A new default plot for multivariate dispersions tribulations of base graphics programming
17 April 2016 /posted in: R
This weekend, prompted by a pull request from Michael Friendly, I finally got round to improving the
plot method for
betadisper() in the vegan package.
betadisper() is an implementation of Marti Anderson’s Permdisp method, a multivariate analogue of Levene’s test for homogeneity of variances. In improving the default plot and allowing customisation of plot features, I was reminded of how much I dislike programming plot functions that use base graphics. But don’t worry, this isn’t going to degenerate into a ggplot love-in nor a David Robinson-esque dig at Jeff Leek.
10 April 2016 /posted in: Science
It’s fair to say I have gotten a bee1 in my bonnet about how palaeolimnologists handle time. For a group of people for whom time is everything, we sure do a poor job (in general) of dealing with it in when it comes time to analyse our data. In many instances, “poor job” means making no attempt at all to account for the special nature of the time series. LOESS comes in for particular criticism because it is widely used by palaeolimnologists despite not being particularly suited to the task. Why this is so is perhaps due to it’s promotion in influential books, papers, and software. I am far from innocent in this regard having taught LOESS and it’s use for many years on the now-defunct ECRC Numerical Course. Here I want to look at further problems with our use of LOESS, and will argue that we need to resign it to the trash can for all but exploratory analyses. I will begin the case for the prosecution with one of my own transgressions.
an entire hive is perhaps more apt!↩
Soap-film smoothers & lake bathymetries
27 March 2016 /posted in: R
A number of years ago, whilst I was still working at ENSIS, the consultancy arm of the ECRC at UCL, I worked on a project for the (then) Countryside Council for Wales (CCW; now part of Natural Resources Wales). I don’t recall why they were doing this project, but we were tasked with producing a standardised set of bathymetric maps for Welsh lakes. The brief called for the bathymetries to be provided in standard GIS formats. Either CCW’s project manager or the project lead at ENSIS had proposed to use inverse distance weighting (IWD) to smooth the point bathymetric measurements. This probably stemmed from the person that initiatied our bathymetric programme at ENSIS being a GIS wizard, schooled in the ways of ArcGIS. My involvement was mainly data processing of the IDW results. I was however, at the time, also somewhat familiar with the problem of finite area smoothing1 and had read a paper of Simon Wood’s on his then new soap-film smoother (Wood, Bravington, and Hedley 2008). So, as well as writing scripts to process and present the IDW-based bathymetry data in the report, I snuck a task into the work programme that allowed me to investigate using soap-film smoothers for modelling lake bathymetric data. The timing was never great to write up this method (two children and a move to Canada have occurred since the end of this project), so I’ve not done anything with the idea. Until now…
Wood, Simon N, Mark V Bravington, and Sharon L Hedley. 2008. “Soap Film Smoothing.” Journal of the Royal Statistical Society. Series B, Statistical Methodology 70 (5). Blackwell Publishing Ltd: 931–55. doi:http://doi.org/10.1111/j.1467-9868.2008.00665.x.
smoothing over a domain with known boundaries, like a lake↩
Additive modelling global temperature time series: revisited
25 March 2016 /posted in: R
Quite some time ago, back in 2011, I wrote a post that used an additive model to fit a smooth trend to the then-current Hadley Centre/CRU global temperature time series data set. Since then the media and scientific papers have been full of reports of record warm temperatures in the past couple of years, of controversies (imagined) regarding data-changes to suit the hypothesis of human induce global warming, and the brouhaha over whether global warming had stalled; the great global warming hiatus or pause. So it seemed like a good time to revisit that analysis and update it using the latest HadCRUT data.
Better use of transfer functions?
