A checklist for maximizing reproducibility of ecological niche models
Open accessAbstract
Reporting specific modelling methods and metadata is essential to the reproducibility of ecological studies, yet guidelines rarely exist regarding what information should be noted. Here, we address this issue for ecological niche modelling or species distribution modelling, a rapidly developing toolset in ecology used across many aspects of biodiversity science. Our quantitative review of the recent literature reveals a general lack of sufficient information to fully reproduce the work. Over two-thirds of the examined studies neglected to report the version or access date of the underlying data, and only half reported model parameters. To address this problem, we propose adopting a checklist to guide studies in reporting at least the minimum information necessary for ecological niche modelling reproducibility, offering a straightforward way to balance efficiency and accuracy. We encourage the ecological niche modelling community, as well as journal reviewers and editors, to utilize and further develop this framework to facilitate and improve the reproducibility of future work. The proposed checklist framework is generalizable to other areas of ecology, especially those utilizing biodiversity data, environmental data and statistical modelling, and could also be adopted by a broader array of disciplines.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
MaxEnt has a predictive performance that is consistently competitive with other high-performing methods.
“This method also has a predictive performance that is consistently competitive with other high-performing methods (Elith et al., 2006; Feng et al., 2019).”
From Projecting future climate change impacts on the distribution of the ‘Octopus vulgaris species complex’ (2022) · cites this paper as Feng et al., 2019
The Ecological niche modelling section calls Maxent popular, and Model calibration (C) discusses how settings can affect model performance. Neither compares Maxent’s predictive performance with other high-performing methods; searches for that comparison found no such passage in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
The Elements of Statistical Learning
Hastie, T., Tibshirani, R., & Friedman, J. (2009) · Springer Series in Statistics · doi:10.1007/978-0-387-84858-7 · Cited by 25,970 · see citing works
DeLong, E. R., DeLong, D. M., & Clarke-Pearson, D. L. (1988) · Biometrics · doi:10.2307/2531595 · Cited by 22,649 · see citing works
Very high resolution interpolated climate surfaces for global land areas
Hijmans, R. J., Cameron, S. E., Parra, J. L., Jones, P. G., & Jarvis, A. (2005) · International Journal of Climatology · doi:10.1002/joc.1276 · Cited by 19,860 · see citing works
Maximum entropy modeling of species geographic distributions
Phillips, S. J., Anderson, R. P., & Schapire, R. E. (2005) · Ecological Modelling · doi:10.1016/j.ecolmodel.2005.03.026 · Cited by 17,870 · see citing works
WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas
Fick, S. E., & Hijmans, R. J. (2017) · International Journal of Climatology · doi:10.1002/joc.5086 · Cited by 17,783 · see citing works
Dormann, C. F., Elith, J., Bacher, S., Buchmann, C. M., Carl, G., Carré, G., Marquéz, J. R. G., Gruber, B., Lafourcade, B., Leitão, P. J., et al. (2012) · Ecography · doi:10.1111/j.1600-0587.2012.07348.x · Cited by 11,116 · see citing works
Measuring the Accuracy of Diagnostic Systems
Swets, J. A. (1988) · Science · doi:10.1126/science.3287615 · Cited by 10,058 · see citing works
Novel methods improve prediction of species’ distributions from occurrence data
Elith*, J., H. Graham*, C., P. Anderson, R., Dudík, M., Ferrier, S., Guisan, A., J. Hijmans, R., Huettmann, F., R. Leathwick, J., Lehmann, A., et al. (2006) · Ecography · doi:10.1111/j.2006.0906-7590.04596.x · Cited by 9,088 · see citing works
Predictive habitat distribution models in ecology
Guisan, A., & Zimmermann, N. E. (2000) · Ecological Modelling · doi:10.1016/s0304-3800(00)00354-9 · Cited by 7,359 · see citing works
A review of methods for the assessment of prediction errors in conservation presence/absence models
FIELDING, A. H., & BELL, J. F. (1997) · Environmental Conservation · doi:10.1017/s0376892997000088 · Cited by 6,956 · see citing works
Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation
Phillips, S. J., & Dudı́k, M. (2008) · Ecography · doi:10.1111/j.0906-7590.2008.5203.x · Cited by 6,851 · see citing works
A statistical explanation of MaxEnt for ecologists
Elith, J., Phillips, S. J., Hastie, T., Dudík, M., Chee, Y. E., & Yates, C. J. (2011) · Diversity and Distributions · doi:10.1111/j.1472-4642.2010.00725.x · Cited by 6,699 · see citing works
A working guide to boosted regression trees
Elith, J., Leathwick, J. R., & Hastie, T. (2008) · Journal of Animal Ecology · doi:10.1111/j.1365-2656.2008.01390.x · Cited by 6,484 · see citing works
Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator
Matsumoto, M., & Nishimura, T. (1998) · ACM Transactions on Modeling and Computer Simulation · doi:10.1145/272991.272995 · Cited by 5,780 · see citing works
Allouche, O., Tsoar, A., & Kadmon, R. (2006) · Journal of Applied Ecology · doi:10.1111/j.1365-2664.2006.01214.x · Cited by 5,518 · see citing works
Conjectures and Refutations: The Growth of Scientific Knowledge.
