Adrien Gelle

Barau’s Petrel: Reunion’s Endangered Seabird and Cultural Icon

Mon, 24 Nov 2025 00:00:00 +0000

A Brief History

The Barau’s Petrel was only formally described in 1964 by Christian Jouanin (Jouanin and Gill, 1967; Mayr, 1971), making it one of the most recently discovered seabird species, despite being well-known to local communities for centuries. Its name honors Armand Barau, a Réunion-born ornithologist and agricultural engineer who contributed significantly to the island’s natural history.

Nesting Cavity of Barau’s Petrel (Pterodroma baraui) in the Grand Bénare colony (©Merlène Saunier)

Range and Endemism

This species is strictly endemic to Réunion Island, nesting in remote, high-altitude colonies between 2,200 and 2,800 meters on volcanic massifs such as Piton des Neiges and Grand Bénare. These burrows, dug into soft volcanic soil, are among the most inaccessible seabird nesting sites in the world. After breeding, Barau Petrels migrate thousands of kilometers across the Indian Ocean, reaching areas near Madagascar, South Africa, and even the Ninety East Ridge, with only one nest found on Rodrigues Island at low altitude (Van Den Berg et al., 1991).

Approximate breeding distribution of Barau’s Petrel (Pterodroma baraui) on the two central massifs of Réunion Island, Piton des Neiges and Grand Bénare (Pinet et al., 2009)

Conservation Status and Threats

The IUCN lists Barau’s Petrel as Endangered, with an estimated population of 30,000–40,000 mature individuals and a declining trend (BirdLife International, 2018). Its survival is impacted by:

Light Pollution: Fledglings mistake city lights for moonlight guiding them to the sea, leading to fatal grounding. Up to 40% of fledglings are affected each season.
Introduced Predators: Feral cats and rats prey on eggs, chicks, and even adults. Modeling suggests extinction within 100 years without cat control (Pinet et al., 2009)
Habitat Modification: Urban expansion and invasive plants threaten nesting areas.
Climate Change: Shifts in oceanic conditions may reduce suitable wintering habitats by 11% by 2100 (Legrand et al., 2016)

Socio-Cultural Significance

Known locally as “taille-vent” or “fouquet,” the Barau Petrel is more than a bird - it’s a cultural emblem. Its eerie, plaintive cry once haunted Réunion’s nights, inspiring myths like that of “Grand-mère Kalle”, a legendary witch said to roam the mountains and manifest through the petrel’s calls.

Today, the species symbolizes ecological pride. Community-led rescue campaigns, such as “Nuits sans lumière” (Lights-Off Nights), uniting schools, associations, and municipalities to save the species. These events have become powerful moments of environmental awareness, reinforcing the bond between people and nature.

Conservation Efforts

The fight to save Barau’s Petrel is funded by the LIFE+ Pétrels program, a €3.1 million EU-funded initiative that brings together the Parc National de La Réunion, SEOR (Société d’Études Ornithologiques de La Réunion), and other partners. Actions include:

Predator control in breeding colonies.
Public awareness campaigns to reduce light pollution.
Scientific monitoring of nesting sites and migration routes.

Adult Barau’s Petrel (Pterodroma baraui) incubating egg in Grand Bénare colony (©Merlène Saunier)

References and further reading

BirdLife International, 2018. Species factsheet: Barau’s Petrel Pterodroma baraui [WWW Document]. BirdLife DataZone. URL https://datazone.birdlife.org/species/factsheet/baraus-petrel-pterodroma-baraui (accessed 11.24.25).

Grand-mère Kalle : la légende de la terrifiante sorcière Grand-mère Kalle : la légende de la terrifiante sorcière [WWW Document], n.d. . Île de la Réunion Tourisme. URL https://www.reunion.fr/decouvrez/histoires-et-fables/la-legende-de-grand-mere-kalle/ (accessed 11.24.25).

Jouanin, C., Gill, F.B., 1967. Recherche du pétrel de Barau Pterodroma baraui. Oiseau Rev Fr Ornithol 37, 1–19.

Le Pétrel de Barau | Parc national de la Réunion [WWW Document], n.d. URL https://www.reunion-parcnational.fr/fr/des-connaissances/la-faune/la-faune-indigene/le-petrel-de-barau (accessed 11.24.25).

Legrand, B., Benneveau, A., Jaeger, A., Pinet, P., Potin, G., Jaquemet, S., Le Corre, M., 2016. Current wintering habitat of an endemic seabird of Réunion Island, Barau’s petrel Pterodroma baraui, and predicted changes induced by global warming. Mar. Ecol. Prog. Ser. 550, 235–248. https://doi.org/10.3354/meps11710

Life + Pétrel | Parc national de la Réunion [WWW Document], n.d. URL https://www.reunion-parcnational.fr/fr/des-actions/proteger-et-gerer/les-projets-de-conservation/life-petrel (accessed 11.24.25).

LIFE 3.0 - LIFE Project Public Page [WWW Document], n.d. URL https://webgate.ec.europa.eu/life/publicWebsite/project/LIFE13-BIO-FR-000075/halting-the-decline-of-endemic-petrels-from-reunion-island-demonstration-of-large-scale-innovative-conservation-actions (accessed 11.24.25).

Mayr, E., 1971. New species of birds described from 1956 to 1965. Journal für Ornithologie.

Nuits sans lumière 2025 : campagne de sauvetage des Pétrel de Barau | Mairie de Saint-Pierre [WWW Document], n.d. URL https://www.saintpierre.re/tous/nuits-sans-lumiere-2025-campagne-de-sauvetage-des-petrel-de-barau (accessed 11.24.25).

Pinet, P., Salamolard, M., Probst, J.-M., Russell, J.C., Jaquemet, S., Corre, M.L., 2009. Barau’s petrel (Pterodroma baraui): history, biology and conservation of an endangered endemic petrel.

