Coding Club in Ghent and a visit to the Forest and Nature Lab in Ghent

At the beginning of March, something strange happened here in Edinburgh – a snow storm! A proper blizzard and what very much looked and felt like real snow, real enough to cause a bit of traveling havoc! On my way to Ghent, it was Beast from the East – a standard snow storm really, but quite unusual for for the rainy Edinburgh winter. On my way back to Edinburgh, of course, came Beast from the East number two – a smaller snow storm, but still enough to make the ground go white. Though I had storms accompanying me all along the way, my journeys all went safely and even more excitingly, they were full to the brim with science!

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Edinburgh snowscapes. Photo by Sandra Angers-Blondin

Coding Club workshop for the EVENET network

Coding Club is growing! It’s quite exciting, and one of the best parts is learning about similar initiatives around the world – the joys and challenges of coding can definitely bring people together. At the Ecology Across Borders conference in Ghent last December, we organised a workshop on sharing quantitative skills among ecologists – seeing so many people keen to only get better at R, but also share their knowledge with others, was definitely one of the conference highlights for me. So imagine how exciting it was when I got the invite to go back to Ghent to lead a Coding Club workshop for EVENET – a network of ecologists from different institutions around Belgium.

The theme of the workshop was developing an efficient and reproducible workflow, so we squeezed in as much data manipulation, visualisation, modelling and then reporting using Markdown into a day-long workshop. If you’re keen to find out about the tidyverse collection of packages and how you can use them to streamline your research, you can check out the tutorial online:

GitHub, Tidyverse and Markdown – efficient data manipulation and visualisation and reproducible workflows

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Red deer populations across space and time – check out the tutorial here https://ourcodingclub.github.io/2018/03/06/tidyverse.html

The Forest and Nature Lab at Ghent University

I’ve been dreaming of visiting a research group – it sounded like something I would really enjoy! I love exploring university campuses and research buildings, checking out the posters on the walls, “feeling the science in the air”, learning about new research and getting to hear different perspectives on my work as well. Visiting the Forest and Nature Lab at Ghent University was indeed a great experience – I shared the preliminary findings of one of my PhD chapters for the first time (how does forest cover influence biodiversity trends?), I learned about a lot of cool forest research and of course, I find land-use history fascinating, so I was very intrigued by the post-agricultural forests in Flanders and the effect of time since last agricultural activity.

You can check out some of the papers below to learn more about the effects of land-use legacy on forest communities:

Hermy & Verheyen (2007) Legacies of the past in the present-day forest biodiversity: a review of past land-use effects on forest plant species composition and diversity, Ecological Research.

Perring et al. (2018) Global environmental change effects on plant community composition trajectories depend upon management legacies, Global Change Biology.

A particularly inspirational moment was getting to walk around the research forest near Gontrode. A research forest! As much as I like coding away with a cup of tea, it’s nice to complement that with seeing real-life plants and animals. I think strong academic communities are so valuable, and in Ghent, I got a small glimpse of such a community! We are all busy and at any point in time, we could be doing many different things. I will definitely remember the feeling of walking around the research forests with a group of PhD students, each showing me some of their experiments and sharing their science.

I had lots of time for daydreaming on my way back to Edinburgh, and I have to say, 12 hour delays sure feel more poetic when 1) you have code running in the background, so you don’t feel totally inefficient, and 2) you are dreaming of future research directions and field research stations!

The Ecology Across Borders conference

It is snowing in Ghent. Delayed or cancelled flights/trains have made travelling a challenge, but as the weather is settling at least a tiny bit, more and more people are arriving to the Ecology Across Borders in Ghent, Belgium. A snowman with a name badge greats those that managed to reach the conference venue. Outside, the cold wind pinches your skin and freezes your toes. Inside, the magic and excitement of science, plus a cup of tea or several, warms you up.

Here are my conference highlights so far.