HESSE, M. B., & Popper, K. R. (1965) · The Philosophical Quarterly · doi:10.2307/2218271 · Cited by 4,233 · see citing works
1,500 scientists lift the lid on reproducibility
Baker, M. (2016) · Nature · doi:10.1038/533452a · Cited by 4,209 · see citing works
Merow, C., Smith, M. J., & Silander, J. A. (2013) · Ecography · doi:10.1111/j.1600-0587.2013.07872.x · Cited by 3,830 · see citing works
Self-citationCross‐validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure
Roberts, D. R., Bahn, V., Ciuti, S., Boyce, M. S., Elith, J., Guillera‐Arroita, G., Hauenstein, S., Lahoz‐Monfort, J. J., Schröder, B., Thuiller, W., et al. (2017) · Ecography · doi:10.1111/ecog.02881 · Cited by 3,689 · see citing works
AUC: A misleading measure of the performance of predictive distribution models
Lobo, J. M., Jiménez‐Valverde, A., & Real, R. (2008) · Global Ecology and Biogeography · doi:10.1111/j.1466-8238.2007.00358.x · Cited by 3,499 · see citing works
F. Dormann, C., M. McPherson, J., B. Araújo, M., Bivand, R., Bolliger, J., Carl, G., G. Davies, R., Hirzel, A., Jetz, W., Daniel Kissling, W., et al. (2007) · Ecography · doi:10.1111/j.2007.0906-7590.05171.x · Cited by 3,433 · see citing works
A manifesto for reproducible science
Munafò, M. R., Nosek, B. A., Bishop, D. V. M., Button, K. S., Chambers, C. D., Percie du Sert, N., Simonsohn, U., Wagenmakers, E.-J., Ware, J. J., & Ioannidis, J. P. A. (2017) · Nature Human Behaviour · doi:10.1038/s41562-016-0021 · Cited by 3,397 · see citing works
Pearson, R. G., Raxworthy, C. J., Nakamura, M., & Peterson, A. T. (2006) · Journal of Biogeography · doi:10.1111/j.1365-2699.2006.01594.x · Cited by 3,146 · see citing works
Self-citationPhillips, S. J., Dudík, M., Elith, J., Graham, C. H., Lehmann, A., Leathwick, J., & Ferrier, S. (2009) · Ecological Applications · doi:10.1890/07-2153.1 · Cited by 2,996 · see citing works
A standard protocol for describing individual-based and agent-based models
Grimm, V., Berger, U., Bastiansen, F., Eliassen, S., Ginot, V., Giske, J., GOSS‐CUSTARD, J. D., Grand, T. C., Heinz, S. K., Huse, G., et al. (2006) · Ecological Modelling · doi:10.1016/j.ecolmodel.2006.04.023 · Cited by 2,988 · see citing works
Raise standards for preclinical cancer research
Begley, C. G., & Ellis, L. M. (2012) · Nature · doi:10.1038/483531a · Cited by 2,979 · see citing works
Opening the black box: an open‐source release of Maxent
Phillips, S. J., Anderson, R. P., Dudı́k, M., Schapire, R. E., & Blair, M. E. (2017) · Ecography · doi:10.1111/ecog.03049 · Cited by 2,891 · see citing works
The art of modelling range-shifting species: <i>The art of modelling range-shifting species</i>
Elith, J., Kearney, M., & Phillips, S. (2010) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2010.00036.x · Cited by 2,813 · see citing works
Selecting pseudo‐absences for species distribution models: how, where and how many?
