Extrapolating with B splines and GAMs

03 June 2020 /posted in: R

An issue that often crops up when modelling with generlaized additive models (GAMs), especially with time series or spatial data, is how to extrapolate beyond the range of the data used to train the model? The issue arises because GAMs use splines to learn from the data using basis functions. The splines themselves are built from basis functions that are typically setup in terms of the data used to fit the model. If there are no basis functions beyond the range of the input data, what exactly is being used if we want to extrapolate? A related issue is that of the wiggliness penalty; depending on the type of basis used, the penalty could extend over the entire real line (-∞–∞), or only over the range of the input data. In this post I want to take a practical look the extrapolation behaviour of splines in GAMs fitted with the mgcv package for R. In particular I want to illustrate how flexible the B spline basis is.

Read on »

gratia 0.4.1 released

31 May 2020 /posted in: R

After a slight snafu related to the 1.0.0 release of dplyr, a new version of gratia is out and available on CRAN. This release brings a number of new features, including differences of smooths, partial residuals on partial plots of univariate smooths, and a number of utility functions, while under the hood gratia works for a wider range of models that can be fitted by mgcv.

Read on »

Rendering your README with GitHub Actions

30 April 2020 /posted in: R

There’s one thing that has bugged me for a while about developing R packages. We have all these nice, modern tools we have for tracking our code, producing web sites from the roxygen documentation, an so on. Yet for every code commit I make to the master branch of a package repo, there’s often two or more additional steps I need to take to keep the package README.md and pkgdown site in sync with the code. Don’t get me wrong; it’s amazing that we have these tools available to help users get to grips with our R packages. It’s just that there’s a lot of extra things to remember to do to keep everything up to date. The development of free-to-use services such as Travis CI or Appveyor have been very useful as they can automate many of these repetitive tasks. A more recent newcomer to the field is GitHub Actions. The other day I was grappling with getting a GitHub Actions workflow to render a README.Rmd file to README.md on GitHub, so that I didn’t have to do it locally all the time. After a lot of trial and error, this is how I got it working.

Read on »

What evaluating Discovery Grants for the last three years has taught me

26 February 2020 /posted in: Science

For the last three years I have been a member of NSERC’s Discovery Grant Evaluation Group for Ecology and Evolution (that’s 1503 in NSERC-speak). In that time I’ve evaluated over 130 Discovery Grant submissions, read the same number of Canadian CCVs, and even chaired a few evaluations. This is what I learned, through this process, about writing a successful Discovery Grant.

Read on »

Pivoting tidily

25 October 2019 /posted in: R

One of the fun bits of my job is that I have actual time dedicated to helping colleagues and grad students with statistical or computational problems. Recently I’ve been helping one of our Lab Instructors with some data that from their Plant Physiology Lab course. Whilst I was writing some R code to import the raw data for the lab from an Excel sheet, it occurred to me that this would be a good excuse to look at the new pivot_longer() and pivot_wider() functions from the tidyr package. In this post I show how these new functions facilitate common data processing steps; I was personally surprised how little data wrangling was actually needed in the end to read in the data from the lab.

Read on »

radian: a modern console for R

18 June 2019 /posted in: R

Whenever I’m developing R code or writing data wrangling or analysis scripts for research projects that I work on I use Emacs and its add-on package Emacs Speaks Statistics (ESS). I’ve done so for nigh on a couple of decades now, ever since I switched full time to running Linux as my daily OS. For years this has served me well, though I wouldn’t call myself an Emacs expert; not even close! With a bit of help from some R Core coding standards document I got indentation working how I like it, I learned to contort my fingers in weird and wonderful ways to execute a small set of useful shortcuts, and I even committed some of those shortcuts to memory. More recently, however, my go-to methods for configuring Emacs+ESS were failing; indentation was all over the shop, the smart _ stopped working or didn’t work as it had for over a decade, syntax highlighting of R-related files, like .Rmd was hit and miss, and polymode was just a mystery to me. Configuring Emacs+ESS was becoming much more of a chore, and rather unhelpfully, my problems coincided with my having less and less time to devote to tinkering with my computer setups. Also, fiddling with this stuff just wasn’t fun any more. So, in a fit of pique following one to many reconfiguration sessions of Emacs+ESS, I went in search of some greener grass. During that search I came across radian, a neat, attractive, simple console for working with R.