Van Den Berg, A.B., Smeenk, C., Bosman, C.A.W., Haase, B.J.M., Van Der Niet, A.M., Cadée, G.C., 1991. Barau’s Petrel Pterodroma baraui, Jouanin’s Petrel Bulweria fallax and other seabirds in the northern Indian Ocean in June–July 1984 and 1985. Ardea 79, 1–14.

The Dodo: Extinction icon and mistaken identity

Fri, 21 Nov 2025 00:00:00 +0000

Introduction

When Dutch sailors first landed on Mauritius in 1598, they encountered a peculiar flightless bird unlike anything in Europe. The dodo (Raphus cucullatus) had evolved in isolation, a ground-dwelling pigeon that had lost its ability to fly in the absence of predators (clostest living relative being the Nicobar pigeon). Within decades, this remarkable creature would vanish forever…

Copper engraving of Dutch activity on Mauritius in 1598 from Het Tvveede Boeck (1601)

Dead as a Dodo

The dodo’s extinction happened very rapidly, with the last sightings occurring between 1662 and 1680. This rapid decline and disappearance was driven by direct hunting and, more significantly, by the introduction of invasive species such as cats, dogs, pigs, and rats, which preyed on dodo nests and juveniles.

The Dodo and the Guinea Pig, George Edwards (1757)

The Great Chain of Being

The dodo needed to wait a century and a half before its extinction being recognized. In the days of naturalists like Cuvier and Buffon, the concept of extinction was religiously wrong. If God had created all of nature according to a divine plan at the beginning, it would seem irrational for him to let some parts of that creation being wiped out. “The Great Chain of Being” (scala naturae): life was fundamentally perfect and unchangeable. In other words, the concept of “extinction” was considered impossible…Species might move to unexplored regions, but they could not simply cease to exist. It was Georges Cuvier who, through meticulous comparative anatomy of elephants and mammoths fossils in the early 19th century, finally established extinction as scientific fact. Recognizing humanity’s role in driving species to extinction.

The Dodo that never was…

For over a century, scientists believed that a second species of dodo had lived on the nearby island of Réunion.

Reunion white dodo (Raphus solitarus), watercolour drawing by Pieter Holsteyn II (1614-1687), undated.

The confusion persisted for decades. This supposed “Réunion white dodo” was given various scientific names, including Raphus solitarius. Modern investigations by Arturo Valledor de Lozoya (2003) and Anthony Cheke and Julian Hume (2004) unraveled the mystery:

The paintings described a Mauritian dodo, not a Réunion species. Holsteyn’s and Withoos’s white dodo images were based on an earlier 1611 painting by Roelant Savery, which showed a whitish specimen from the Prague collection of Holy Roman Emperor Rudolf II. This was likely a pale or albino individual of the Mauritian dodo (Raphus cucullatus).
The “solitaires” described historically were actually ibises. Subfossil discoveries in the 1970s revealed that the large white birds early explorers encountered on Réunion were not dodos but rather a species of flightless ibis (Threskiornis solitarius), now called the Réunion ibis (no specimens were brought to Europe alive or dead). This ibis was indeed white and flightless, matching the travelers’ descriptions, but it was an entirely different species.
Dodos never reached Réunion. Geological evidence shows that Mauritius is older than Réunion, and dodos had already become flightless before Réunion emerged from the sea. They could not have colonized the younger island.

References and further reading

De Lozoya, A.V., 2003. An unnoticed painting of a white dodo. Journal of the History of Collections 15, 201–210. https://doi.org/10.1093/jhc/15.2.201

Hume, J.P., 2006. The history of the Dodo Raphus cucullatus and the penguin of Mauritius. Historical Biology 18, 69–93. https://doi.org/10.1080/08912960600639400

Hume, J.P., Cheke, A.S., 2004. The white dodo of Réunion Island: unravelling a scientific and historical myth. Archives of Natural History 31, 57–79. https://doi.org/10.3366/anh.2004.31.1.57

Mauremootoo, J., Cheke, A., Watt, I., 2015. Mauritius & Rodrigues Historical Context. https://doi.org/10.13140/RG.2.1.3372.6169

The dodo bird: The real facts about this icon of extinction | Natural History Museum [WWW Document], n.d. URL https://www.nhm.ac.uk/discover/the-dodo-bird-the-real-facts-about-this-icon-of-extinction.html (accessed 11.22.25).

Turvey, S.T., Cheke, A.S., 2008. Dead as a dodo: the fortuitous rise to fame of an extinction icon. Historical Biology 20, 149–163. https://doi.org/10.1080/08912960802376199

Skomer Island: A Volunteer's Journey Into Seabirds Hidden Kingdom

Thu, 08 May 2025 00:00:00 +0000

Introduction

Skomer Island is located off the Pembrokeshire coast of Wales, formed primarily of volcanic rock. Archaeological evidence indicates human settlements dating back to the Iron Age, though today it functions as a protected nature reserve managed by the Wildlife Trust of South Wales. The island’s geology—predominantly volcanic rock covered by thin, fertile soil—provides an optimal habitat for numerous species, particularly burrowing seabirds.

The Arrival

We arrived on Skomer on April 26th, 2025, as weekly volunteers. Our boat departed from Martin’s Haven on the mainland and landed at North Haven on Skomer Island. Weather conditions upon arrival included mist, which is relatively common in this maritime environment during spring.

North Haven embarkation point The team heading towards the farm on the first day The farm (staff accommodation)

The Team

Our operational team consisted of six weekly volunteers, two long-term volunteers, and four staff members. Daily tasks were systematically assigned, including walks and talks with visitors around the island, observation point staffing at the Wick with spotting scopes to facilitate species identification, and logistical support during boat arrivals (landing, binoculars renting). The Wick viewpoint

The Avian Fauna

Skomer’s ecological significance is particularly evident in its burrowing seabird populations. The island substrate is extensively tunneled, resembling a biological honeycomb structure. Two primary burrowing species inhabit these tunnels: approximately 360,000 pairs of Manx Shearwaters (Puffinus puffinus) and 43,000 Atlantic Puffins (Fratercula arctica).