Ecology Hackathon

On Monday, I joined the full day Ecology Hackathon. Our goal was to make an R package to download and harmonise differed gridded datasets to facilitate their use in answering research questions. We have written code and drafted the key goals of our package, and are excited to continue building on this.

Speed review from the BES journal editors

The speed review session was a great opportunity to get feedback from the editors of some of the BES journals. The session was very useful and  it was great to meet some of the editors and talk about the winning elements of a manuscript.

GBIF stall in the exhibition hall

I had a riveting discussion with Dmitry Schigel from the Global Biodiversity Information Facility (GBIF). I’m using GBIF data in my analysis of how rarity metrics (geographic range, mean population size and habitat specificity) affect population change, and it was fantastic to learn more about GBIF and how to best use GBIF data. We love open source data, and we are looking forward to continuing using GBIF – both in our research, and in teaching at Coding Club.

Catching up with people and meeting others for the first time

It’s exciting to see people you haven’t met with for a while, to chat about science and life, and share the conference experience. Equally, it is exciting to meet new people, to ponder a subject area you’ve never though about before, or to see your own area in a different light.

Taking it all in – three floors of people enthusiastic about science, a buzzing conference venue, beautiful photos spread around, and lots of inspiration – it is worth to stop running for a moment (though I find that hard!) to just breathe in the ecology magic.
For those of us that didn’t bring appropriate footwear and are walking around in socks, the conference very much feels like home! And what better home for an ecologist than one where we get to share and discuss our research, pick up new skills along the way and start new collaborations.

Workshop: Transferring quantitative skills among ecologists

Coding Club brings together people at different career stages to create a supportive environment for knowledge exchange and collective advancement of quantitative skills. We combine peer-to-peer workshops and online tutorials to promote statistical and programming fluency. In our EAB workshop, we used a tutorial on analysing big data in ecology to demonstrate how we can deliver quantitative training across academic institutions, after which we made our own tutorials and uploaded them to GitHub!

Interested in learning how to write coding tutorials and create a positive space for knowledge and skills exchange? All of our workshop materials are freely available online and we welcome future collaborations.

We were thrilled that many people attended and engaged with our workshop – it’s fantastic to meet more people keen to build a community around coding and quantitative training!

Talk: Does rarity influence population change in the UK and across global biomes?

Straight from our workshop, I ran to the Conservation science session to give my talk! An exciting jam-packed day!

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Species’ attributes such as rarity status, distribution and taxa are often assumed to predict population declines and extinction risk. However, empirical tests of the influence of rarity on population change across tax and biomes have yet to be undertaken, hindering proactive conservation. We combined open source data from the Living Planet Index, the Global Biodiversity Information Facility and the IUCN to examine (1) the effects of rarity on rates of vertebrate population change in the UK, (2) the variation in global vertebrate population trends across biomes, and (3) the relationship between detected population change, species’ conservation status, and study duration.

I loved the 2016 BES conference in Liverpool, and the join conference in 2017 was no different!

One year of Coding Club

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This November, we are celebrating Coding Club’s first birthday – one year full of workshops, lots of code and many moments of joy as we finally figure out how to get our code to work and improve our quantitative skills together! It’s been such an exciting year, and we are thrilled to see many new faces joining us, as well as familiar faces returning workshop after workshop. We have developed 19 tutorials for our website on topics such as mixed effects models, using Markdown, and following a coding etiquette. We went to Aberdeen to co-lead a workshop with Francesca from the University of Aberdeen, and we also made it to the University of Edinburgh Impact awards!

But most of all, we are lucky to have many keen people, from different career stages and different disciplines, join us as we get better at coding by either coming to our workshops in Edinburgh or completing the tutorials online! It’s wonderful to have a supportive community where we can ask all of the R questions that pop into our minds, a place where we can all be learners and teachers, and help each other learn how to run models, make beautiful graphs and more!

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A map of the countries from where people visit our website!

