functions, several bug fixes and a major change arising from additions to R 2.14.x requiring all packages to have a … Continue reading → [Read more...]

Generating sets of permutations

October 21, 2011 | ucfagls

In previous posts I discussed how to generate a single permutation from a fully-randomised or restricted permutation design using shuffle(). Here I want to briefly mention the shuffleSet() function and illustrate it’s usage. Every time you call shuffle() it has to interpret the … Continue reading → [Read more...]

Generating restricted permutations with permute

October 18, 2011 | ucfagls

In a previous post I introduced the permute package and the function shuffle(). In that post I got as far as replicating R’s base function sample(). Here I’ll briefly outline how shuffle() can be used to generate restricted permutations. shuffle() … Continue reading → [Read more...]

permute: a package for generating restricted permutations

October 4, 2011 | ucfagls

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 → [Read more...]

Smoothing temporally correlated data

July 21, 2011 | ucfagls

Something I have been doing a lot of work with recently are time series data, to which I have been fitting additive models to describe trends and other features of the data. When modelling temporally dependent data, we often need … Continue reading → [Read more...]

No lake is an island: PhD Opportunity

June 14, 2011 | ucfagls

NERC recently funded the formation of the UK Lake Ecological Observation Network (UKLEON) as part of the its Networks of Sensors programme. UKLEON is lead by Ian Jones at CEH Lancaster. A fully-funded PhD project is associated with the UKLEON … Continue reading → [Read more...]
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