The Manx Shearwaters return to their burrows at night, vocally active with their distinctive calls . These vocalisations are characterised by a high-pitched, repetitive sound pattern that historically contributed to Skomer’s ancient designation as the “island of lost souls.” Overnight stays on Skomer provide valuable opportunities to observe these nocturnal avian activities, which are not accessible to day visitors.

Diurnal raptor species observable on the island include Common Buzzard (Buteo buteo), Common Kestrel (Falco tinnunculus), Peregrine Falcon (Falco peregrinus), and Short-eared Owl (Asio flammeus). All avian observations (from any observers) were systematically recorded in the daily bird log at 8 pm. A comprehensive list of all the bird species that I identified is available in my eBird trip report.

Manx Shearwater (Puffinus puffinus) at the breeding grounds on Skomer Island ©Martin Reith Atlantic Puffin (Fratercula arctica) cleaning his burrow, photographed at the Wick by ©Nigel Blake. Atlantic Puffin (Fratercula arctica) photographed at the Wick by ©Nigel Blake.

The Experience

We were very lucky to have great weather during the week, with clear skies and temperatures reaching maximums of 25°C. The last days featured strong northerly winds, creating conditions unsuitable for boat landings. This resulted in a 24-hour extension of our stay, with a 48-hour period without any visitors (the island was ours!).

These days without visitors were an opportunity for infrastructure maintenance (painting, repairs & cleaning) and targeted monitoring. I participated in Short-eared Owl (Asio flammeus) monitoring. During this survey, I got the amazing luck of seeing an individual flying just above my head, calling and showing territorial behaviors (“wing-clapping”). The nest was not very far…

Short-eared Owl (Asio flammeus) photographed by ©Nigel Blake in April 2008

Acknowledgment

I would like to thank the entire team on the island: Ceris, Rob, Bob, Elana, Caroline & Becca. A special acknowledgement to Dai who helped me significantly improve my species identification during the stay. It was a wonderful team and I strongly believe that the experience would not have been the same without you all. Thank you Nigel Blake for the conversations and sharing amazing photos with me. The weekly volunteering team (Dai, Caroline, Becca, Bob, Me(Adrien), Elana)

Final Thoughts

I strongly encourage anyone who hasn’t been to Skomer to visit the island, or to apply for volunteering. There is something very captivating and emotional about this island, and I feel like my simple human brain could only capture a small proportion of what was going on there… I hope to come back very soon. Goodbye (for now), Skomer.

Skomer Island South coast Sunset view from the North coast of Skomer Island

CMR - Data transformation App

Tue, 29 Oct 2024 00:00:00 +0000

CMR data transformation app example (user interface)

Mauritius kestrel

Fri, 08 Mar 2024 00:00:00 +0000

The Mauritius Kestrel (Falco punctatus) is a small bird of prey endemic to the island of Mauritius. Once abundant throughout the island, the population of Mauritius Kestrels began to decline rapidly in the 20th century due to a combination of factors, primarily habitat loss, introduced predators, and the widespread use of pesticides like DDT.

By the 1970s, the Mauritius Kestrel had become one of the rarest birds in the world, with only a handful of individuals remaining in the wild. At its lowest point in 1974 it was estimated that there were only four individuals left.

However, the story of the Mauritius Kestrel took a remarkable turn thanks to the efforts of conservationists. In 1973, the Durrell Wildlife Conservation Trust, led by conservationist Gerald Durrell, launched a captive breeding program for the Mauritius Kestrel in collaboration with the Mauritian government and other conservation organizations.

Despite initial challenges and setbacks, including difficulties in breeding the birds in captivity and concerns about inbreeding, the breeding program eventually began to yield results. Through careful management and dedication, the population of Mauritius Kestrels in captivity began to increase steadily.

In 1987, the first captive-bred Mauritius Kestrels were released back into the wild, marking a major milestone in the species’ conservation. Over the following years, additional releases were conducted, and supplementary feeding programs were implemented to support the reintroduced birds as they adjusted to their natural habitat.

Carl Jones in 1982 with one of the first Mauritius kestrels that hatched in captivity

The efforts to save the Mauritius Kestrel paid off, and the population began to rebound. By the early 2000s, the population had increased to over 400 individuals, with breeding populations established in various parts of the island.

Today, the Mauritius Kestrel stands as a symbol of successful conservation efforts and serves as a reminder of the importance of protecting endangered species and their habitats. While challenges remain, particularly in addressing ongoing threats such as habitat destruction and invasive species, the recovery of the Mauritius Kestrel is a proof of what can be achieved through dedication, collaboration, and innovation in conservation efforts.

Holding a juvenile Mauritius kestrel from the 2020-21 breeding season

Facts

Is a bird of prey endemic to the island of Mauritius in the Indian Ocean.
Small in Size: relatively small birds, measuring about 25 to 30 centimeters in length.
Varied Diet: primarily consists of small birds, lizards, insects, and occasionally small mammals.
Habitat: forests, scrublands, and agricultural areas.
Conservation Status: no longer critically endangered, it remains classified as “Endangered” on the IUCN Red List due to ongoing threats such as habitat degradation and competition with introduced species.

Publications

Thu, 29 Feb 2024 00:00:00 +0000

These are the projects on which I worked

Gellé, A., Fontaine, B., Jiguet, F., Lagrange, P., Gilg, O., 2026. Effectiveness of nature reserves in France in protecting common birds: Evidence from long-term monitoring. Biological Conservation 319, 111907. https://doi.org/10.1016/j.biocon.2026.111907

Dilshan, Y., Gellé, A., 2026. Empowering communities through biodiversity dashboards: A case study from Kumbalgama Tank, Sri Lanka.

