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Ouvrir le dossier des exemples de fichiers audioGoogle Colab
Google Colab est un service permettant d’éxécuter du code (R, Python) sur un ordinateur à distance.
Nous fournissons quelques exemples permettant de se familiariser avec les bases de l’analyse de données pour le suivi acoustique passif.
- Détection automatique avec BirdNET
- Lecture des données et métadonnées audio
- Échantillons audio et spectrogrammes
- Calcul d’indices acoustiques avec Python
- Calcul d’indices acoustiques avec R
Références
Références clés
- Bradfer-Lawrence, T., Desjonqueres, C., Eldridge, A., Johnston, A., Metcalf, O., 2023. Using acoustic indices in ecology: guidance on study design, analyses and interpretation. Methods Ecol. Evol. 14, 2192–2204. https://doi.org/10.1111/2041- 210X.14194
- Browning, E., Gibb, R., Glover-Kapfer, P., & Jones, K. E. (2017). Passive acoustic monitoring in ecology and conservation (No. 2; WWF Conservation Technology Series, p. 75). WWF-UK
- Gibb, R., Browning, E., Glover‐Kapfer, P., & Jones, K. E. (2019). Emerging opportunities and challenges for passive acoustics in ecological assessment and monitoring. Methods in Ecology and Evolution, 10(2), 169-185. https://doi.org/10.1111/fwb.13356
- Sugai, L.S.M., Desjonquères, C., Silva, T.S.F. and Llusia, D. (2020), A roadmap for survey designs in terrestrial acoustic monitoring. Remote Sens Ecol Conserv, 6: 220-235. https://doi.org/10.1002/rse2.131
- Bittencourt, L., Barbosa, M., Secchi, E., Lailson-Brito, J. & Azevedo, A. (2016). Acoustic habitat of an oceanic archipelago in the Southwestern Atlantic. Deep Sea Res. Part I Oceanogr. Res. Pap., 115, 103–111.
- Boelman, N. T., Asner, G. P., Hart, P. J., & Martin, R. E. (2007). Multitrophic invasion resistance in Hawaii: Bioacoustics, field surveys, and airborne remote sensing. Ecological Applications, 17(8), 21372144. https:// doi.org/10.1890/07-0004.1
- Bonthoux, S., and G. Balent. 2012. Point count duration: five minutes are usually sufficient to model the distribution of bird species and to study the structure of communities for a French landscape. J. Ornithol. 153, 491.
- Bradfer-Lawrence, T., B. Duthie, C. Abrahams, M. Adam, R. J. Barnett, A. Beeston, J. Darby, B. Dell, N. Gardner, A. Gasc, B. Heath, N. Howells, M. Janson, M.-V. Kyoseva, T. Luypaert, O. C. Metcalf, A. E. Nousek-McGregor, F. Poznansky, S. R. P.-J. Ross, S. Sethi, S. Smyth, E. Waddell, et J. S. P. Froidevaux. 2024. The Acoustic Index User’s Guide : A practical manual for defining, generating and understanding current and future acoustic indices. Methods in Ecology and Evolution.
- Buxton, R. T., M. F. McKenna, M. Clapp, E. Meyer, E. Stabenau, L. M. Angeloni, K. Crooks, et G. Wittemyer. 2018. Efficacy of Extracting Indices from Large-Scale Acoustic Recordings to Monitor Biodiversity. Conservation Biology 32 :11741184.
- Campos-Cerqueira, M., & Aide, T. M. (2016). Improving distribution data of threatened species by combining acoustic monitoring and occupancy modelling. Methods in Ecology and Evolution, 7, 1340–1348. https://doi.org/10.1111/2041-210x.12599
- Depraetere, M., S. Pavoine, F. Jiguet, A. Gasc, S. Duvail, and J. Sueur. 2012. Monitoring animal diversity using acoustic indices: implementation in a temperate woodland. Ecol. Indic. 13, 46.
