R & github = open science

So, after birds/birdwatching my favourite thing in the world is R https://cran.r-project.org/

Why R? Well, number one, it lets me do pretty much any data manipulation, analysis, modelling, visualization task that I need to do. And number two, it’s free and supported by an amazing community of super smart people, which means it is getting better all the time. And three – because we all know that, in science, you haven’t got your analysis right until you’ve done it three times. In R you can write some code to do your [analysis/manipulation/visualization thing] and then just rerun that analysis. So next time my colleague/supervisor says ‘hey what if we just change that [small parameter]’ I no longer have to spend 3 months redoing everything manually, instead just tweek the code and hit run. Brilliant!

Combine R with github and you have #openscience! Advantages 1) Never lose code again when you change jobs/computer dies/dog ate it. 2) Easily revert to a previous version when you realise your late night coding session was fueled by a little too much wine/coffee 3) Copy the github url for your project’s repository into the methods section of your paper and Voila! transparent and reproducible science. Best thing since….R.

However, having travelled the long path from newbie to expeRt I know just how hard and confusing it can be to learn. So I’ve put together some of my favourite R sites for your neRding pleasure.

Tips for beginners – you don’t need to know each and every function or package – use google and copy code liberally!


http://adv-r.had.co.nz/  This site will take you into the upper echelons of R excellence. We took this on as a weekly ‘R club’, running through a chapter or so each week. Requires a basic  knowledge of R.

Learn to make plots in R: https://www.datacamp.com/community/blog/the-easiest-way-to-learn-ggplot2

oh and while we are on the topic of plotting, if you haven’t already, check out this awesome new resource!


Global collaboration needed to save migratory birds

Each year millions of migratory birds in every country across the globe make the perilous annual journey from their breeding grounds to wintering grounds. These journeys can span vast distances, like arctic terns, who over the course of their lifetime travel the equivalent of to the moon and back three times. They can require incredible feats of endurance, like that of E7, the bar-tailed godwit who made a single flight of over 11,000km. Some of them return year after year to the same location, navigating across landscapes now vastly changed by humans.

Migratory birds rely on multiple places – their breeding grounds, non-breeding (or wintering) areas and the places they rely on to rest and refuel in between. These higher demands make migrants vulnerable. Any threat to one of these areas, such as habitat loss or hunting, can impact the whole population. This unique aspect of migratory birds presents a major conservation challenge: how can we look after these incredible species that rely on so many different landscapes, often across multiple political boundaries? One of the best ways to protect migratory birds is to put aside land for their use, in protected areas.

In our recent paper, we looked at how well current protected areas cover the distribution of migratory birds. We discovered that when you take into account their need for protection in their breeding grounds, non-breeding grounds and stop-over sites they rely on in between, migratory birds are woefully under protected.  More than 90% of the 1451 migratory species we looked at are missing protection in one or more of their seasonal ranges. Without these protections, they can be very vulnerable to threats. Far Eastern Curlew, a large brown shorebird with a long curved bill, breed in Siberian tundra, then migrate to Australia and New Zealand. Along the way, they stop to rest and feed at mudflats in coastal China and Korea. Land reclamation activities owing to urban, industrial and agricultural expansion and changes in river flow from dams have destroyed many of these critical sites and the species is suffering a rapid decline. Protection of these key stopover sites will be crucial to the long-term survival of these birds.

Some countries are doing well at protecting their birds but being let down by countries elsewhere along their migratory route. For example, Germany’s protected areas adequately cover the distributions of 98% of the migratory bird species within its borders, but less than 13% of those species are have sufficient overseas.

But there is hope. Currently, nations across the world are undergoing a big drive to increase the amount of land and sea that is protected, with international agreements like the Convention on Biodiversity Conservation driving a rapid increase in global protected areas. Portugal recently announced two new protected areas filling in key gaps for migratory birds, including the Critically Endangered Balearic Shearwater, Europe’s rarest seabird. We need to make sure these new protected areas go in the right places to fill the gaps for migratory species. There is a real danger that countries will meet their 17% and 10% terrestrial and marine protected area commitments in the wrong places, places that are of limited conservation value to migrants. Increased international cooperation will be essential, plus more information about what locations might be the most critical to the long term future of each migratory species.

With strong commitment from governments across the world, and some smart science, these incredible migrations will be around to capture the imagination of future generations.

Extinction risk in dynamic species

In a world where the money available for conservation is never enough, we need to prioritise which species we choose to conserve. One of the main ways this is done is to work out the extinction risk for each species (e.g., IUCN Red List) and then spend money on the ones most likely to disappear. But we often don’t have very much information to help us decide how at risk a species is, and so just base the decision on the area of its distribution (geographic range size), with the idea being that species with a small distribution are more at risk than those that occupy a big area. However many species move around and these movements can lead to substantial temporary expansion and contraction of geographic ranges, to levels which may pose an extinction risk. For instance, nomadic birds can contract down to very small areas during time of drought and this makes them very vulnerable to threats during that time.


Highly dynamic species, like this nomadic orange chat Epthianura aurifrons can contract down to small areas during times of drought


In this paper we modelled the dynamic distributions of 43 arid-zone nomadic bird species across the Australian continent for each month over 11 years and calculated minimum range size and extent of fluctuation in geographic range size from these models. There was enormous variability in predicted spatial distribution over time; during times of poor environmental conditions, several species not currently classified as globally threatened contracted their ranges to very small areas, despite their normally large geographic range size. This finding raises questions about the adequacy of conventional assessments of extinction risk based on static geographic range size (e.g., IUCN Red Listing). Our approach provides a tool for discovering spatial dynamics in data-poor and highly mobile species and can be used to unlock valuable information for improved extinction risk assessment and conservation planning.