Data scientist trained as a theoretical and computational ecologist
In my compagny I develop computational tools to help academics, governments and small buinesses solve data problems.
In my research, I use algebra, analysis, probability, statistics, data science and computational science to study ecological networks and how global change affects them in order to conserve ecosystem functions and biodiversity that are essential to our good health and well being.
Great Lakes Fishery Commission, Guelph, ON, Canada
Work on the research project “Forecasting fisheries productivity responses to management options under multiple stressors in the Great Lakes”.
10/2020–present: Data scientist
inSileco, Montreal, QC, Canada
Co-founded a consulting company that supports academics and governments with data challenges and develops data science workshops and micro scientific applications.
02/2022–07/2023: Data scientist
Omnimed, Cookshire, QC, Canada
Developed data tools to assess data quality and to generate dynamic internal reports including data. Analyzed the possibility of using Artificial Intelligence to improve user experience.
03/2021–02/2022: Research Associate
McCann Lab, University of Guelph, ON, Canada
Worked on ecological networks, meta-ecosystems and food provenance.
06/2017–10/2020: Postdoctoral Researcher
McCann Lab, University of Guelph, ON, Canada
Worked on biogeography, ecological networks, meta-ecosystems and food provenance.
10/2012–12/2016: PhD candidate
Université de Montpellier, France/ Université du Québec à Rimouski, QC, Canada
Ph.D. thesis on the relationship between co-occurrence and ecological interactions.
06/2012–09/2012: Research Associate
École Normale Supérieure, Paris, France
Worked on applying wavelets analysis to the spread of dengue in Southern Asia.
Education
2016: Doctor of Philosophy in Ecology (grade: Excellent). Université du Québec À Rimouski, Canada / Université de Montpellier, France (Joint PhD).
2012: M.Sc, Ecology and Evolution. AgroParisTech, Paris, France.
2011: General agronomy diploma. AgroParisTech, Paris, France.
Computational Skills
Scientific programming
■ ■ ■ ■ ■ R
■ ■ ■ ■ □ Julia
■ ■ ■ □ □ Python
■ ■ ■ □ □ Matlab/Octave
■ ■ ■ □ □ C/C++
■ ■ ■ □ □ Java
■ ■ ■ □ □ Sage
■ ■ ■ ■ □ Bash
Reproducibility
■ ■ ■ ■ □ Git
■ ■ ■ ■ □ GitHub Actions
■ ■ ■ ■ □ Docker
■ ■ ■ □ □ Dagster
■ ■ □ □ □ Kubernetes
■ ■ ■ □ □ Torque/Slurm
Database
■ ■ ■ ■ □ SQL (postgreSQL, SQLite, Oracle, etc.)
■ ■ □ □ □ DuckDB
■ ■ □ □ □ Arrow
■ ■ □ □ □ mongoDB
Modern web technologies
■ ■ ■ ■ □ HTML/CSS/Javascript
■ ■ ■ ■ □ Hugo
■ ■ ■ ■ □ Shiny App
■ ■ □ □ □ Spring Framework
Document preparation
■ ■ ■ ■ □ Markdown/R Markdown/Quarto
■ ■ ■ ■ □ Latex
■ ■ ■ ■ □ Pandoc
■ ■ ■ ■ □ Inkscape
■ ■ ■ ■ □ LibreOffice / Microsoft Office
Teaching and workshops
2022: Led a workshop on building Shiny applications
. Environment and Climate Change Canada, Dartmouth, NS, Canada, 2 days.
2022: Led a workshop to learn how to use git, GitHub and R Markdown to work more collaboratively
. Environment and Climate Change Canada, Dartmouth, NS, Canada, 2 days.
2022: Led a workshop to learn how to use git and GitHub to work more collaboratively
. Bedford Institute of Oceanography, Halifax NS, Canada, 4 days.
2021: Led a workshop on manipulating and visualising spatial data with R
. Environment and Climate Change Canada, Dartmouth, NS, Canada, 2 days.
2021: Led a workshop on creating reproducible workflows
. Bedford Institute of Oceanography, Halifax NS, Canada, 2 days.
2021: Led a workshop on manipulating and visualising rasters with R
. Bedford Institute of Oceanography, Halifax NS, Canada, 2 days.
2020: Led an advanced statistics workshop (QCBS R workshop series)
. Université du Québec à Rimouski, Rimouski QC, Canada, 1 week.
2019: Led an introduction to R
. Université du Québec à Montréal, Montreal QC, Canada, 2 days.