Gellé, A., Henshaw, S., Tatayah, V., 2021. Where have all the birds gone? - A multi-species approach to confirm distribution of threatened Mauritian birds in the Bambou Mountains (Mauritius) in the aftermath of Covid-19, through AudioMoth.

Fontaine, B., Moussy, C., Carricaburu, J.C., Dupuis, J., Corolleur, E., Schmaltz, L., Lorrillière, R., Loïs, G. and Gaudard, C., 2021. Suivi des oiseaux communs en France 1989-2019: 30 ans de suivis participatifs.

Claessens, O., Gellé, A., 2020. Le Suivi des Oiseaux Communs (programme STOC-EPS) en Guyane : Bilan 2012-2018.

Gellé, A., 2019. Evaluation de l’effet du réseau des Réserves naturelles sur les tendances d’effectifs des populations d’oiseaux nicheurs communs en France métropolitaine sur les 15 dernières années. Rapport de stage, Master 2 Biodiversité, écologie et évolution, Sciences Sorbonne Université (Paris VI).

Echo parakeet

Thu, 29 Feb 2024 00:00:00 +0000

Male Echo parakeet with juvenile (© Vanousha Pillay)

The Mauritius or ‘echo’ parakeet (Alexandrinus eques) is perhaps the most acutely studied bird in Mauritius and maybe one of the most studied in the world. Due to human settlement and expansion since the 17th century, which led to habitat loss and fragmentation (Cheke and Hume, 2020; Safford, 1997; Vaughan and Wiehe, 1937), as well as the introduction of exotic plants and animals (Lorence and Sussman, 1986), two endemic species of parrot went extinct ( Lophopsittacus mauritianus and Lophopsittacus bensoni (Cheke, 1987)) and the Echo Parakeet population size and range began to decline (Jones, 1980). By the 1980s, this decline had progressed to the point where the species was classified as ‘critically endangered’ on the IUCN Red List. The extinction of the species seemed imminent by the early 1990s, when the echo parakeet was considered not only the rarest parrot in the world (Venning, 1993), but also one of the world’s rarest and most endangered bird of any group (Collar et al., 1994). However, intensive conservation efforts helped the species to recover from a population size of fewer than 20 individuals in the 1980s (Jones 1987, Jones and Duffy 1993) to over 150 breeding pairs and 800 individuals in 2020 (MWF, 2020). As a result, the species was downlisted on the IUCN Red List twice this century, from Critically Endangered to Endangered in 2007 (BirdLife International, 2007), and to Vulnerable in 2019 (BirdLife International, 2019).

“Like most Mauritian naturalists I believe that the echo parakeet will become extinct in the very near future.” (Jones, 1980)

Female Echo parakeet (© Jacques de Speville)

The conservation success of the echo parakeet was achieved through intensive conservation management (including captive breeding, nest manipulation, installation of artificial nest boxes, supplementary food, predator and competitor control) and monitoring (Jones and Duffy, 1993; Thorsen and Jones, 1998). Population recovery is largely due to the provision of artificial nest boxes (Tatayah et al., 2007) and supplemental food (Tollington et al., 2018).

Echo parakeets at feeding station (© Rebecca Louch)

Facts

The only survivor of six parrot species once found in the Mascarenes islands.
Diet: leaves, fruits, flowers and stems of primarily native plant species (also includes exotic species).
Cavity nesters (naturally nesting in cavities in endemic trees).
The Echo Parakeet project is the world’s most successful parrot recovery programme.

More information about the project on Mauritian Wildlife Foundation.

Acknowledgement

The monitoring and management of the Echo parakeet population is part of a long-term species recovery programme conducted by the Mauritian Wildlife Foundation (MWF), with support from the Institute of Zoology (ZSL), University of Kent, and Durrell Wildlife Conservation Trust. All data was provided by MWF.

LICENSE: CC-BY-SA

Wed, 28 Feb 2024 00:00:00 +0100

My blog posts are released under a Creative Commons Attribution-ShareAlike 4.0 International License.

Hi there

Tue, 28 Feb 2023 13:38:41 -0600

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Formspree requires a (free) account and new form to be set up. The link is made on the final published url in the field: Restrict to Domain. It is possible to register up to 2 emails free and you can select which one you want the forms to go to within Formspree in the Settings tab. **

The happiest notebooks on Earth

Thu, 10 Nov 2022 13:00:00 +0000

Notebooks hold a special place in every data scientist’s heart. They may treasure every moment creating their own, or commenting on others’ notebooks. Or they may sincerely and truly hate notebooks. But notebooks are useful. How could we “imagineer” better notebooks? I’ve made and read hundreds of notebooks in the past decade. In this talk, I share key principles for developing happier notebooks – ones that are more fun to write, more fun to read, and more fun as an onramp to the next ride.

The happiest notebooks on Earth

Thu, 27 Oct 2022 18:50:00 +0000

The untold story of palmerpenguins

Tue, 21 Jun 2022 08:45:00 +0000

The palmerpenguins R package provides a modern, approachable dataset containing body size measurements for three penguin species that nest on islands throughout the Palmer Archipelago, Western Antarctic Peninsula. Since palmerpenguins was released on the Comprehensive R Archive Network (CRAN) in July 2020, the package has been downloaded over 340,000 times, was quickly adapted for use in other languages including Python’s seaborn package and Google’s TensorFlow datasets, and has become a go-to option for data science and statistics educators worldwide. In this talk, we share the untold story of the palmerpenguins package. From original data collection on rocky Antarctic shores to CRAN submission and beyond, we describe the penguins’ journey from polar research project to global teaching product. What started out as a simple methods paper for a dissertation project turned into a widely used data science product mainly because of initial efforts to make the data publicly available and easily accessible by others. The success of the palmerpenguins R package underscores the importance of proper data archiving for unknown future applications.