Read on »

Tibbles, checking examples, & character encodings

22 January 2019 /posted in: R

Recently I’ve been preparing my gratia package for submission to CRAN. During my pre-flight testing I noticed an issue under Windows checking the examples in the package against the reference output I generated on linux. In the latest release of the tibble package, the way tibbles are printed has changed subtly and in a way that leads to cross-platform differences. As I write this, tibbles with more than a set number of rows are printed in a truncated form, showing only the first 10 rows of data. In such cases, a final line is printed with an ellipsis and a note as to how many more rows are in the tibble. It was this ellipsis that was causing the cross-platform issue where differences between the output generated on windows and the reference output were being identified during R CMD check on Windows. If this is causing you an issue, here’s one way to solve the problem.

Read on »

What's wrong with software paper preprints on EarthArXiv?

20 December 2018 /posted in: Science

Via Twitter I recently found out that EarthArXiv, a new preprint server for the geosciences doesn’t accept software paper submissions. Actually, EarthArXiv doesn’t accept quite a few types of publication — some justifiably, like ad hominem attack pieces, others unjustifiably like correspondence or opinion pieces. I find this general stance very odd indeed; commentary, editorial or opinion pieces and software papers are accepted in a large number of the general and specialized journals that serve the geoscience field, so why wouldn’t EarthArxiv want to host these prior to publication of the version of record in one of those journals?

Read on »

Confidence intervals for GLMs

10 December 2018 /posted in: R

You’ve estimated a GLM or a related model (GLMM, GAM, etc.) for your latest paper and, like a good researcher, you want to visualise the model and show the uncertainty in it. In general this is done using confidence intervals with typically 95% converage. If you remember a little bit of theory from your stats classes, you may recall that such an interval can be produced by adding to and subtracting from the fitted values 2 times their standard error. Unfortunately this only really works like this for a linear model. If I had a dollar (even a Canadian one) for every time I’ve seen someone present graphs of estimated abundance of some species where the confidence interval includes negative abundances, I’d be rich! Here, following the rule of “if I’m asked more than once I should write a blog post about it!” I’m going to show a simple way to correctly compute a confidence interval for a GLM or a related model.

Read on »

Introducing gratia

23 October 2018 /posted in: R

I use generalized additive models (GAMs) in my research work. I use them a lot! Simon Wood’s mgcv package is an excellent set of software for specifying, fitting, and visualizing GAMs for very large data sets. Despite recently dabbling with brms, mgcv is still my go-to GAM package. The only down-side to mgcv is that it is not very tidy-aware and the ggplot-verse may as well not exist as far as it is concerned. This in itself is no bad thing, though as someone who uses mgcv a lot but also prefers to do my plotting with ggplot2, this lack of awareness was starting to hurt. So, I started working on something to help bridge the gap between these two separate worlds that I inhabit. The fruit of that labour is gratia, and development has progressed to the stage where I am ready to talk a bit more about it.

gratia is an R package for working with GAMs fitted with gam(), bam() or gamm() from mgcv or gamm4() from the gamm4 package, although functionality for handling the latter is not yet implement. gratia provides functions to replace the base-graphics-based plot.gam() and gam.check() that mgcv provides with ggplot2-based versions. Recent changes have also resulted in gratia being much more tidyverse aware and it now (mostly) returns outputs as tibbles.

In this post I wanted to give a flavour of what is currently possible with gratia and outline what still needs to be implemented.

Read on »