Publications
Peer-reviewed publications
(last automatic update: 2024-09-29)
- Sonabend R, Gruson H, Wolansky L, Kiragga A, Katz D (2024). “FAIR-USE4OS: Guidelines for creating impactful open-source software.” PLoS Computational Biology, 20(5), e1012045. doi:10.1371/journal.pcbi.1012045, https://hal.science/hal-04711753.
- Grenié M, Gruson H (2023). “fundiversity: a modular R package to compute functional diversity indices.” Ecography, 2023(3), e06585. doi:10.1111/ecog.06585, https://hal.science/hal-04022533.
- Sherratt K, Gruson H, Grah R, Johnson H, Niehus R, Prasse B, Sandmann F, Deuschel J, Wolffram D, Abbott S, Ullrich A, Gibson G, Ray E, Reich N, Sheldon D, Wang Y, Wattanachit N, Wang L, Trnka J, Obozinski G, Sun T, Thanou D, Pottier L, Krymova E, Meinke J, Barbarossa MV, Leithauser N, Mohring J, Schneider J, Wlazlo J, Fuhrmann J, Lange B, Rodiah I, Baccam P, Gurung H, Stage S, Suchoski B, Budzinski J, Walraven R, Villanueva I, Tucek V, Smid M, Zajicek M, Perez Alvarez C, Reina B, Bosse N, Meakin S, Castro L, Fairchild G, Michaud I, Osthus D, Alaimo Di Loro P, Maruotti A, Eclerova V, Kraus A, Kraus D, Pribylova L, Dimitris B, Li ML, Saksham S, Dehning J, Mohr S, Priesemann V, Redlarski G, Bejar B, Ardenghi G, Parolini N, Ziarelli G, Bock W, Heyder S, Hotz T, Singh D, Guzman-Merino M, Aznarte J, Morina D, Alonso S, Alvarez E, Lopez D, Prats C, Burgard JP, Rodloff A, Zimmermann T, Kuhlmann A, Zibert J, Pennoni F, Divino F, Catala M, Lovison G, Giudici P, Tarantino B, Bartolucci F, Jona Lasinio G, Mingione M, Farcomeni A, Srivastava A, Montero-Manso P, Adiga A, Hurt B, Lewis B, Marathe M, Porebski P, Venkatramanan S, Bartczuk R, Dreger F, Gambin A, Gogolewski K, Gruziel-Slomka M, Krupa B, Moszyński A, Niedzielewski K, Nowosielski J, Radwan M, Rakowski F, Semeniuk M, Szczurek E, Zielinski J, Kisielewski J, Pabjan B, Holger K, Kheifetz Y, Scholz M, Przemyslaw B, Bodych M, Filinski M, Idzikowski R, Krueger T, Ozanski T, Bracher J, Funk S (2023). “Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations.” eLife, 12. doi:10.7554/elife.81916, https://hal.science/hal-04224083.
- Meakin S, Abbott S, Bosse N, Munday J, Gruson H, Hellewell J, Sherratt K, Chapman L, Prem K, Klepac P, Jombart T, Knight G, Jafari Y, Flasche S, Waites W, Jit M, Eggo R, Villabona-Arenas CJ, Russell T, Medley G, Edmunds WJ, Davies N, Liu Y, Hué S, Brady O, Pung R, Abbas K, Gimma A, Mee P, Endo A, Clifford S, Sun FY, Mccarthy C, Quilty B, Rosello A, Sandmann F, Barnard R, Kucharski A, Procter S, Jarvis C, Gibbs H, Hodgson D, Lowe R, Atkins K, Koltai M, Pearson C, Finch E, Wong K, Quaife M, O’reilly K, Tully D, Funk S (2022). “Comparative assessment of methods for short-term forecasts of COVID-19 hospital admissions in England at the local level.” BMC Medicine, 20(1), 86. doi:10.1186/s12916-022-02271-x, https://hal.science/hal-03596660.
- Gruson H, Elias M, Parra JL, Andraud C, Berthier S, Doutrelant C, Gomez D (2021). “Distribution of iridescent colours in hummingbird communities results from the interplay between selection for camouflage and communication.” Peer Community Journal, 1, e64. doi:10.24072/pcjournal.7, https://hal.science/hal-02372238.