Empowering women in data (science)

Mon, 21 Feb 2022 10:00:00 +0000

R-Ladies Cologne is kicking off with a roundtable on “Empowering Women in Data (Science)” on February 21, 2022, at 7 pm CET. We are excited to have four fantastic speakers from across the globe working in different fields to share their experiences, tips, tricks, and challenges with us! 🚀

Our four amazing panelists are:

✨ Alison Hill (Ph.D., Senior Data Scientist, AI Strategy & Innovation @IBM)

✨ Ana Carolina Leote (PhD Candidate @ Cologne Graduate School of Ageing Research)

✨ Angélica Becerra (Data Scientist @ cynkra GmbH)

✨ Nina Hauser (Head of Data Literacy @ CorrelAid e.V.)

Tidy your mental models

Tue, 25 Jan 2022 09:00:00 +0000

In this talk, I shared some lessons learned from teaching and learning tidymodels over the past two years.

R Markdown Notebooks for Scientific Communication

Wed, 15 Dec 2021 10:45:00 +0000

Speakers

Alison Hill, RStudio
Fernando Pérez, University of California, Berkeley
Simon Goring, University of Wisconsin / Leah Wasser, Earth Lab at CU Boulder / Laura DeCicco, USGS
Loren Shure, MathWorks
Hugh Shanahan, University of London / RDA
Chris Erdmann, American Geophysical Union
Kenton McHenry or Dan Katz (moderator), University of Illinois

Panel abstract

As science becomes more and more dependent on data and software, capturing these elements of the modern scientific procedure has become critical in achieving reproducibility. Computational notebooks have emerged as an increasingly valued way of capturing not only the traditional elements of a scientific paper but also the software steps in an executable and reproducible manner. As part of the 2020 EarthCube Annual Meeting, the EarthCube office, Leadership Council, and Technical Architecture Committee experimented by issuing a call focused on notebook submissions as peer reviewed publications. The call was well received by the community: 21 Jupyter notebooks were submitted, and 12 of these were accepted for publication. As part of the 2021 call for notebooks, the idea of expanding this call to more types of “notebooks” is being discussed, with the goal of eliciting submissions from a wider group of researchers, who may be more comfortable with other notebook technologies.

The proposed session will bring together representatives from the major “notebook” efforts, efforts such as Jupyter, RStudio, and commercial efforts such as MATLAB live scripts. Presenters will discuss the latest developments in each of their technologies, emphasizing elements that support the notions of ease of use, long-term executability, interoperability, and software publication. Lessons learned from building a geoscience-focused notebook directory, notebook template, and long-term preservation in AGU’s ESSOaR will be discussed as well as how this relates to international efforts to elevate notebooks and make them FAIR.

Talk abstract

In this talk, I’ll describe the R Markdown ecosystem for computational notebooks that support the full lifecycle of scientific communication, including basic reports, presentations, peer-reviewed journal article submissions, and long-form books. The ecosystem has roots in the Pandoc open source project, and includes a family of R packages scientists can use for research.

Introduction to Machine Learning with Tidymodels

Wed, 15 Sep 2021 03:00:00 +0000

Due to COVID-19, the conference was held remotely instead of in Bari, Italy.

This six-hour workshop will provide a gentle introduction to machine learning with R using the modern suite of predictive modeling packages called tidymodels. We will build, evaluate, compare, and tune predictive models. Along the way, we’ll learn about key concepts in machine learning including overfitting, the holdout method, the bias-variance trade-off, ensembling, cross-validation, and feature engineering. Learners will gain knowledge about good predictive modeling practices, as well as hands-on experience using tidymodels packages like parsnip, rsample, recipes, yardstick, tune, and workflows.

R Markdown

Tue, 15 Jun 2021 12:00:00 +0000

Speakers

Kenton McHenry (University of Illinois) and Dan Katz (University of Illinois) will moderate a discussion with presenters:

Alison Hill (RStudio),
Chris Holdgraf (2i2c - Jupyter),
Chris Erdmann (American Geophysical Union), and
Loren Shure (MathWorks - Matlab).

The talks will focus on the latest developments in each of the presenters’ technologies, emphasizing elements that support the notions of ease of use, long-term executability, interoperability, and software publication. Lessons learned from building a geoscience-focused notebook directory, notebook template, and long-term preservation in AGU’s ESSOaR will also be discussed - as well as how this all relates to international efforts to elevate notebooks and make them FAIR. This session has been designed for attendees that are already developing notebooks, those interested in doing so, and organizers who want to support these technologies in their events and proceedings.

Introduce yourself online with blogdown & Hugo Apéro

Wed, 26 May 2021 11:00:00 +0000

“You should have a website!” You may have heard this one before, or even said it yourself. In this workshop, you’ll learn how to build and customize a website from the comfort of the RStudio IDE with R Markdown. We’ll use the blogdown package and the Hugo Apéro theme to build and deploy a personal website. We’ll cover basic website care and feeding like using R Markdown to create content, how to use GitHub for version control and Netlify for publishing, and how to use the latest upgrades to the blogdown R package to keep your site up and running.

The goal of this workshop is to equip participants with tools that amplify their own contributions, build a more visible presence in the R/data community, and share their knowledge and insights with others.

