Blog Archives

Pangaea and R and open palaeo data

December 16, 2016
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Pangaea and R and open palaeo data

For a while now, I’ve been wanting to experiment with rOpenSci’s pangaear package (Chamberlain et al. 2016), which allows you to search, and download data from, the Pangaea, a major data repository for the earth and environmental sciences. Earlier in the year, as a member of the editorial board of Scientific Data, Springer Nature’s open data journal...

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Simultaneous intervals for smooths revisited

December 15, 2016
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Simultaneous intervals for smooths revisited

Eighteen months ago I wrote a post in which I described the use of simulation from the posterior distribution of a fitted GAM to derive simultaneous confidence intervals for the derivatives of a penalised spline. It was a nice post that attracted some interest. It was also wrong. I have no idea what I was thinking when I...

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Rootograms

June 7, 2016
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Rootograms

Assessing the fit of a count regression model is not necessarily a straightforward enterprise; often we just look at residuals, which invariably contain patterns of some form due to the discrete nature of the observations, or we plot observed versus fitted values as a scatter plot. Recently, while perusing the latest statistics offerings on ArXiv I came across Kleiber...

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Harvesting more Canadian climate data

May 24, 2016
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Harvesting more Canadian climate data

A while back I wrote some code to download climate data from Government of Canada’s historical climate/weather data website for one of our students. In May this year (2016) the Government of Canada changed their website a little and the API code that responded to requests had changed URL and some of the GET parameters had also changed....

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A new default plot for multivariate dispersions

April 17, 2016
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A new default plot for multivariate dispersions

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...

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Soap-film smoothers & lake bathymetries

March 27, 2016
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Soap-film smoothers & lake bathymetries

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...

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Additive modelling global temperature time series: revisited

March 25, 2016
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Additive modelling global temperature time series: revisited

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...

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Are some seasons warming more than others?

November 23, 2015
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Are some seasons warming more than others?

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,...

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Climate change and spline interactions

November 21, 2015
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Climate change and spline interactions

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...

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User-friendly scaling

October 8, 2015
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User-friendly scaling

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...

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