- Vergne T, Gubbins S, Guinat C, Bauzile B, Delpont M, Chakraborty D, Gruson H, Roche B, Andraud M, Paul M, Guérin J (2021). “Inferring within-flock transmission dynamics of highly pathogenic avian influenza H5N8 virus in France, 2020.” Transboundary and emerging diseases, 68(6), 3151-3155. doi:10.1111/tbed.14202, https://hal.inrae.fr/hal-03479732.
- Gruson H (2020). “Digest: Evolution of camouflage patterns in geckos.” Evolution - International Journal of Organic Evolution, 74(6), 1224-1225. doi:10.1111/evo.13999, This article is a digest of Allen W, Moreno N, Gamble T, Chiari Y. Ecological, behavioral and phylogenetic influences on the evolution of dorsal color pattern in geckos. Evolution. 2020. https://doi.org/10.1111/evo.13915. https://onlinelibrary.wiley.com/doi/10.1111/evo.13915, https://hal.science/hal-02570373.
- Gruson H (2020). “Estimation of colour volumes as concave hypervolumes using \(\alpha\)-shapes.” Methods in Ecology and Evolution, 11(8), 955-963. doi:10.1111/2041-210X.13398, https://hal.science/hal-02558986.
- Gruson H, Andraud C, Daney de Marcillac W, Berthier S, Elias M, Gomez D (2019). “Quantitative characterization of iridescent colours in biological studies: a novel method using optical theory.” Interface Focus, 9(1), 20180049. doi:10.1098/rsfs.2018.0049, https://hal.science/hal-01961448.
- Gruson H, White T, Maia R (2019). “lightr: import spectral data and metadata in R.” Journal of Open Source Software, 4(43), 1857. doi:10.21105/joss.01857, https://hal.science/hal-02342889.
- Maia R, Gruson H, Endler J, White T (2019). “pavo 2: new tools for the spectral and spatial analysis of colour in R.” Methods in Ecology and Evolution, 10(7), 1097-1107. doi:10.1111/2041-210X.13174, https://hal.science/hal-02063659.
- Gruson H (2019). “Digest: Disentangling plumage and behavior contributions to iridescent signals.” Evolution - International Journal of Organic Evolution, 73(3), 623-625. doi:10.1111/evo.13685, This article is a digest of Simpson, R. K., and K. J. McGraw. 2018. Experimental trait mis-matches uncover specificity of evolutionary links between multiple signaling traits and their interactions in hummingbirds. Evolution, doi: 10.1111/evo.13662, https://onlinelibrary.wiley.com/doi/10.1111/evo.13662, https://hal.science/hal-01987390.
Invited blog posts and news items
Things that can go wrong when using renv (2024), featured on the Epiverse-TRACE blog.
- Commented in the R Weekly Highlights podcast
System dependencies in R packages and automatic testing (2023), featured on the R-hub blog
- Commented in the R Weekly Highlights podcast
From hidden to visisble: how can we recognise research software? (2023), featured on the Software Sustainability Institute blog
Ensuring & Showcasing the Statistical Correctness of your R Package (2023), featured on the Epiverse-TRACE blog
- Commented in the R Weekly Highlights podcast
Minimum R version dependency (2022), featured on the R-hub blog
Opening the door to new contributors in open source projects (2022), featured on the Software Sustainability Institute blog.
Why You Should (or Shouldn’t) Build an API client? (2022), featured on rOpenSci blog.
- Commented in the R Weekly Highlights podcast
Dealing with flaky GitHub Actions (2022), featured on EpiForecasts blog.
Checking the Inputs of your R Functions (2022), featured on R-hub blog.
Covidpreprints.com: Automating Website Updates with the europepmc and rAltmetric Packages (2020), featured on rOpenSci blog preLights blog.
Community Captioning of rOpenSci Community Calls (2020), featured on rOpenSci blog.
Access Publisher Copyright & Self-Archiving Policies via the ‘SHERPA/RoMEO’ API (2019), featured on rOpenSci blog.
When Standards Go Wild - Software Review for a Manuscript (2019), featured on rOpenSci blog and Methods in Ecology and Evolution blog.
Observatoire des oiseaux des jardins : premiers résultats (2014), in L’Oiseau Mag (trimestrial magazine of BirdLife France).