Free & Open Source Software

Tue, 18 May 2021 10:00:00 +0000

Crafting Kind Tools

Mon, 12 Apr 2021 18:00:00 +0000

Abstract:

We are all tool-makers. If you are an educator, your lessons are tools. You make them to be used by students. Students use your lessons to build mental models piece-by-piece, and learn processes step-by-step. If you are a researcher, you design experiments as tools to be used by participants. As a scientist, your analyses are tools used by other researchers to replicate and extend what you did. And finally, if you use software for making any of these tools, you are also using a tool that was crafted by someone else. Is it kind? What makes a tool kind? In this talk, I’ll share ideas and insights I’ve gained while working to make tools for everyday data science communication kinder for users. I’ll discuss some case studies from my work on free and open-source software at RStudio over the past 2.5 years.

Making R Markdown work better for you

Wed, 24 Mar 2021 18:00:00 +0000

Take a Sad Plot & Make It Better

Thu, 25 Feb 2021 12:00:00 +0000

Alison Hill (I think her unofficial nickname is RMarkdown Whisperer) is going to talk to us on another of her strengths. Making things beautiful, and informative. She’s going to do her “Take a Sad Plot & Make it Better” talk, for us. In this talk, Alison will discuss one plot’s life cycle, from a sad Powerpoint slide to the finished product made with the ggplot2 package in R, and what she learnt from it.

Alison doesn’t need much introduction, she’ll be the main search result if you’re looking for RMarkdown info, xaringan inspiration, blogging and teaching online using R, among many other topics! Read about her here: https://alison.rbind.io/about/. If you’re on Twitter, you’d learn a lot by following https://twitter.com/apreshill.

Aside: Also have a look at Hugo Apéro, for some inspiration on building a presence online ( https://hugo-apero.netlify.app/).

Introduce yourself online

Mon, 25 Jan 2021 13:00:00 +0000

“You should have a website!” You may have heard this one before, or even said it yourself. In this workshop, you’ll learn how to build and customize a website from the comfort of the RStudio IDE using the blogdown package. We’ll also cover basic website care and feeding like using R Markdown to create content, and how to use GitHub and Netlify to improve your workflow. Pre-work will be shared with participants ahead of time, but to get the most out of this workshop, you’ll want to have a GitHub account and be able to push and pull files from a GitHub repository using your local RStudio IDE.

The download

Tue, 08 Dec 2020 20:30:00 +0000

The R Markdown family of packages has grown a lot over the past few years! While each new package is truly a bundle of joy, the past few months we have worked hard to make our family of existing packages more consistent, supportive, and intuitive. In this talk, I’ll share some of what we are up to lately and what to expect, with highlights from the distill, blogdown, bookdown, and xaringan packages.

InspiRing InstRuction: A panel on teaching #rstats for all audiences

Thu, 12 Nov 2020 09:00:00 +0000

Someone in your department, company, or class comes to you and says: “I want to learn R; where do I start?” Or, “how do I take my R skills to the next level?”

Come hear from 3 R-Ladies on how to make R pedagogy work for different groups of people!

R Markdown for Pharma

Wed, 07 Oct 2020 13:00:00 +0000

A four-hour workshop that will take you on a tour of how to get from data to manuscript using R Markdown. You’ll learn:

The basics of Markdown and knitr
How to add tables for different outputs
Workflows for working with data
How to include and style graphics

Presented with Tom Mock from RStudio.

Learning without a net

Wed, 07 Oct 2020 09:00:00 +0000

In this talk, I shared my experiences learning new data science skills on my own, and some broader strategies for learning when you have to do it by yourself.

Teaching in Production

Wed, 23 Sep 2020 09:00:00 +0000

This goal of this workshop is to equip educators with the tools that can help them make their teaching more robust and reproducible with R Markdown.

Trainings offered:

2020-09-23
2020-09-20

Introduction to Machine Learning with the Tidyverse

Thu, 27 Aug 2020 13:00:00 +0000

This four-hour workshop will provide a gentle introduction to machine learning with R using the modern suite of predictive modeling packages called tidymodels. We will build, evaluate, compare, and tune predictive models. Along the way, we’ll learn about key concepts in machine learning including overfitting, the holdout method, the bias-variance trade-off, ensembling, cross-validation, and feature engineering. Learners will gain knowledge about good predictive modeling practices, as well as hands-on experience using tidymodels packages like parsnip, rsample, recipes, yardstick, tune, and workflows.

The workshop was adapted from a 2-day in-person workshop delivered at rstudio::conf(2020) in San Francisco, CA.

An Introduction to R Markdown for the CDC

Wed, 13 May 2020 14:00:00 +0000

R Markdown is an authoring format that enables easy creation of dynamic documents, presentations, and reports from R. It combines the core syntax of markdown with embedded R code chunks that are run so their output can be included in the final document. R Markdown documents are fully reproducible and can be updated whenever underlying R code or data changes.

This is a great opportunity to learn and get inspired about the capabilities for generating reports in R.

This session will introduce flexible and powerful tools for sharing your research and reports, covering topics like:

The basics of R Markdown and knitting
Output formats
Working with data
Adding text
Adding code
Adding tables
Adding plots
Options for sharing R Markdown reports

The talk will introduce R Markdown and include an overview of the core content types one can create, such as websites, PDF’s, PowerPoints, and more.

No prior knowledge of R or RStudio is needed to attend this session. There is no registration required for this Webinar.

Sharing on Short Notice

Tue, 31 Mar 2020 09:00:00 +0000

This webinar was designed to help educators who needed to quickly transition to remote teaching due to COVID-19.

Educators create a lot of files for teaching- slides, exercises, solutions, assignments, data, figures- that all ultimately need to be shared with other people. Having a link for sharing your teaching materials can save you time and pain, but it is hard to get started if you’ve never shared your resources online before. In this webinar, we’ll give a tour of the R Markdown ecosystem for educators that you can start to use right away. We’ll show how it can help you make your teaching more shareable, reproducible, and resilient.

Read the accompanying Q&A blog post on the RStudio Education blog.