- Desjonquères, C., Rybak, F., Depraetere, M., Gasc, A., Le Viol, I., Pavoine, S., et al. (2015). First description of underwater acoustic diversity in three temperate ponds. PeerJ, 3, e1393.
- Dorcas, M. E., S. J. Price, S. C. Walls, and W. J. Barichivich. 2009. Auditory monitoring of anuran population. in C. K. Dodd, ed. Conservation and ecology in amphibians: 281–298. Oxford University Press, Oxford, UK.
- Erbe, C., Verma, A., McCauley, R., Gavrilov, A. & Parnum, I. (2015). The marine soundscape of the Perth Canyon. Prog. Oceanogr., 137, 38–51.
- Farina, A., Pieretti, N. & Piccioli, L. (2011). The soundscape methodology for long-term bird monitoring: A Mediterranean Europe case-study. Ecol. Inform., 6, 354–363.
- Fuller, S., Axel, A.C., Tucker, D. & Gage, S.H. (2015). Connecting soundscape to landscape: Which acoustic index best describes landscape configuration? Ecol. Indic., 58, 207–215.
- Halfwerk, W., Holleman, L.J.M., Lessells, C.M. & Slabbekoorn, H. (2011). Negative impact of traffic noise on avian reproductive success. J. Appl. Ecol., 48, 210–219.
- Kaczmarski, M., Kaczmarek, J.M., Radzińska, A. et al. Passive acoustic monitoring reveals seasonal patterns in European green toad calling activity but fails to accurately reflect population abundance. Sci Rep 15, 26447 (2025). https://doi.org/10.1038/s41598-025-11706-3
- Kasten, E. P., Gage, S. H., Fox, J., & Joo, W. (2012). The remote environmental assessment laboratory’s acoustic library: An archive for studying soundscape ecology. Ecological Informatics, 12, 50–67. https:// doi.org/10.1016/j.ecoinf.2012.08.001
- Lucas, T. C. D., Moorcroft, E. A., Freeman, R., Rowcliffe, J. M., & Jones, K. E. (2015). A generalised random encounter model for estimating animal density with remote sensor data. Methods in Ecology and Evolution, 6, 500–509. https://doi.org/10.1111/2041-210X.12346
- Marques, T. A., Thomas, L., Martin, S. W., Mellinger, D. K., Ward, J. A., Moretti, D. J., & Tyack, P. L. (2013). Estimating animal population density using passive acoustics. Biological Reviews, 88, 287–309. https://doi.org/10.1111/brv.12001
- Merchant, N. D., Fristrup, K. M., Johnson, M. P., Tyack, P. L., Witt, M. J., Blondel, P., & Parks, S. E. (2015). Measuring acoustic habitats. Methods in Ecology and Evolution, 6, 257–265. https://doi. org/10.1111/2041-210X.12330
- Nedelec, S.L., Simpson, S.D., Holderied, M., Radford, A.N., Lecellier, G., Radford, C., et al. (2015). Soundscapes and living communities in coral reefs: temporal and spatial variation. Mar. Ecol. Prog. Ser., 524, 125–135.
- Petrusková, T., Pišvejcová, I., Kinštová, A., Brinke, T., & Petrusek, A. (2016). Repertoire-based individual acoustic monitoring of a migratory passerine bird with complex song as an efficient tool for tracking territorial dynamics and annual return rates. Methods in Ecology and Evolution, 7, 274–284. https://doi.org/10.1111/2041-210X.12496
- Pieretti, N., Farina, A., & Morri, D. (2011). A new methodology to infer the singing activity of an avian community: The Acoustic Complexity Index (ACI). Ecological indicators, 11(3), 868-873.
- Shirose, L. J., C. A. Bishop, D. M. Green, J. M. Cameron, R. J. Brooks, and J. H. Natalie. 1997. Validation tests of an amphibian call count survey technique in Ontario, Canada. Herpetologica 53, 312.
- Sueur, J., T. Aubin, et C. Simonis. 2008. Seewave, a free modular tool for sound analysis and synthesis. Bioacoustics 18 :213‑226.
- Towsey, M., Wimmer, J., Williamson, I., & Roe, P. (2014). The use of acoustic indices to determine avian species richness in audio-recordings of the environment. Ecological Informatics, 21, 110–119. https://doi. org/10.1016/j.ecoinf.2013.11.007
- Tucker, D., Gage, S.H., Williamson, I. & Fuller, S. (2014). Linking ecological condition and the soundscape in fragmented Australian forests. Landsc. Ecol., 29, 745–758.
- Villanueva-Rivera, L. J., Pijanowski, B. C., Doucette, J., & Pekin, B. (2011). A primer of acoustic analysis for landscape ecologists.Landscape Ecology, 26(9), 1233–1246. https:// doi.org/10.1007/s10980- 011-9636-9
- Bonthoux, S., and G. Balent. 2012. Point count duration: five minutes are usually sufficient to model the distribution of bird species and to study the structure of communities for a French landscape. J. Ornithol. 153, 491.
- Bradfer-Lawrence, T., Desjonqueres, C., Eldridge, A., Johnston, A., Metcalf, O., 2023. Using acoustic indices in ecology: guidance on study design, analyses and interpretation. Methods Ecol. Evol. 14, 2192–2204. https://doi.org/10.1111/2041- 210X.14194
- Browning, E., Gibb, R., Glover-Kapfer, P., & Jones, K. E. (2017). Passive acoustic monitoring in ecology and conservation (No. 2; WWF Conservation Technology Series, p. 75). WWF-UK
- Dorcas, M. E., S. J. Price, S. C. Walls, and W. J. Barichivich. 2009. Auditory monitoring of anuran population. in C. K. Dodd, ed. Conservation and ecology in amphibians: 281–298. Oxford University Press, Oxford, UK.
- Gibb, R., Browning, E., Glover‐Kapfer, P., & Jones, K. E. (2019). Emerging opportunities and challenges for passive acoustics in ecological assessment and monitoring. Methods in Ecology and Evolution, 10(2), 169-185. https://doi.org/10.1111/fwb.13356
- Shirose, L. J., C. A. Bishop, D. M. Green, J. M. Cameron, R. J. Brooks, and J. H. Natalie. 1997. Validation tests of an amphibian call count survey technique in Ontario, Canada. Herpetologica 53, 312.
- Sugai, L.S.M., Desjonquères, C., Silva, T.S.F. and Llusia, D. (2020), A roadmap for survey designs in terrestrial acoustic monitoring. Remote Sens Ecol Conserv, 6: 220-235. https://doi.org/10.1002/rse2.131
- Hanf‐Dressler, T., Nouioua, R., Thomisch, K., Cazau, D., De Selys Longchamps, S., & Darras, K. (2026). Software Tools for Passive Acoustic Monitoring in Aquatic and Terrestrial Bio- and Ecoacoustics: A Living Systematic Review. F1000Research, 15. https://doi.org/10.12688/f1000research.173495.1.
- Mellinger, D. K., Stafford, K. M., Moore, S. E., Dziak, R. P., & Matsumoto, H. (2007). An overview of fixed passive acoustic observation methods for cetaceans. Oceanography, 20(4), 36-45.
- Clare, J. D. J., P. A.Townsend, and B.Zuckerberg. 2021. Generalized model-based solutions to false-positive error in species detection/nondetection data. Ecology102(2):e03241. 10.1002/ecy.3241
- Pijanowski BC, Villanueva-Rivera LJ, Dumyahn SL, Farina A, Krause BL, Napoletano BM, Gage SH, Pieretti N. 2011. Soundscape ecology: The science of sound in the landscape. BioScience 61: 203–216.
- Sueur J, Farina A. 2015. Ecoacoustics: The ecological investigation and interpretation of environmental sound. Biosemiotics 8: 493–502.