2018: Led a workshop on how to R as a geographic information system
. Institut de recherche en biologie végétale, Montreal QC, Canada, 3 h.
2017: Instructor in a meta-analyses workshop
. Centre de la Science de la Biodiversité du Québec (CSBQ), Canada, 3 days.
2017: Instructor in the summer school “Bayesian Statistics for Ecologists”
. University of Sherbrooke, Sherbrooke QC, Canada, 5 days.
2016: Organized a two-days event on data visualisation in biodiversity science for graduate students
. Quebec Centre For Biodiversity Science, Canada, 2 days.
2015: “Led an introduction to Markov chains”
. Université du Québec à Rimouski, Canada, 3 h.
2014–2016: Presenter for the QCBS R workshop series
. Université du Québec à Rimouski, Canada, 16 h/year.
2014–2015: Advanced R course on data visualisation and graphics editing
. Université du Québec à Rimouski, Canada, 1 day/year.
2013–2015: Practical course for first year undergraduates in developmental biology (TA)
. Université de Montpelier, France, 64 h/year.
2014: Led an advanced R course on map editing. Universidade Federal de Minas Gerais, Brazil, 1 day.
Alexandra Huybregts, undergraduate student (2021). Co-supervisor/second reader of Honours Thesis
.
Sarah Marshall, undergraduate student (2018). Co-supervisor/second reader of Honours Thesis
.
Valesca de Groot, undergraduate student (2018). Co-supervisor/second reader of Honours Thesis
.
Emelia Myles-Gonzales, B.Sc. student (2018). Mentored student in development of statistical modeling
.
Publications
Peer reviewed
Cazelles K. (2023). Isolating interactions from co-occurrences. Nature Ecology & Evolution. doi: 10.1038/s41559-023-02245-z.
Harvey E., Marleau J., Gounand I., Leroux S., Firkowski C., Altermatt F., Guillaume Blanchet F., Cazelles K., Chu C., D’Aloia C., Donelle L., Gravel D., Guichard F., McCann K., Ruppert J., Ward C. & Fortin M. (2023). A general meta‐ecosystem model to predict ecosystem functions at landscape extents. Ecography. doi: 10.1111/ecog.06790.
Cazelles B., Cazelles K., Tian H., Chavez M. & Pascual M. (2023). Disentangling local and global climate drivers in the population dynamics of mosquito-borne infections. Science Advances. doi: 10.1126/sciadv.adf7202.
Beauchesne D., Cazelles K., Daigle R., Gravel D. & Archambault P. (2023). Ecological interactions amplify cumulative effects in marine ecosystems. Preprint. doi: 10.21203/rs.3.rs-3296860/v1.
Saulnier-Talbot É., Duchesne E., Antoniades D., Arseneault D., Barnard C., Berteaux D., Bhiry N., Bouchard F., Boudreau S., Cazelles K., Comte J., Corbeil-Robitaille M., Côté S., Couture R., Fontaine G., Domine F., Fauteux D., Fortier D., Garneau M., Gauthier G., Gravel D., Laurion I., Lavoie M., Lecomte N., Legagneux P., Lévesque E., Naud M., Paquette M., Payette S., Pienitz R., Rautio M., Roy A., Royer A., Simard M., Vincent W. & Bêty J. (2023). State shifts and divergent sensitivities to climate warming across northern ecosystems. Preprint. doi: 10.21203/rs.3.rs-3026284/v1.
Gutgesell M., McCann K., Gellner G., Cazelles K., Greyson-Gaito C., Bieg C., Guzzo M., Warne C., Ward C., O’Connor R., Scott A., Graham B., Champagne E. & McMeans B. (2022). On the dynamic nature of omnivory in a changing world. BioScience. doi: 10.1093/biosci/biab144.
Galiana N., Lurgi M., Bastazini V., Bosch J., Cagnolo L., Cazelles K., Claramunt-López B., Emer C., Fortin M., Grass I., Hernández-Castellano C., Jauker F., Leroux S., McCann K., McLeod A., Montoya D., Mulder C., Osorio-Canadas S., Reverté S., Rodrigo A., Steffan-Dewenter I., Traveset A., Valverde S., Vázquez D., Wood S., Gravel D., Roslin T., Thuiller W. & Montoya J. (2022). Ecological network complexity scales with area. Nature Ecology & Evolution. doi: 10.1038/s41559-021-01644-4.
