Tag Archives: R package

Issue 10.12: Statistical Ecology, UAVs, Invasive Species and More

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The December issue of Methods is now online!

The final 2019 issue of Methods in Ecology and Evolution is online now.

To close out another brilliant year, we’ve got papers on invasive species, convolutional neural networks, rapid spatial risk modelling, species distribution models and much more.

You can find out more about our Featured Articles (selected by the Senior Editor) below. We also discuss this month’s Open Access and freely available papers we’ve published in our latest issue (Practical Tools and Applications articles are always free to access, whether you have a subscription or not) .

Continue reading →

‘Tis the Season for Modelling Mortalities

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Post provided by ELIE GURARIE

A warning: Halloween is nigh, and the following post contains graphic real-life imagery of maggot-eaten eye-sockets and deadly pianos. Read on… if you dare!

A Death in the Woods 

In the vast and often frozen boreal forest of northern Canada there is a slow-burning forensic investigation into a death. The victim: a woodland caribou, an iconic species that is threatened or endangered throughout its range.

Kyle Joly

The scene is very much made for TV neo-Scandinavian neo-noir. From a not-too-luxurious regional office in the town of Fort Smith, just north of the Alberta border, over a steaming cup of coffee, world-weary biologist Allicia Kelly – who’s seen it all and then some – is monitoring the movements of collared animals on her computer screen. It’s the middle of May. The females, nearly all pregnant, are scattering to higher ground to find suitably cozy and secluded sites to calve. All is as peaceful and idyllic as a bunch of blips on a computer screen can be.

But then (cue slightly unsettling dissonance in the soundtrack) one of the little blips seems to have stopped moving. Kelly raises her eyebrow, tells herself to keep an eye out. A moment later she makes the call: “Team, we’ve got another ringer … let’s roll!” Continue reading →

Meaningful Monitoring or Monitoring for the Sake of Monitoring? epower Helps You Tell the Difference

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Post provided by REBECCA FISHER and GLENN R SHIELL

As environmental managers, we’re frequently asked to make judgements about the relative health of the environment. This is often difficult because, by its nature, the environment is highly variable in space and time. Ideally, such judgements should be informed by robust scientific investigation, or more precisely, the reliable interpretation of the resulting data.

Type I and Type II Errors

Even with robust investigations and good data, our interpretations can sometimes be wrong. In general, this happens when:

  • the investigation concludes that an impact has occurred, when in fact it hasn’t (Type I error)
  • fails to detect an impact, when an impact has actually occurred (Type II error).

Understanding the circumstances that lead to these errors is unfortunately complicated, and difficult unless you have a strong statistical background. Continue reading →

Speeding Up Systematic Reviews: This New Method for Automated Keyword Selection Will Save You Time

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Post provided by ELIZA GRAMES

The number of studies published every year in ecology and evolutionary biology has increased rapidly over the past few decades. Each new study contributes more to what we know about a topic, adding nuance and complexity that helps improve our understanding of the natural world. To make sense of this wealth of evidence and get closer to a complete picture of the world, researchers are increasingly turning to systematic review methods as a way to synthesise this information.

What is a Systematic Review?

Systematic reviews, first developed in public health fields, take an experimental design approach to reviewing the literature. They treat the search for primary studies as a transparent and reproducible data gathering process. The rigorous methods used in systematic reviews make them a trusted form of evidence synthesis. Researchers use them to summarise the state of knowledge on a topic and make policy and practice recommendations. Continue reading →

Introducing fishtree and fishtreeoflife.org

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This post was originally published on Jonathan Chang’s blog.

In our recent publication (Rabosky et al. 2018) we assembled a huge phylogeny of ray-finned fishes: the most comprehensive to date! While all of our data are accessible via Dryad, we felt like we could go the extra mile to make it easy to repurpose and reuse our work. I’m pleased to report that this effort has resulted in two resources for the community: the Fish Tree of Life website, and the fishtree R package. The package is available on CRAN now, and you can install it with:

install.packages("fishtree")

The source is on GitHub in the repository jonchang/fishtree. The manuscript describing these resources has been published in Methods in Ecology and Evolution (Chang et al. 2019).

Continue reading →

Spatial Cross-Validation of Species Distribution Models in R: Introducing the blockCV Package

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Post provided by Roozbeh Valavi

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Modelling species distributions involves relating a set of species occurrences to relevant environmental variables. An important step in this process is assessing how good your model is at figuring out where your target species is. We generally do this by evaluating the predictions made for a set of locations that aren’t included in the model fitting process (the ‘testing points’).