Introduction to Machine Learning with the Tidyverse

Mon, 27 Jan 2020 09:00:00 +0000

This two-day workshop provided a gentle introduction to supervised machine learning: concepts, methods, and R code. Participants learned how to train and assess predictive models with several common machine learning algorithms, as well as how to do feature engineering to improve the predictive accuracy of their models. We focused on teaching intuitive explanations of the models and best practices for predictive modeling. Along the way, we introduced several core tidymodels packages, which provide a grammar for modeling that makes it easy to the right thing, and harder to accidentally do the wrong thing.

Plot Twist: 10 Bake Offs, Visualized 11 Ways

Fri, 04 Oct 2019 18:00:00 +0000

Using data from 10 series of The Great British Bake Off, we will walk through eleven ways to visualize the same data using the ggplot2 package. We’ll talk a lot about geoms and variable mappings, but also about what it means to “tidy your data”, plus the new pivot functions in the tidyr package.

You won’t need your laptops but you will get the most out of this talk if you know some basics about using ggplot2. To brush up (or start learning now), you may want to play with the free RStudio.cloud data visualization primer (you may use an existing Google or GitHub account to log in). Or of course you can check out R-Ladies Sydney’s own VizW(h)iz Module of #RYouWithMe!

The Art of Literate Projecting

Wed, 02 Oct 2019 09:00:00 +0000

“Literate programming” is an approach to writing software programs that weaves together the source code and documentation at the time of creation. The idea is to create programs that are easier for users to understand. But they are also easier for programmers to work on and maintain. In this talk, I will describe how data scientists can be inspired by this programming approach and start what I refer to as “literate projecting.” Literate projects are not only more pleasant to work on — they are also easier for others to discover and explore. In my experiences as a researcher and now a data scientist at RStudio, I’ve had the pleasure to work on many literate projects, and I’ve felt the pain of working on illiterate ones too. What is the difference? What are the benefits? Based on my experiences, I’ll share good literate projecting practices that have the potential to shift your mindset and reshape your workflow.

Communicating with R Markdown Workshop

Mon, 30 Sep 2019 09:00:00 +0000

A full-day workshop for users who want to get more out of R Markdown (and friends). In this workshop, you will create, publish, and share some beautiful data products. You’ll learn to make:

Parameterized reports
Version-controlled R Markdown projects
Templates within a package
Shareable scientific/technical articles, slides, dashboards, and websites

Take a Sad Plot & Make It Better

Thu, 26 Sep 2019 18:15:00 +0000

In this talk, Alison will talk about one plot’s life cycle, from a sad Powerpoint slide to an Excel chart and finally to the finished product made with the ggplot2 package in R. Along the way, she will discuss why each version of the plot fails in different ways and how each iteration improved on the last one.

Latest event

This talk was most recently given at the University of South Wales on 2019/10/04.

R Markdown for Medicine Workshop

Thu, 12 Sep 2019 08:00:00 +0000

Teaching Students to Talk about Data Science

Mon, 29 Jul 2019 14:00:01 -0700

Data science educators have a unique opportunity to teach students the skills they need in their future careers. We know that practical skills matter, like being able to wrangle, explore, analyze, and visualize data (preferably using code), but what is easy to overlook is teaching students how to communicate about data science with other people. Being able to communicate about data, code, and insights gained are important skills we can strengthen in the classroom to make a real impact on students. I will talk about three ways to help strengthen data science communication skills that matter: self-reflection, iteration, and broadcasting. Self-reflection involves asking students to reflect on concepts and/or code that they struggled with to increase engagement with materials and independent problem-solving. Iteration involves revisiting old concepts/code, identifying areas for improvement, and making them better, either independently or in collaboration with peers or other experts/advanced users. Broadcasting involves practice (practice, practice, practice) “wrapping up” code with words into coherent narratives about what a data analysis or visualization means.

Summer of blogdown: Day 04

Thu, 13 Jun 2019 09:00:00 +0000

A hands-on workshop to creating a personal website using blogdown and the Hugo Academic theme.

Four daily 1-hour sessions (see slides) plus 30-60 minutes of homework for 3 nights.

See the project link for all the days of the summer of blogdown.

Summer of blogdown: Day 03

Wed, 12 Jun 2019 09:00:00 +0000

A hands-on workshop to creating a personal website using blogdown and the Hugo Academic theme.

Four daily 1-hour sessions (see slides) plus 30-60 minutes of homework for 3 nights.

See the project link for all the days of the summer of blogdown.

Summer of blogdown: Day 02

Tue, 11 Jun 2019 09:00:00 +0000

A hands-on workshop to creating a personal website using blogdown and the Hugo Academic theme.

Four daily 1-hour sessions (see slides) plus 30-60 minutes of homework for 3 nights.

See the project link for all the days of the summer of blogdown.

Summer of blogdown: Day 01

Mon, 10 Jun 2019 09:00:00 +0000

A hands-on workshop to creating a personal website using blogdown and the Hugo Academic theme.

Four daily 1-hour sessions (see slides) plus 30-60 minutes of homework for 3 nights.

See the project link for all the days of the summer of blogdown.

Using blogdown to Connect Beyond the Classroom

Thu, 30 May 2019 08:00:00 +0000

Meet blogdown

Tue, 15 Jan 2019 16:00:00 +0000

Meet bookdown

Tue, 15 Jan 2019 14:00:00 +0000

Meet flexdashboard

Tue, 15 Jan 2019 11:00:00 +0000

Meet xaringan

Tue, 15 Jan 2019 09:00:00 +0000

Data Visualization in the Tidyverse

Mon, 29 Oct 2018 16:00:00 +0000

Using one dataset from The Great British Bake Off, I show eleven ways to visualize one dataset using eleven different versions of “tidy data.” Take-away messages:

Tidy data is the start of your data wrangling journey, not the end
There is not a single “tidy” version of a dataset
Tidy data does make you more nimble!

