Mitchell Lyons

Role: Research Fellow | Lecturer

Bio: I am a postdoc in the Centre for Ecosystem Science, and my research can be described as a mixture of Ecology, Geography and Statistics. I finished my PhD in 2013, at the University of Queensland, which focused on developing new remote sensing methods for long term monitoring and change detection in terrestrial and marine ecosystems. After this I focused on automated monitoring of seagrass environments using remote sensing and autonomous underwater vehicles (AUVs). On moving to the University of New South Wales, I shifted focus to application of modern statistical and modelling approaches for large scale vegetation classification and mapping problems, with a side interest in drone-acquired image data. I also teach remote sensing in some of the courses in the School of Biological, Earth and Environmental Sciences, as well as programming and statistics in various short courses and workshops (http://environmentalcomputing.net/). I am also involved in a project at the University of Queensland - the Paul Allen Coral Atlas - that is mapping every coral reef in the world, and my focus is on developing object-based and machine learning classification and mapping routines.

Technically speaking, my expertise lies in remote sensing and ecological modelling (statistics and machine learning), and I generally take a computational programming (R and Python specifically, and JavaScript on the Google Earth Engine) approach. Non-technically speaking, I love getting into the bush or into the ocean, love bare feet on grass and I have a penchant for cricket and homebrewing.

Research field keywords: ecology, remote sensing and GIS, ecological modelling, vegetation science, statistical ecology

Publications: see my Google Scholar profile (http://scholar.google.com.au/citations?user=9PnIKHYAAAAJ), and please contact me if you would like a copy of any of my papers.

Code + software: see my github page (https://github.com/mitchest/), and check out my R packages/tool if you are so inclined:

optimus - model-based clustering diagnostics - https://cran.r-project.org/web/packages/optimus/index.html

c2c - comparing classification and clustering solutions to eachother - https://cran.r-project.org/web/packages/c2c/index.html

online quantatative vegetation classificaiton tool -  https://mitchest.shinyapps.io/vegplot/

 

phone: +61 2 9385 8296 | email: mitchell.lyons@unsw.edu.au | location: level 5, E26 (biological sciences south) | twitter: @mitchest

 

Organisational units

Publications

Journal articles
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B. Lyons M; M. Roelfsema C; V. Kennedy E; M. Kovacs E; Borrego-Acevedo R; Markey K; Roe M; M. Yuwono D; L. Harris D; R. Phinn S; Asner GP; Li J; E. Knapp D; S. Fabina N; Larsen K; Traganos D; J. Murray N, 2020, 'Mapping the world's coral reefs using a global multiscale earth observation framework', Remote Sensing in Ecology and Conservation, http://dx.doi.org/10.1002/rse2.157
2020
Callaghan CT; Major RE; Cornwell WK; Poore AGB; Wilshire JH; Lyons MB, 2020, 'A continental measure of urbanness predicts avian response to local urbanization', Ecography, vol. 43, pp. 528 - 538, http://dx.doi.org/10.1111/ecog.04863
2020
Inman VL; Lyons MB, 2020, 'Automated Inundation Mapping Over Large Areas Using Landsat Data and Google Earth Engine', Remote Sensing, vol. 12, pp. 1348 - 1348, http://dx.doi.org/10.3390/rs12081348
2020
Francis RJ; Lyons MB; Kingsford RT; Brandis KJ, 2020, 'Counting mixed breeding aggregations of animal species using drones: Lessons from waterbirds on semi-automation', Remote Sensing, vol. 12, pp. 1185 - 1185, http://dx.doi.org/10.3390/rs12071185
2020
Callaghan CT; Major RE; Lyons MB; Martin JM; Wilshire JH; Kingsford RT; Cornwell WK, 2019, 'Using citizen science data to define and track restoration targets in urban areas', Journal of Applied Ecology, vol. 56, pp. 1998 - 2006, http://dx.doi.org/10.1111/1365-2664.13421
2019
McGinness H; Brandis K; Robinson F; Piper M; O'Brien L; Langston A; Hodgson J; Wenger L; Martin J; Bellio M; Callaghan D; Webster E; Francis R; McCann J; Lyons M; Doerr V; Kingsford R; Mac Nally R, 2019, Murray‒Darling Basin Environmental Water Knowledge and Research Project — Waterbird Theme Research Report, https://doi.org/10.26181/5d2eb0ed77159
2019
Morales-Barquero L; Lyons MB; Phinn SR; Roelfsema CM, 2019, 'Trends in remote sensing accuracy assessment approaches in the context of natural resources', Remote Sensing, vol. 11, pp. 2305 - 2305, http://dx.doi.org/10.3390/rs11192305
2019
Lyons MB; Brandis KJ; Murray NJ; Wilshire JH; McCann JA; Kingsford RT; Callaghan CT, 2019, 'Monitoring large and complex wildlife aggregations with drones', Methods in Ecology and Evolution, vol. 10, pp. 1024 - 1035, http://dx.doi.org/10.1111/2041-210X.13194
2019
Webster E; Kingsford RT; Lyons M; Brandis K; Fisher A, 2019, Tracking the Flow Water Pilot Technology Program Final Report
2019
Callaghan CT; Poore AGB; Major RE; Cornwell W; Wilshire J; Lyons M, 2019, 'How to build a biodiverse city: environmental determinants of bird diversity within and among 1,581 cities', EcoEvoRxiv, http://dx.doi.org/10.32942/osf.io/ur4fe
2019
Callaghan CT; Bino G; Major RE; Martin JM; Lyons MB; Kingsford RT, 2019, 'Heterogeneous urban green areas are bird diversity hotspots: insights using continental-scale citizen science data', Landscape Ecology, vol. 34, pp. 1231 - 1246, http://dx.doi.org/10.1007/s10980-019-00851-6
2019
Lee MR; Powell JR; Oberle B; Cornwell WK; Lyons M; Rigg JL; Zanne AE, 2019, 'Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats', Ecology, vol. 100, pp. e02790, http://dx.doi.org/10.1002/ecy.2790
2019
Murray NJ; Phinn SR; DeWitt M; Ferrari R; Johnston R; Lyons MB; Clinton N; Thau D; Fuller RA, 2019, 'The global distribution and trajectory of tidal flats', Nature, vol. 565, pp. 222 - 225, http://dx.doi.org/10.1038/s41586-018-0805-8
2019
Callaghan CT; Major RE; Lyons MB; Martin JM; Kingsford RT, 2018, 'The effects of local and landscape habitat attributes on bird diversity in urban greenspaces', Ecosphere, vol. 9, http://dx.doi.org/10.1002/ecs2.2347
2018
Lyons M; Gordon C; Mills C; Letnic MI, 2018, 'Linking trophic cascades to changes in desert dune geomorphology using high-resolution drone data', Journal of the Royal Society Interface, vol. 15, http://dx.doi.org/10.1098/rsif.2018.0327
2018
O'Brien KR; Waycott M; Maxwell P; Kendrick GA; Udy JW; Ferguson AJP; Kilminster K; Scanes P; McKenzie LJ; McMahon K; Adams MP; Samper-Villarreal J; Collier C; Lyons M; Mumby PJ; Radke L; Christianen MJA; Dennison WC, 2018, 'Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance', Marine Pollution Bulletin, vol. 134, pp. 166 - 176, http://dx.doi.org/10.1016/j.marpolbul.2017.09.006
2018
Lyons M; Brandis K; Callaghan C; McCann J; Mills C; Ryall S; Kingsford RT, 2018, 'Bird interactions with drones, from individuals to large colonies', Australian Field Ornithology, vol. 35, pp. 51 - 56, http://dx.doi.org/10.20938/afo35051056
2018
Addicott E; Laurance S; Lyons M; Butler D; Neldner J, 2018, 'When rare species are not important: Linking plot-based vegetation classifications and landscape-scale mapping in Australian savanna vegetation', Community Ecology, vol. 19, pp. 67 - 76, http://dx.doi.org/10.1556/168.2018.19.1.7
2018
Callaghan CT; Brandis KJ; Lyons MB; Ryall S; Kingsford RT, 2018, 'A comment on the limitations of UAVS in wildlife research – the example of colonial nesting waterbirds', Journal of Avian Biology, vol. 49, http://dx.doi.org/10.1111/jav.01825
2018
Phinn S; Roelfsema C; Kovacs E; Canto R; Lyons M; Saunders M; Maxwell P, 2018, 'Mapping, monitoring and modelling seagrass using remote sensing techniques', in , Springer, pp. 445 - 487, http://dx.doi.org/10.1007/978-3-319-71354-0
2018
Kendrick G; Hovey R; Lyons M; Roelfsema C; Ruiz Montoya L; Phinn S, 2018, 'Australian Seagrass Seascapes: Present Understanding and Future Research Directions', in , Springer, pp. 257 - 286, http://dx.doi.org/10.1007/978-3-319-71354-0
2018
Kendrick GA; Hovey RK; Lyons M; Roelfsema C; Montoya LR; Phinn S, 2018, 'Australian seagrass seascapes: Present understanding and future research directions', in Larkum AWD; Kendrick GA; Ralph PJ (ed.), Seagrasses of Australia: Structure, Ecology and Conservation, Springer, pp. 257 - 286, http://dx.doi.org/10.1007/978-3-319-71354-0_9
2018
Lyons MB; Keith DA; Phinn SR; Mason TJ; Elith J, 2018, 'A comparison of resampling methods for remote sensing classification and accuracy assessment', Remote Sensing of Environment, vol. 208, pp. 145 - 153, http://dx.doi.org/10.1016/j.rse.2018.02.026
2018
Phinn S; Roelfsema C; Kovacs E; Canto R; Lyons M; Saunders M; Maxwell P, 2018, 'Mapping, monitoring and modelling seagrass using remote sensing techniques', in Larkum AWD; Kendrick GA; Ralph PJ (ed.), Seagrasses of Australia: Structure, Ecology and Conservation, Springer, pp. 445 - 487, http://dx.doi.org/10.1007/978-3-319-71354-0_15
2018
Bugnot AB; Lyons MB; Scanes P; Clark GF; Fyfe SK; Lewis A; Johnston EL, 2018, 'A novel framework for the use of remote sensing for monitoring catchments at continental scales', Journal of Environmental Management, vol. 217, pp. 939 - 950, http://dx.doi.org/10.1016/j.jenvman.2018.03.058
2018
Roelfsema C; Kovacs E; Roos P; Terzano D; Lyons M; Phinn S, 2018, 'Use of a semi-automated object based analysis to map benthic composition, Heron Reef, Southern Great Barrier Reef', Remote Sensing Letters, vol. 9, pp. 324 - 333, http://dx.doi.org/10.1080/2150704X.2017.1420927
2018
Lyons M; Lucas R, 2018, 'Remote sensing of wetland types: Sea grasses', in The Wetland Book: I: Structure and Function, Management, and Methods, pp. 1659 - 1663, http://dx.doi.org/10.1007/978-90-481-9659-3_313
2018
Kovacs E; Roelfsema C; Lyons M; Zhao S; Phinn S, 2018, 'Seagrass habitat mapping: How do landsat 8 OLI, sentinel-2, ZY-3A, and worldview-3 perform?', Remote Sensing Letters, vol. 9, pp. 686 - 695, http://dx.doi.org/10.1080/2150704X.2018.1468101
2018
Murray NJ; Keith DA; Bland LM; Ferrari R; Lyons MB; Lucas R; Pettorelli N; Nicholson E, 2018, 'The role of satellite remote sensing in structured ecosystem risk assessments', Science of the Total Environment, vol. 619-620, pp. 249 - 257, http://dx.doi.org/10.1016/j.scitotenv.2017.11.034
2018
Lyons MB; Foster SD; Keith DA, 2017, 'Simultaneous vegetation classification and mapping at large spatial scales', Journal of Biogeography, vol. 44, pp. 2891 - 2902, http://dx.doi.org/10.1111/jbi.13088
2017
Callaghan CT; Lyons MB; Martin JM; Major RE; Kingsford RT, 2017, 'Assessing the reliability of avian biodiversity measures of urban greenspaces using ebird citizen science data', Avian Conservation and Ecology, vol. 12, http://dx.doi.org/10.5751/ACE-01104-120212
2017
Dyer F; Broadhurst B; Tschierschke A; Thiem J; Thompson R; Bowen S; Asmus M; Brandis K; Lyons M; Spencer J; Callaghan D; Lenehan J, 2017, Commonwealth Environmental Water Office Long Term Intervention Monitoring Project: Lower Lachlan river system Selected Area 2016-17 Monitoring and Evaluation Report, Commonwealth of Australia
2017
Foster SD; Hill NA; Lyons M, 2017, 'Ecological grouping of survey sites when sampling artefacts are present', Journal of the Royal Statistical Society. Series C: Applied Statistics, vol. 66, pp. 1031 - 1047, http://dx.doi.org/10.1111/rssc.12211
2017
Samper-Villarreal J; Roelfsema C; Kovacs EM; Adi NS; Lyons M; Mumby PJ; Lovelock CE; Saunders MI; Phinn SR, 2017, 'Seagrass morphometrics at species level in Moreton Bay, Australia from 2012 to 2013', Scientific Data, vol. 4, http://dx.doi.org/10.1038/sdata.2017.60
2017
Warton DI; Lyons M; Stoklosa J; Ives AR, 2016, 'Three points to consider when choosing a LM or GLM test for count data', Methods in Ecology and Evolution, vol. 7, pp. 882 - 890, http://dx.doi.org/10.1111/2041-210X.12552
2016
Lyons MB; Keith DA; Warton DI; Somerville M; Kingsford RT, 2016, 'Model-based assessment of ecological community classifications', Journal of Vegetation Science, vol. 27, pp. 704 - 715, http://dx.doi.org/10.1111/jvs.12400
2016
Roff A; Lyons M; Jones H; Thonell J, 2016, 'Reliability of map accuracy assessments: A comment on Hunter et al. (2016)', ECOLOGICAL MANAGEMENT & RESTORATION, vol. 17, pp. 124 - 127, http://dx.doi.org/10.1111/emr.12213
2016
Roelfsema C; Lyons M; Dunbabin M; Kovacs EM; Phinn S, 2015, 'Integrating field survey data with satellite image data to improve shallow water seagrass maps: The role of AUV and snorkeller surveys?', Remote Sensing Letters, vol. 6, pp. 135 - 144, http://dx.doi.org/10.1080/2150704X.2015.1013643
2015
Lyons M; Roelfsema C; Kovacs E; Samper-Villarreal J; Saunders M; Maxwell P; Phinn S, 2015, 'Rapid monitoring of seagrass biomass using a simple linear modelling approach, in the field and from space', Marine Ecology Progress Series, vol. 530, pp. 1 - 14, http://dx.doi.org/10.3354/meps11321
2015
Kilminster K; McMahon K; Waycott M; Kendrick GA; Scanes P; McKenzie L; O'Brien KR; Lyons M; Ferguson A; Maxwell P; Glasby T; Udy J, 2015, 'Unravelling complexity in seagrass systems for management: Australia as a microcosm', Science of the Total Environment, vol. 534, pp. 97 - 109, http://dx.doi.org/10.1016/j.scitotenv.2015.04.061
2015
Roelfsema CM; Lyons M; Kovacs EM; Maxwell P; Saunders MI; Samper-Villarreal J; Phinn SR, 2014, 'Multi-temporal mapping of seagrass cover, species and biomass: A semi-automated object based image analysis approach', Remote Sensing of Environment, vol. 150, pp. 172 - 187, http://dx.doi.org/10.1016/j.rse.2014.05.001
2014
Kennedy RE; Andréfouët S; Cohen WB; Gómez C; Griffiths P; Hais M; Healey SP; Helmer EH; Hostert P; Lyons MB; Meigs GW; Pflugmacher D; Phinn SR; Powell SL; Scarth P; Sen S; Schroeder TA; Schneider A; Sonnenschein R; Vogelmann JE; Wulder MA; Zhu Z, 2014, 'Bringing an ecological view of change to landsat-based remote sensing', Frontiers in Ecology and the Environment, vol. 12, pp. 339 - 346, http://dx.doi.org/10.1890/130066
2014
Saunders MI; Leon J; Phinn SR; Callaghan DP; O'Brien KR; Roelfsema CM; Lovelock CE; Lyons MB; Mumby PJ, 2013, 'Coastal retreat and improved water quality mitigate losses of seagrass from sea level rise', Global Change Biology, vol. 19, pp. 2569 - 2583, http://dx.doi.org/10.1111/gcb.12218
2013
Roelfsema C; Kovacs EM; Saunders MI; Phinn S; Lyons M; Maxwell P, 2013, 'Challenges of remote sensing for quantifying changes in large complex seagrass environments', Estuarine, Coastal and Shelf Science, vol. 133, pp. 161 - 171, http://dx.doi.org/10.1016/j.ecss.2013.08.026
2013
Dudaniec RY; Rhodes JR; Worthington Wilmer J; Lyons M; Lee KE; McAlpine CA; Carrick FN, 2013, 'Using multilevel models to identify drivers of landscape-genetic structure among management areas', Molecular Ecology, vol. 22, pp. 3752 - 3765, http://dx.doi.org/10.1111/mec.12359
2013
Knudby A; Jupiter S; Roelfsema C; Lyons M; Phinn S, 2013, 'Mapping Coral Reef Resilience Indicators Using Field and Remotely Sensed Data', Remote Sensing, vol. 5, pp. 1311 - 1334, http://dx.doi.org/10.3390/rs5031311
2013
Lyons MB; Roelfsema CM; Phinn SR, 2013, 'Towards understanding temporal and spatial dynamics of seagrass landscapes using time-series remote sensing', Estuarine, Coastal and Shelf Science, vol. 120, pp. 42 - 53, http://dx.doi.org/10.1016/j.ecss.2013.01.015
2013
Lyons MB; Phinn SR; Roelfsema CM, 2012, 'Long term land cover and seagrass mapping using Landsat and object-based image analysis from 1972 to 2010 in the coastal environment of South East Queensland, Australia', ISPRS Journal of Photogrammetry and Remote Sensing, vol. 71, pp. 34 - 46, http://dx.doi.org/10.1016/j.isprsjprs.2012.05.002
2012
Dekker AG; Phinn SR; Anstee J; Bissett P; Brando VE; Casey B; Fearns P; Hedley J; Klonowski W; Lee ZP; Lynch M; Lyons M; Mobley C; Roelfsema C, 2011, 'Intercomparison of shallow water bathymetry, hydro-optics, and benthos mapping techniques in Australian and Caribbean coastal environments', Limnology and Oceanography: Methods, vol. 9, pp. 396 - 425, http://dx.doi.org/10.4319/lom.2011.9.396
2011
Lyons M; Phinn S; Roelfsema C, 2011, 'Integrating Quickbird Multi-Spectral Satellite and Field Data: Mapping Bathymetry, Seagrass Cover, Seagrass Species and Change in Moreton Bay, Australia in 2004 and 2007', Remote Sensing, vol. 3, pp. 42 - 64, http://dx.doi.org/10.3390/rs3010042
2011
Knudby A; Roelfsema C; Lyons M; Phinn S; Jupiter S, 2011, 'Mapping Fish Community Variables by Integrating Field and Satellite Data, Object-Based Image Analysis and Modeling in a Traditional Fijian Fisheries Management Area', Remote Sensing, vol. 3, pp. 460 - 483, http://dx.doi.org/10.3390/rs3030460
2011