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Conservation in the Cairngorms

Five rainbows, ptarmigan, beautiful autumn colours and exciting chats with students and conservation practitioners – the Conservation Science course fieldtrip was a wonderful conservation-themed weekend! I’ve been dreaming of going to the fieldtrip for two years, and this year it finally happened!

I took the Conservation Science course as a student two years ago, and I loved it! The opinion piece was definitely one of my favourite assignments ever, and earlier this year, it got published in the Biosphere magazine – you can check it out here if you are keen to learn about conservation in the Australian Outback. I was also very excited about the course having a blog, so I couldn’t stop myself at writing just the blog post that was part of the course assignments, and wrote one more about how our obsession with rare species might be hampering conservation. Overall, I was very inspired and motivated by the course. I was also very bummed out, because I couldn’t go along to the fieldtrip back then, so I only got to hear the amazing stories and look at the beautiful photos. When I came back to the University of Edinburgh this fall as a PhD student, I was thrilled that not only will I get to do my dream research, but I will also be able to do my dream tutoring on the Conservation Science and GeoScience Outreach courses. As we headed out to the Cairngorms, well, you probably couldn’t see my enthusiasm and excitement, because I get motion sickness very easily, but once we arrived, I was all ready for adventure!

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Hiking at Glen Feshie

For me, the highlight of fieldtrips is that students and staff get to know each other, and explore and learn together. I loved that as a student, and I love it now as a member of the teaching staff. It was great to talk about conservation, academia, careers and life with the students – be it by the fire, on hikes, or just at breakfast, it’s wonderful to hear students’ thoughts. Aside from all the talking, we also got to play a game together!

The activity I led was a game called “Species on the move”.

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The cards for the game – you can download a pdf here.

Here is the premise: faced with climate change, habitat change, conflicts with human activities and naturally occurring environmental change, species have three options: adapt, move, or go extinct. We focused on moving, or changes in distribution ranges, as this strategy might be particularly relevant in Scotland, where climate change and land use change might force species to move. Each student drew a species card and joined one of two ecological communities. The students, each representing a species, lined up – their current habitats were no longer suitable, so they had to move. Species traits, human attitude and conservation support all influence the success of species on the move. I then called out various criteria for movement, like: “If you can fly, take one step forward”, “If fences can’t stop you, take one step forward”. Half way through we introduced lynx and beaver in our ecological communities, which then had effects on the success of some of the already present species.

The aim of the game was to find out which species first reach their new, more suitable habitat. As students were taking steps forwards and sometimes back (poor rare alpine plants!), we could already put together a picture of how intrinsic factors, like species’ traits, interact with extrinsic factors like land management and conservation interventions, to create dynamic ecosystems, where some species will be winners, and others losers, Afterwards, we heard from our winning and losing species, who all shared their strategies for success or what held them back. Haydn, our Scottish crossbill, shared why he was way behind Thomas, the Common crossbill. Or were those meant to be the same species? Afterwards all of us, winners and losers, had a warm cup of tea and ate delicious cake, a lovely finish to our adventures in the Highlands!

You can download the cards for “Species on the move” here.

The RSE Spotlight on Scotland’s Biodiversity Conference

Last week I took part in the Scotland’s Biodiversity conference at the Royal Society of Edinburgh. As conference go, there was knowledge and inspiration filling the rooms, there were questions I hadn’t pondered before, some answers that surprised me, some that re-affirmed what I already suspected. What was special about this conference though, was that I got to share the whole experience with an enthusiastic group of students from the Conservation Science honours course!

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For the students, it was their first ever conference, and it certainly was inspiring to see them chat to speakers and engage with wide-ranging conservation topics – from policy, natural capital, agri-environment management, peatland restoration all the way to the conservation action plan of the Scottish wildcat. Many jolly discussions followed, inspired by the talks we saw and the conversations we had with the speakers. 

Topics I found particularly interesting include whether conservation should be focused on species-specific measures or broader ecosystem functionality, as well as the effect of climate change on species richness-oriented conservation. For example, should one of conservation’s goals be to maintain and/or increase biodiversity (most often quantified through species richness)? Climate change might make Scotland more biodiverse, but we probably wouldn’t be calling that a conservation success story!