Beauchesne D., Cazelles K., Archambault P., Dee L. & Gravel D. (2021). On the sensitivity of food webs to multiple stressors. Ecology Letters. doi: 10.1111/ele.13841.
Poisot T., Bergeron G., Cazelles K., Dallas T., Gravel D., MacDonald A., Mercier B., Violet C. & Vissault S. (2021). Global knowledge gaps in species interaction networks data. Journal of Biogeography. doi: 10.1111/jbi.14127.
McCann K., Cazelles K., MacDougall A., Fussmann G., Bieg C., Cristescu M., Fryxell J., Gellner G., Lapointe B. & Gonzalez A. (2020). Landscape modification and nutrient‐driven instability at a distance. Ecology Letters. doi: 10.1111/ele.13644.
Cazelles K., Zemlak T., Gutgesell M., Myles-Gonzalez E., Hanner R. & Shear McCann K. (2021). Spatial fingerprinting: Horizontal fusion of multi-dimensional bio-tracers as solution to global food provenance problems. Foods. doi: 10.3390/foods10040717.
Blanchet F., Cazelles K. & Gravel D. (2020). Co‐occurrence is not evidence of ecological interactions. Ecology Letters. doi: 10.1111/ele.13525.
Warne C., McCann K., Rooney N., Cazelles K. & Guzzo M. (2020). Geography and morphology affect the ice duration dynamics of northern hemisphere lakes worldwide. Geophysical Research Letters. doi: 10.1029/2020gl087953.
Solarik K., Cazelles K., Messier C., Bergeron Y. & Gravel D. (2019). Priority effects will impede range shifts of temperate tree species into the boreal forest. Journal of Ecology. doi: 10.1111/1365-2745.13311.
Poisot T., Bergeron G., Cazelles K., Dallas T., Gravel D., Macdonald A., Mercier B., Violet C. & Vissault S. (2020). Environmental biases in the study of ecological networks at the planetary scale. Preprint. doi: 10.1101/2020.01.27.921429.
Brice M., Cazelles K., Legendre P. & Fortin M. (2019). Disturbances amplify tree community responses to climate change in the temperate–boreal ecotone. Global Ecology and Biogeography. doi: 10.1111/geb.12971.
Cazelles K. & Vissault S. (2019). Rmangal: Making ecological networks easily accessible. Preprint. doi: 10.59350/51nby-5v347.
Cazelles K., Bartley T., Guzzo M., Brice M., MacDougall A., Bennett J., Esch E., Kadoya T., Kelly J., Matsuzaki S., Nilsson K. & McCann K. (2019). Homogenization of freshwater lakes: Recent compositional shifts in fish communities are explained by gamefish movement and not climate change. Global Change Biology. doi: 10.1111/gcb.14829.
Albouy C., Archambault P., Appeltans W., Araújo M., Beauchesne D., Cazelles K., Cirtwill A., Fortin M., Galiana N., Leroux S., Pellissier L., Poisot T., Stouffer D., Wood S. & Gravel D. (2019). The marine fish food web is globally connected. Nature Ecology & Evolution. doi: 10.1038/s41559-019-0950-y.
Cazelles K. & McCann K. (2019). Diversity-stability and the structure of perturbations. Peer Community In Ecology. doi: 10.24072/pci.ecology.100017.
Bartley T., Guzzo M., Cazelles K., Verville A., McMeans B. & McCann K. (2019). Thermal preference influences depth use but not biomass of predatory fishes in response to lake morphometry. Preprint. doi: 10.1101/572925.
Bartley T., McCann K., Bieg C., Cazelles K., Granados M., Guzzo M., MacDougall A., Tunney T. & McMeans B. (2019). Food web rewiring in a changing world. Nature Ecology & Evolution. doi: 10.1038/s41559-018-0772-3.
Bartomeus I., Cazelles K. & Geschke J. (2018). Rcites - the story behind the package. Preprint. doi: 10.59350/4q40p-bxr56.
Wheeler H., Berteaux D., Furgal C., Cazelles K., Yoccoz N. & Grémillet D. (2019). Identifying key needs for the integration of social–ecological outcomes in arctic wildlife monitoring. Conservation Biology. doi: 10.1111/cobi.13257.
Geschke J., Cazelles K. & Bartomeus I. (2018). Rcites: An r package to access the CITES speciesplus database. Journal of Open Source Software. doi: 10.21105/joss.01091.