16 December 2015 /posted in: Science
Transfer functions have had a bit of a hard time of late following Steve Juggins (2013) convincing demonstration that 1) secondary gradients can influence your model, and 2) that variation down-core in a secondary variable can induce a signal in the thing being reconstructed. This was followed up by further comment on diatom-TP reconstructions (Juggins et al. 2013), and not to be left out, chironomid transfer functions have come in from some heat, if the last (that I went to) IPS meeting was any indication. In a session at the 2015 Fall Meeting of the AGU, my interest was piqued by Yarrow Axford’s talk using chironomid temperature reconstructions, but not for the reasons you might be thinking.
Juggins, Steve. 2013. “Quantitative Reconstructions in Palaeolimnology: New Paradigm or Sick Science?” Quaternary Science Reviews 64 (0): 20–32. doi:http://doi.org/10.1016/j.quascirev.2012.12.014.
Juggins, Steve, N John Anderson, Joy M Ramstack Hobbs, and Adam J Heathcote. 2013. “Reconstructing Epilimnetic Total Phosphorus Using Diatoms: Statistical and Ecological Constraints.” Journal of Paleolimnology 49 (3). Springer Netherlands: 373–90. doi:http://doi.org/10.1007/s10933-013-9678-x.
AGU Fall Meeting 2015
14 December 2015 /posted in: Science
My poster, Rapid ecological change in lake ecosystems (GC13G-1236) in the Sedimentary records of threshold change (GC13G Moscone South Poster Hall 1340–1800, monday 14th December) describes some of my recent research into methods to analyse palaeoenvironmental time series from sediment cores. Using data from a varved lake, Baldeggersee, Switzerland, I use location scale generalised additive models to simultaneously model the mean (trend) and the variance of a time series of diatom counts. Wavelets were used to investigate further variation in species dynamics during the well-documented history of eutrophication at the lake.
Are some seasons warming more than others?
23 November 2015 /posted in: R
I ended the last post with some pretty plots of air temperature change within and between years in the Central England Temperature series. The elephant in the room1 at the end of that post was is the change in the within year (seasonal) effect over time statistically significant? This is the question I’ll try to answer, or at least show how to answer, now.
well, one of the elephants; I also wasn’t happy with the AR(7) for the residuals↩
Climate change and spline interactions
21 November 2015 /posted in: R
In a series of irregular posts1 I’ve looked at how additive models can be used to fit non-linear models to time series. Up to now I’ve looked at models that included a single non-linear trend, as well as a model that included a within-year (or seasonal) part and a trend part. In this trend plus season model it is important to note that the two terms are purely additive; no matter which January you are predicting for in a long timeseries, the seasonal effect for that month will always be the same. The trend part might shift this seasonal contribution up or down a bit, but all January’s are the same. In this post I want to introduce a different type of spline interaction model that will allow us to relax this additivity assumption and fit a model that allows the seasonal part of the model to change in time along with the trend.
08 October 2015 /posted in: R
Back in the mists of time, whilst programming early versions of Canoco, Cajo ter Braak decided to allow users to specify how species and site ordination scores were scaled relative to one another via a simple numeric coding system. This was fine for the DOS-based software that Canoco was at the time; you entered
2 when prompted and you got species scaling,
-1 got you site or sample scaling and Hill’s scaling or correlation-based scores depending on whether your ordination was a linear or unimodal method. This system persisted; even in the Windows era of Canoco these numeric codes can be found lurking in the
.con files that describe the analysis performed. This use of numeric codes for scaling types was so pervasive that it was logical for Jari Oksanen to include the same system when the first
rda() functions were written and in doing so Jari perpetuated one of the most frustrating things I’ve ever had to deal with as a user and teacher of ordination methods. But, as of last week, my frustration is no more…
ESA's publishing deal with Wiley Notes from ESA Council
11 August 2015 /posted in: Science
One of the big announcements about the society made by ESA in the run up to the annual meeting in Baltimore this week was the news that ESA has chosen to partner with John Wiley & Sons as publisher of the society journals. At the time of the announcement few details about the deal or the process by which this decision was made were available. I was attending the ESA Council as the incoming Chair of the Paleoecology Section where some further details were provided and members of Council were able to ask questions about the deal. These are my notes from that meeting.