Big Magic with R: Creative Learning Beyond Fear

Sat, 02 Jun 2018 08:00:00 +0000

Inspired by the book “Big Magic: Creative Living Beyond Fear” by Elizabeth Gilbert, Alison will talk about the five essential ingredients needed to creatively learn R and why these elements are also essential for advanced users to take their R skills to the next level. You will hear practical advice for when, where, and how to start a project in R, and how your learning can add value- both to your own knowledge and to contribute to the larger community of R learners. Along the way, she will share recommended resources and evidence-based strategies for project-based learning. Alison’s background working with both new and advanced R users gives her a unique perspective on this topic.

Take a Sad Plot & Make It Better

Fri, 06 Apr 2018 16:00:00 +0000

Join us on April 6 for a walk-through of how to take a sad plot and make it better by Alison Hill, who co-teaches the CS631 Data Visualization course. Alison will take us through one plot’s life cycle, from a sad Powerpoint slide to an Excel chart and finally to the finished product made with the ggplot2 package in R. We will discuss why each version of the plot fails in different ways, how each iteration improved on the last one, and which data visualization principles are at work in the final plot to communicate a clear scientific story.

Following this, Eric Earl (Senior RA in the DCAN Labs) will show a case study of visualization in neuroimaging research.

Labhub Workshop

Fri, 08 Dec 2017 16:00:00 +0000

The landscape of scientific communication is changing dramatically. Diverse stakeholders, including major funders and universities are demonstrating a growing interest and investment in open scientific principles and practices. Researchers, students, and the institutions that support them are needing to navigate new expectations, workflows, and policies against a backdrop of relatively unchanged means and measures of scientific success.

Sound complicated? Join us on December 8th from 3:00 to 4:00 PM for a panel discussion with OHSU leaders and early career researchers on the evolving landscape of scientific communication. We’ll explore the drivers behind the calls for “openness”, what this means in practice, and the real world compatibility and tensions between open science and student, researcher, and institutional success.

Confirmed panelists include:

Dr. Gary Westbrook, Vollum Institute Senior Scientist and Director of the Neuroscience Graduate Program

Dr. Bita Moghaddam, Chair of the Department of Behavioral Neuroscience

Dr. Abhinav Nellore, Assistant Professor, Biomedical Engineering and the Department of Surgery

Dr. Alison Hill, Associate Professor, Center for Spoken Language Understanding

The panel will be followed by food, drinks, and two hands on workshops from 4:00 - 5:30:

In this workshop, Dr. Alison Hill and Robin Champieux demonstrated tools and methods for building transparency within a lab, and onboarding new graduate students and postdocs. We provided a template GitHub repository and code of conduct designed to facilitate a healthy and productive learning and research environment. You are encouraged to use these tools to communicate expectations, document protocols, receive feedback, and facilitate the long-term value of students’ and trainees’ contributions.

Labhub is a work in progress. We created this repository as an education and demonstration tool for faculty, postdocs, and students curious about how documentation, open science workflows, and tools like Github can contribute to a healthy and productive research environment. Your ideas and contributions are welcome!

Up & Running with blogdown

Thu, 14 Sep 2017 00:00:00 +0000

See project links for more details.

Code Your Graph Workshop

Fri, 24 Jun 2016 00:00:00 +0000

Honors & Awards

Mon, 01 Jan 0001 00:00:00 +0000

Conferences

Mon, 01 Jan 0001 00:00:00 +0000

Experience

Mon, 01 Jan 0001 00:00:00 +0000

Education

Mon, 01 Jan 0001 00:00:00 +0000

Adrien Gelle

Barau’s Petrel: Reunion’s Endangered Seabird and Cultural Icon

Table of Contents

A Brief History

Range and Endemism

Conservation Status and Threats

Socio-Cultural Significance

Conservation Efforts

References and further reading

The Dodo: Extinction icon and mistaken identity

Table of Contents

Introduction

Dead as a Dodo

The Great Chain of Being

The Dodo that never was…

References and further reading

Skomer Island: A Volunteer's Journey Into Seabirds Hidden Kingdom

Table of Contents

Introduction

The Arrival

The Team

The Avian Fauna

The Experience

Acknowledgment

Final Thoughts

CMR - Data transformation App

Mauritius kestrel

Facts

Publications

Echo parakeet

Facts

Acknowledgement

LICENSE: CC-BY-SA

Hi there

The happiest notebooks on Earth

The happiest notebooks on Earth

The untold story of palmerpenguins

Empowering women in data (science)

Tidy your mental models

R Markdown Notebooks for Scientific Communication

Speakers

Panel abstract

Talk abstract

Introduction to Machine Learning with Tidymodels

R Markdown

Speakers

Introduce yourself online with blogdown & Hugo Apéro

Free & Open Source Software

Crafting Kind Tools

Abstract:

Making R Markdown work better for you

Take a Sad Plot & Make It Better

Introduce yourself online

The download

InspiRing InstRuction: A panel on teaching #rstats for all audiences

R Markdown for Pharma

Learning without a net

Teaching in Production

Introduction to Machine Learning with the Tidyverse

An Introduction to R Markdown for the CDC

Sharing on Short Notice

Introduction to Machine Learning with the Tidyverse

Plot Twist: 10 Bake Offs, Visualized 11 Ways

The Art of Literate Projecting

Communicating with R Markdown Workshop

Take a Sad Plot & Make It Better

Latest event

R Markdown for Medicine Workshop

Teaching Students to Talk about Data Science

Summer of blogdown: Day 04

Summer of blogdown: Day 03

Summer of blogdown: Day 02

Summer of blogdown: Day 01

Using blogdown to Connect Beyond the Classroom

Meet blogdown

Meet bookdown

Meet flexdashboard

Meet xaringan

Data Visualization in the Tidyverse

Big Magic with R: Creative Learning Beyond Fear