Galiana N., Lurgi M., Claramunt-López B., Fortin M., Leroux S., Cazelles K., Gravel D. & Montoya J. (2018). The spatial scaling of species interaction networks. Nature Ecology & Evolution. doi: 10.1038/s41559-018-0517-3.
MacDougall A., Harvey E., McCune J., Nilsson K., Bennett J., Firn J., Bartley T., Grace J., Kelly J., Tunney T., McMeans B., Matsuzaki S., Kadoya T., Esch E., Cazelles K., Lester N. & McCann K. (2018). Context-dependent interactions and the regulation of species richness in freshwater fish. Nature Communications. doi: 10.1038/s41467-018-03419-1.
Legagneux P., Casajus N., Cazelles K., Chevallier C., Chevrinais M., Guéry L., Jacquet C., Jaffré M., Naud M., Noisette F., Ropars P., Vissault S., Archambault P., Bêty J., Berteaux D. & Gravel D. (2018). Our house is burning: Discrepancy in climate change vs. Biodiversity coverage in the media as compared to scientific literature. Frontiers in Ecology and Evolution. doi: 10.3389/fevo.2017.00175.
Kopelke J., Nyman T., Cazelles K., Gravel D., Vissault S. & Roslin T. (2017). Food‐web structure of willow‐galling sawflies and their natural enemies across europe. Ecology. doi: 10.1002/ecy.1832.
Massol F., Dubart M., Calcagno V., Cazelles K., Jacquet C., Kéfi S. & Gravel D. (2017). Island biogeography of food webs. Advances in ecological research. doi: 10.1016/bs.aecr.2016.10.004.
Cazelles K., Mouquet N., Mouillot D. & Gravel D. (2016). On the integration of biotic interaction and environmental constraints at the biogeographical scale. Ecography. doi: 10.1111/ecog.01714.
Poisot T., Cirtwill A., Cazelles K., Gravel D., Fortin M. & Stouffer D. (2015). The structure of probabilistic networks. Methods in Ecology and Evolution. doi: 10.1111/2041-210x.12468.
Cazelles K., Araújo M., Mouquet N. & Gravel D. (2015). A theory for species co-occurrence in interaction networks. Theoretical Ecology. doi: 10.1007/s12080-015-0281-9.
Le Stradic S., Silveira F., Buisson E., Cazelles K., Carvalho V. & Fernandes G. (2015). Diversity of germination strategies and seed dormancy in herbaceous species of campo rupestre grasslands. Austral Ecology. doi: 10.1111/aec.12221.
Cazelles B. & Cazelles K. (2014). Major urban centers have weak influence on the timing of dengue epidemics in southeast asia. International Journal of Infectious Diseases. doi: 10.1016/j.ijid.2014.03.873.
Cazelles B., Cazelles K. & Chavez M. (2014). Wavelet analysis in ecology and epidemiology: Impact of statistical tests. Journal of The Royal Society Interface. doi: 10.1098/rsif.2013.0585.
Cazelles K., Otten W., Baveye P. & Falconer R. (2013). Soil fungal dynamics: Parameterisation and sensitivity analysis of modelled physiological processes, soil architecture and carbon distribution. Ecological Modelling. doi: 10.1016/j.ecolmodel.2012.08.008.
Reports
Stoyel Q., Finnis S., Gomez C., Lazin G., Daigle R., Lindsay B., Adrian H., Charlotte S., David B., Sean B. & Cazelles K. (2022). An open, efficient, and transparent spatial reproducible reporting tool for data discovery and science advice
. Canadian Technical Report of Fisheries and Aquatic Sciences 3495
.
Popularization
Cazelles K. (2014). La Biodiversité en territoire isolée. Accromath.
Legagneux P., Cazelles K. & Gravel D. (2019). Sommes-nous bien informés ? : écarts entre la couverture du changement climatique et de la biodiversité par les médias et la littérature scientifique. Climatoscope.
Cazelles K., Myles-Gonzalez E., Zemlak T. & McCann K. (2019-12-19). Embracing the blessing of dimensionality to determine species’ provenance. QCBS Annual symposium. Montreal, QC, Canada.
Cazelles K., Gravel D. & McCann K. (2018-08-01). Towards an Energetic Theory of Island biogeography. ESA Annual Meeting. New-Orleans, LA, USA.
Cazelles K., Myles-Gonzalez E., Zemlak T. & McCann K. (2018-07-01). Fighgting Noise with dimensionality. CSEE Annual Meeting. Guelph, ON, Canada.
Cazelles K., Gravel D. & McCann K. (2017-12-01). Towards an Energetic Theory of Island biogeography. Ecology Across Borders. Ghent, Belgium.
Cazelles K., Gravel D. & McCann K. (2017-12-01). Do ecological interactions impact geographic distributions of species?. Ecology Across Borders. Ghent, Belgium.
Vissault S. & Cazelles K. (2017-01-08). Teaser of the alien R package. R à Québec. Québec, QC, Canada.
Cazelles K., Mouquet N. & Gravel D. (2015-12-01). Do ecological interaction impact geographical distributions of species?. QCBS - Annual Symposium. Montreal, QC, Canada.
Cazelles K., Mouquet N., Mouillot D. & Gravel D. (2015-08-01). Integration of ecological networks in a theoretical stochastic model of biogeography. CSEE - Annual Meeting. Saskatoon, SK, Canada.
Cazelles K., Mouquet N., Mouillot D. & Gravel D. (2014-12-01). Integration of ecological networks in a theoretical stochastic model of biogeography. BES-SFE - Joint Annual Meeting. Lille, France.
Cazelles K. & Cazelles B. (2012-08-01). Wavelet Clustering, a tool to integrate spatial and temporal patterns based on their dynamical properties, application to dengue in Thailand. Model in Population Biology. Santa Maria, Brazil.
Seminars
Cazelles K. (2018-10-12). Do biotic interactions affect species distribution?. Université de Sherbrooke. Université de Sherbrooke.
Vissault S., Gravel D., Cazelles K. & Poisot T.. Mangal, a global ecological interactions database. biodiversitynext. Leiden – The Netherlands (2018-08-01).
Brice M., Legendre P., Cazelles K. & Fortin M.. Long-term forest community changes in the boreal-temperate ecotone. ESA Annual Meeting. New-Orleans, LA, USA (2018-08-01).
Beauchesne D., Cazelles K., Archambault P. & Gravel D.. Predicting the spatial distribution of ecological networks. CSEE Annual meeting. Victoria, BC, Canada (2017-08-01).
Legagneux P., Casajus N., Cazelles K., Chevallier C., Chevrinais M., Guéry L., Jacquet C., Jaffré M., Naud M., Noisette F., Ropars P., Vissault S., Archambault P., Bêty J., Berteaux D. & Gravel D.. The Earth Tribune. ArcticNet Meeting. Winnipeg, MB, Canada (2016-12-01).
Software
This section includes a subset of my contributions to open-source software. If you are interested in seeing more, most of my contributions can be found on my GitHub account, see also the section “notes” of my website.
packages
Below is a selection of R packages I significantly contributed to.
rcites (maintainer): R client to access the Speciesplus database via the Speciesplus/CITES Checklist API.
.
inSilecoMisc (maintainer): Miscellaneous R functions
.
disker (maintainer): Rcpp implementation of 5 isotropic dispersal kernels
.
motifcensus (maintainer): Rcpp implementation that counts the different positions occupied by the different species in all the 3 species motifs of a given unipartite network
.
rmangal (contributor): R client for the Mangal database
.
rgovcan (contributor): R package to interact with the Open Canada API
.
Shiny applications
Below are the Shiy applications I significantly contributed to.
Spatial Reproducible Reporting (developer): R Shiny App to select search area(s) and generate reproducible reports (R Markdown)
.
Research compendia
I am strongly committed to making the research I do reproducible. To that end, every study I lead comes with a research compendium. Below is a list of selected research compendia that were published along side with the corresponding paper.
Spatial Fingerprinting: Creation of spatial fingerprint combining biotracers, determination of geographic origin using machine learning
(paper’s doi: 10.3390/foods10040717). 10.5281/zenodo.4602032
NDID: Theoretical investigations in meta-ecosystem theory, build and solve ordinary differential equations
(paper’s doi: 10.1111/ele.13644). 10.5281/zenodo.4081347
coocNotInteract: Probabilistic modelling to explain why co-occurrence is not evidence of ecological interaction
(paper’s doi: 10.1111/ele.13525). 10.5281/zenodo.3733206
monitoringOutcomes: Networks analysis to identify desired outcomes of arctic wildlife monitoring and the links between them
(paper’s doi: 10.1111/cobi.13257). 10.5281/zenodo.1652737
burningHouse: Comparison of media coverage of climate change and media coverage of biodiversity crisis
(paper’s doi: 10.1111/cobi.13257). 10.5281/zenodo.1134897