Eladio Fernandez-Galiano from the Council of Europe brought up the issue of Scotland potentially losing the species that make Scottish nature Scottish. Invasive species also made an appearance among talks, and it was intriguing to ponder whether species, colonising a certain area due to climate change and range shifts, should be classified as native or invasive. A particularly strong point of the conference for me were the three presentations delivered by pupils, part of the Scottish Natural Heritage’s ReRoute programme, and researchers and academics. It was fantastic to hear about young people’s views on conservation directly from them, and what excellent speakers they were – their presentations were clear, well-organised, and they answered questions from the audience like pros!

I was happy to present the results of my research with John Godlee and Isla Myers-Smith at the conference. It was my first time being part of a panel discussion, along with some of the other presenters, which was also fun!

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Overall, it was great to have a biodiversity event right here in Edinburgh, only a quick cycle away!

Pondering the effects of habitat fragmentation

Are the negative effects of habitat fragmentation a zombie idea? Do we see positive or negative effects of habitat fragmentation more often? And even before we do that, can we make broad generalisations about the effects of habitat fragmentations; if we can, should we be? What would be the potential effects on conservation policy and actions?

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Journal club joy

This week we had our first EdGE meeting, under the theme of a Biodiversity Journal Club, and we pondered all of those questions and more in a lovely thought-provoking and stimulating atmosphere! We focused on the following paper:

Fahrig, L. (2017). Ecological responses to habitat fragmentation per se. Annual Review of Ecology, Evolution, and Systematics48(1).

Check out the full blog post summarising our thoughts on the EdEN website!

PhD begins, Coding Club returns

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After a field season in Northern Scotland and a field season in the Arctic, I am back in Edinburgh to delve into the world of biodiversity change and its drivers. I have started a PhD! My project aims to quantify the effects of land use change on global and local patterns of species richness, abundance and composition, and develop a computational framework to facilitate answering ecological questions using big data and global synthesis of long-term observations. In particular, I will investigate whether: 1) changes in species richness, abundance and composition can be attributed to land use change over recent decades, 2) land intensification and land abandonment are both causing species homogenisation, and 3) biodiversity change processes are more pronounced in areas of high land use change rates.

We have also led the first Coding Club workshop – exciting to see Coding Club back for a second year of coding and statistics inspiration and knowledge sharing! With Coding Club, we want to create a friendly environment in which we can learn about quantitative analysis together. Coding Club is for everyone – all students and staff are welcome to come along and participate, regardless of their current R knowledge. We were thrilled to see people returning to our workshops, as well as many new faces – with new students come new ideas, new research projects and new data presents to open – ah, imagine the graphs!

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The Coding Club cookies, featuring some pipes we piped!

Coding Club will soon celebrate its first birthday – in one year there have been many lines of code, majority of them working, many workshops, posters and emails to spread the word. Every week there is a little pocket of R magic in our university building, and with over 50 people coming to our two workshops last week, the pocket doesn’t feel so little anymore! We have ambitious plans for developing Coding Club further, sharing what we have learned so far, and forming new collaborations. You can check out our tutorials on efficient data manipulation, data visualisation, mixed effects models and more on the Coding Club website. We are also very happy to have other people use our tutorials to deliver Coding Club workshops around the world, and would also love to have more people contribute online tutorials. If you are interested, you can get in touch with us at ourcodingclub (at) gmail.com.

A particularly great aspect of Coding Club’s first week back was that the workshops were lead by Sam and Claudia – two of Team Shrub’s new honours students. We hope to spread inspiration and motivation to learn through our workshops, and we were definitely inspired by Sam and Claudia’s great work! Coding can be scary and intimidating, but among the occasional fear and many R errors, we are glad that there is a place where we can brave the errors together and get better at finding the answers to our research questions.