Barbet-Massin, M., Jiguet, F., Albert, C., & Thuiller, W. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00172.x · Cited by 2,715 · see citing works
Selecting thresholds of occurrence in the prediction of species distributions
Liu, C., Berry, P. M., Dawson, T. P., & Pearson, R. G. (2005) · Ecography · doi:10.1111/j.0906-7590.2005.03957.x · Cited by 2,701 · see citing works
Evaluating resource selection functions
Boyce, M. S., Vernier, P. R., Nielsen, S. E., & Schmiegelow, F. K. A. (2002) · Ecological Modelling · doi:10.1016/s0304-3800(02)00200-4 · Cited by 2,580 · see citing works
Citizen Science: A Developing Tool for Expanding Science Knowledge and Scientific Literacy
Bonney, R. E., Cooper, C. B., Dickinson, J. L., Kelling, S., Phillips, T., Rosenberg, K. V., & Shirk, J. (2009) · BioScience · doi:10.1525/bio.2009.59.11.9 · Cited by 2,542 · see citing works
Aiello‐Lammens, M. E., Boria, R. A., Radosavljević, A., Vilela, B., & Anderson, R. P. (2015) · Ecography · doi:10.1111/ecog.01132 · Cited by 2,385 · see citing works
Warren, D. L., & Seifert, S. N. (2011) · Ecological Applications · doi:10.1890/10-1171.1 · Cited by 2,312 · see citing works
Muscarella, R., Galante, P. J., Soley‐Guardia, M., Boria, R. A., Kass, J. M., Uriarte, M., & Anderson, R. P. (2014) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12261 · Cited by 2,110 · see citing works
Barve, N., Barve, V., Jiménez‐Valverde, A., Lira‐Noriega, A., Maher, S. P., Peterson, A. T., Soberón, J. M., & Villalobos, F. (2011) · Ecological Modelling · doi:10.1016/j.ecolmodel.2011.02.011 · Cited by 1,901 · see citing works
Self-citationWisz, M. S., Pottier, J., Kissling, W. D., Pellissier, L., Lenoir, J., Damgaard, C. F., Dormann, C. F., Forchhammer, M. C., Grytnes, J., Guisan, A., et al. (2013) · Biological Reviews · doi:10.1111/j.1469-185x.2012.00235.x · Cited by 1,769 · see citing works
(2010) · Cited by 1,762 · see citing works
Rethinking receiver operating characteristic analysis applications in ecological niche modeling
Peterson, A. T., Papeş, M., & Soberón, J. M. (2008) · Ecological Modelling · doi:10.1016/j.ecolmodel.2007.11.008 · Cited by 1,715 · see citing works
Self-citationFranklin, J. (2010) · Cambridge University Press eBooks · doi:10.1017/cbo9780511810602 · Cited by 1,650 · see citing works
Selecting thresholds for the prediction of species occurrence with presence‐only data
Liu, C., White, M. D., & Newell, G. R. (2013) · Journal of Biogeography · doi:10.1111/jbi.12058 · Cited by 1,639 · see citing works
Thermal tolerance and the global redistribution of animals
Sunday, J. M., Bates, A. E., & Dulvy, N. K. (2012) · Nature Climate Change · doi:10.1038/nclimate1539 · Cited by 1,585 · see citing works
On the relationship between niche and distribution
Pulliam, H. R. (2000) · Ecology Letters · doi:10.1046/j.1461-0248.2000.00143.x · Cited by 1,559 · see citing works
Punctuated equilibrium and criticality in a simple model of evolution
Bak, P., & Sneppen, K. (1993) · Physical Review Letters · doi:10.1103/physrevlett.71.4083 · Cited by 1,517 · see citing works
Habitat Suitability and Distribution Models
Guisan, A., Thuiller, W., & Zimmermann, N. E. (2017) · Cambridge University Press eBooks · doi:10.1017/9781139028271 · Cited by 1,483 · see citing works
Spatial filtering to reduce sampling bias can improve the performance of ecological niche models
Boria, R., Olson, L., Goodman, S., & Anderson, R. (2014) · Ecological Modelling · doi:10.1016/j.ecolmodel.2013.12.012 · Cited by 1,458 · see citing works
Random graph models of social networks
Newman, M. E. J., Watts, D. J., & Strogatz, S. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.012582999 · Cited by 1,340 · see citing works
Niches and distributional areas: Concepts, methods, and assumptions
Soberón, J. M., & Nakamura, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901637106 · Cited by 1,311 · see citing works
CoordinateCleaner : Standardized cleaning of occurrence records from biological collection databases
Zizka, A., Silvestro, D., Andermann, T., Azevedo, J. A. R., Ritter, C. D., Edler, D., Farooq, H. M., Herdean, A., Ariza, M., Scharn, R., et al. (2019) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.13152 · Cited by 1,233 · see citing works
Darwin Core: An Evolving Community-Developed Biodiversity Data Standard
Wieczorek, J. R., Bloom, D., Guralnick, R., Blum, S., Döring, M., Giovanni, R. D., Robertson, T., & Vieglais, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029715 · Cited by 1,216 · see citing works
Fourcade, Y., Engler, J. O., Rödder, D., & Secondi, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097122 · Cited by 1,175 · see citing works
Standards for distribution models in biodiversity assessments
Araújo, M. B., Anderson, R. P., Barbosa, A. M., Beale, C. M., Dormann, C. F., Early, R., