Statistical comparison of additive regression tree methods on ecological grassland data

Article


Plant, Emily, King, Rachel and Kath, Jarrod. 2021. "Statistical comparison of additive regression tree methods on ecological grassland data." Ecological Informatics. 61, pp. 1-23. https://doi.org/10.1016/j.ecoinf.2020.101198
Article Title

Statistical comparison of additive regression tree methods on ecological grassland data

ERA Journal ID124225
Article CategoryArticle
AuthorsPlant, Emily (Author), King, Rachel (Author) and Kath, Jarrod (Author)
Journal TitleEcological Informatics
Journal Citation61, pp. 1-23
Article Number101198
Number of Pages23
Year2021
PublisherElsevier
Place of PublicationNetherlands
ISSN1574-9541
Digital Object Identifier (DOI)https://doi.org/10.1016/j.ecoinf.2020.101198
Web Address (URL)https://www.sciencedirect.com/science/article/pii/S1574954120301485
Abstract

Additive tree methods are widely used in ecology. To date most ecologists have used boosted regression tree (BRT) methods. However, Bayesian additive regression tree (BART) models may offer advantages to ecologists previously unexamined.

Here we test whether BART has some benefits over the widely used BRT method. To do this we use two grassland data and 13 hydroclimatic and land use predictor variables. The dataset contained data from a period of drought as well as during a recovery phase after the drought. The response variable was the trend in the Enhanced Vegetation Index (EVI), which is an remotely sensed indicator of grassland degradation and recovery.

The settable parameters of both methods (BRT and BART) were varied to compare the performance of each method. BRT and BART models were evaluated using three prediction error statistics; root mean square error (RMSE), mean absolute error (MAE), and the coefficient of determination (R2). The best models across the two methods were assessed by inspecting the relative importance of predictor variables and the prediction error statistics.

BRT and BART models exhibited similar variable selection abilities, but the BART method generated models with similar or more favourable prediction error statistics than the BRT method (BART explained an additional 10.17% to 11.92% of the variation than BRT models). Our results indicate that BARTs may be more effective at modelling ecological data than BRTs.

BARTs also had shorter run times, more reasonable defaults in its software implementation, and greater functionality of said software implementation, beyond model building and prediction functions. Ecologists using additive regression approaches may benefit from using BART approaches and we suggest their use alongside more commonly used BRT methods in ecological studies.

KeywordsBayesian additive regression tree; Boosted regression tree; Remote sensing; Satellite; Grassland; Pasture
ANZSRC Field of Research 2020300206. Agricultural spatial analysis and modelling
490501. Applied statistics
300202. Agricultural land management
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Byline AffiliationsSchool of Sciences
Faculty of Health, Engineering and Sciences
Centre for Applied Climate Sciences
Institution of OriginUniversity of Southern Queensland
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Reardon-Smith, Kate, Kath, Jarrod, Le Brocque, Andy and Dyer, Fiona. 2014. "Identifying groundwater thresholds for drought resilience in floodplain tree species in the northern Murray-Darling Basin." Andersen, Alan (ed.) 2014 Conference of the Ecological Society of Australia (ESA 2014). Alice Springs, Australia 28 Sep - 03 Oct 2014 Canberra, Australia.
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Kath, Jarrod, Le Brocque, Andrew, Leyer, Ilona and Mosner, Eva. 2014. "Hydrological and land use determinants of Eucalyptus camaldulensis occurrence in floodplain wetlands." Austral Ecology: a journal of ecology in the Southern Hemisphere. 39 (6), pp. 643-655. https://doi.org/10.1111/aec.12126
Groundwater depth thresholds for tree condition
Kath, Jarrod, Reardon-Smith, Kate, Le Brocque, Andi, Dafny, Elad, Dyer, Fiona, Fritz, L. and Batterham, Megan. 2013. "Groundwater depth thresholds for tree condition." 52nd Australian Society for Limnology Congress (ASL 2013): From Theory to Practice in Water Science. Canberra, Australia 02 - 05 Dec 2013 Canberra, Australia.
Groundwater decline and tree change in floodplain landscapes: identifying non-linear threshold responses in canopy condition
Kath, J., Reardon-Smith, K., Le Brocque, A. F., Dyer, F. J., Dafny, E., Fritz, L. and Batterham, M.. 2014. "Groundwater decline and tree change in floodplain landscapes: identifying non-linear threshold responses in canopy condition." Global Ecology and Conservation. 2, pp. 148-160. https://doi.org/10.1016/j.gecco.2014.09.002
Foraging guild perturbations and ecological homogenization driven by a despotic native bird species
Howes, Alison, MacNally, Ralph, Loyn, Richard, Kath, Jarrod, Bowen, Michiala, McAlpine, Clive and Maron, Martine. 2014. "Foraging guild perturbations and ecological homogenization driven by a despotic native bird species." IBIS: The International Journal of Avian Science. 156 (2), pp. 341-354. https://doi.org/10.1111/ibi.12136
Outcrossing rates and reproductive success in xanthorrhoea johnsonii (xanthorrhoeaceae), in south east Queensland, Australia
Zalucki, Jacinta M., King, Rachel and Hughes, Jane M.. 2013. "Outcrossing rates and reproductive success in xanthorrhoea johnsonii (xanthorrhoeaceae), in south east Queensland, Australia." Biological Journal of the Linnean Society. 110 (2), pp. 335-345. https://doi.org/10.1111/bij.12135
An integrated model to examine the effects of sustainable diversion limits: a case study in the Lower Campaspe catchment
El Sawah, S., Kelly, R. A., Beverly, C., Stott, K., Patrick, M. J., Kath, J., Croke, B. F. W., Qureshi, M. E., Courtney-Barrer, B., Asher, M. J., Roberts, A. and Jakeman, A. J.. 2013. "An integrated model to examine the effects of sustainable diversion limits: a case study in the Lower Campaspe catchment." Piantadosi, J., Anderssen, R. S. and Boland, J. (ed.) 20th International Congress on Modelling and Simulation (MODSIM2013). Adelaide, Australia 01 - 06 Dec 2013 Canberra, Australia. Modelling and Simulation Society of Australia and New Zealand .
Potential inbreeding in a small population of a mass flowering species, Xanthorrhoea johnsonii (Xanthorrhoaceae): is your mother my father?
King, Rachel and Zalucki, Jacinta M.. 2012. "Potential inbreeding in a small population of a mass flowering species, Xanthorrhoea johnsonii (Xanthorrhoaceae): is your mother my father?" American Journal of Plant Sciences. 3 (3), pp. 303-312. https://doi.org/10.4236/ajps.2012.33036
Integrating hydrology and land use to understand the ecology of floodplain wetlands in the Condamine Catchment, southern Queensland, Australia
Kath, Jarrod Michael. 2012. Integrating hydrology and land use to understand the ecology of floodplain wetlands in the Condamine Catchment, southern Queensland, Australia. PhD Thesis Doctor of Philosophy. University of Southern Queensland.
Interspecific competition and small bird diversity in an urbanizing landscape
Kath, Jarrod, Maron, Martine and Dunn, Peter K.. 2009. "Interspecific competition and small bird diversity in an urbanizing landscape." Landscape and Urban Planning. 92 (2), pp. 72-79. https://doi.org/10.1016/j.landurbplan.2009.02.007
Ephemeral wetlands: their ecological function and resilience and climate change
Kath, Jarrod, Le Brocque, Andrew F. and Miller, Craig. 2008. "Ephemeral wetlands: their ecological function and resilience and climate change." 11th International Riversymposium: A Future of Extremes. Brisbane, Australia 01 - 04 Sep 2008 Brisbane, Australia.
Relative influence of habitat modification and interspecific competition on woodland bird assemblages in eastern Australia
Maron, M., Main, A., Bowen, M., Howes, A., Kath, J., Pillette, C. and McAlpine, C. A.. 2011. "Relative influence of habitat modification and interspecific competition on woodland bird assemblages in eastern Australia." Emu: austral ornithology. 111 (1), pp. 40-51. https://doi.org/10.1071/MU09108
Different landscape factors explain establishment and persistence of river red gum (Eucalyptus camaldulensis) in agricultural landscapes of southeast Queensland
Kath, Jarrod, Le Brocque, Andrew F., Miller, Craig, Leyer, Ilona and Mosner, Eva. 2010. "Different landscape factors explain establishment and persistence of river red gum (Eucalyptus camaldulensis) in agricultural landscapes of southeast Queensland." Lonsdale, Mark (ed.) 2010 Conference of the Ecological Society of Australia (ESA 2010). Canberra, Australia 06 - 10 Dec 2010 Alice Springs, Australia. Ecological Society of Australia.
Mapping habitat of threatened reptiles in Western Downs, Queensland: a spatial modelling approach using 'presence-only' occurrence data
Apan, Armando, Phinn, Stuart, McAlpine, Clive and Kath, Jarrod. 2010. "Mapping habitat of threatened reptiles in Western Downs, Queensland: a spatial modelling approach using 'presence-only' occurrence data." Queensland Surveying and Spatial Conference 2010 (QSSC 2010). Brisbane, Australia 01 - 03 Sep 2010 Brisbane, Australia.
Eco-hydrology of dynamic wetlands in an Australian agricultural landscape: a whole of system approach for understanding climate change impacts
Kath, Jarrod, Le Brocque, Andrew and Miller, Craig. 2010. "Eco-hydrology of dynamic wetlands in an Australian agricultural landscape: a whole of system approach for understanding climate change impacts." BALWOIS 2010: Water Observation and Information System for Decision Support. Ohrid, Macedonia 25 - 29 May 2010 Macedonia.
Wetland hydrology in an agricultural landscape: implications for biodiversity
Kath, Jarrod, Le Brocque, Andrew and Miller, Craig. 2010. "Wetland hydrology in an agricultural landscape: implications for biodiversity." BALWOIS 2010: Water Observation and Information System for Decision Support. Ohrid, Macedonia 25 - 29 May 2010 Macedonia.
Resilience of ephemeral wetlands in production landscapes
Kath, Jarrod, Le Brocque, Andrew F. and Miller, Craig. 2008. "Resilience of ephemeral wetlands in production landscapes." McArthur, Clare (ed.) 2008 Conference of the Ecological Society of Australia (ESA 2008). Sydney, Australia 01 - 05 Dec 2008 Canberra, Australia. Ecological Society of Australia.
Resilience of temporary wetlands in production landscapes and potential impacts of climate change
Kath, Jarrod, Le Brocque, Andrew F. and Miller, Craig. 2009. "Resilience of temporary wetlands in production landscapes and potential impacts of climate change." James, Craig D. (ed.) INTECOL 2010: Ecology in a Changing Climate: Two Hemispheres, One Globe. Brisbane, Australia 16 - 21 Aug 2009 Australia.