Random splitting of the species occurrence data into training and testing points

Random splitting of the species occurrence data into training and testing points

The normal, practical advice people give about this suggests that, for reliable validation, the testing points should be independent of the points used to train the model. But, truly independent data are often not available. Instead, modellers usually split their data into a training set (for model fitting) and a testing set (for model validation), and this can be done to produce multiple splits (e.g. for cross-validation). The splitting is typically done randomly. So testing points sometimes end up located close to training points. You can see this in the figure to the right: the testing points are in red and training points are in blue. But, could this cause any problem? Continue reading →

R2ucare: An Interview with Olivier Gimenez

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At the International Statistical Ecology Conference in St Andrews this July (ISEC 2018) David Warton interviewed Olivier Gimenez about R2ucare. R2ucare is an R package for goodness-of-fit tests for capture-recapture models. The full Methods in Ecology and Evolution article on this package – R2ucare: An r package to perform goodness‐of‐fit tests for capture–recapture models – was published in the July 2018 issue of the journal.

David and Olivier also discuss some tips for creating R packages. They mention that if you’re new to writing R packages, there are some excellent resources online. Here’s one of them: A Quickstart Guide for Building Your First R Package

We’ll have more of David’s interviews from the ISEC coming out over the next few weeks. Keep an eye out for them here and on the Methods in Ecology and Evolution YouTube channel.

You can find David’s first ISEC interview (with Kate Jones) here.

The babette R Package: How to Sooth the Phylogenetic BEAST2

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Post provided by Richel Bilderbeek

 What is babette?

‘babette‘ is an R package that works with the popular phylogenetic tool BEAST2. BEAST2 uses one or more alignments and a model setup to create a Bayesian posterior of jointly estimated model parameters and phylogenies.

babette lets you call BEAST2 from an R script. This makes it easier to explore models and/or alignments than using the graphical user interface programs that BEAST2 provides. It will also help you to improve the reproducibility of your work with BEAST2.

babette Tutorial Videos

If you’re new to phylogentic analyses, the video ‘babette demo‘ demonstrates the package. It has all of the information that you need to be able to start using the package

Continue reading →

HistMapR: 12 Months from Coffee Break Musings to a Debut R Package

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Post provided by Alistair Auffret

I was really happy to hear that our paper, ‘HistMapR: Rapid digitization of historical land‐use maps in R’ was shortlisted for the 2017 Robert May Prize, and to be asked to write a blog to mark the occasion. The paper was already recommended in an earlier blog post by Sarah Goslee (the Associate Editor who took care of our submission), and described by me in an instructional video, so I thought that I would write the story of our first foray into making an R package, and submitting a paper to a journal that I never thought I would ever get published in.

Background: Changing Land-Use and Digitizing Maps

Land-use change in Europe is often typified by land-drainage to create arable fields.

Land-use change in Europe is often typified by land-drainage to create arable fields.

Land-use change is largely accepted to be one of the major threats to biodiversity worldwide at the moment. At the same time, a warming climate means that species’ ranges need to move poleward – something that can be hampered by changing land use. Quantifying how land use has changed in the past can help us to understand how species diversity and distributions respond to environmental change.

Unfortunately, quantifying this change by digitizing historical maps is a pretty tedious business. It involves a lot of clicking around various landscape features in a desktop GIS program. So, in many cases, historical land use is only analyzed in a relatively small number of selected landscapes for each particular study. In our group at Stockholm University, we thought that it would be useful to digitize maps over much larger areas, making it possible to assess change in all types of landscape and assess biodiversity responses to land-use change at macroecological scales. The question was, how could we do this? Continue reading →

Code-Based Methods and the Problem of Accessibility

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Post provided by Jamie M. Kass, Matthew E. Aiello-Lammens, Bruno Vilela, Robert Muscarella, Cory Merow and Robert P. Anderson

The namesake of our software and founder of the field of biogeography, Alfred Russel Wallace. Photo ©G. W. Beccaloni

The namesake of our software and founder of the field of biogeography, Alfred Russel Wallace. Photo ©G. W. Beccaloni

In ecology, new methods are increasingly being accompanied by code, and sometimes even full command-line software packages (usually in R). This is great, as it makes analyses more reproducible and transparent, which is essential for the development of open science. In an ideal world, code would have informative annotation, generalized functions for multipurpose use, and be written in a legible and consistent manner. After all, the code may be used by ecologists with a wide range of programming experience.

In reality, code is often poorly commented (or not commented at all!), hard to reuse for other projects, and difficult to interpret. To add to that, most code isn’t actively maintained, so users are on their own if they try to commandeer it for new purposes. Further, ecologists with little or no programming knowledge are unlikely to benefit from methods that exist only as poorly documented code. In a positive development, some new methods are accessible through software with graphic user interfaces (GUIs) developed by programmers spending significant time and effort. But too often these end up as tools with flashy controls and insufficient instruction manuals. Continue reading →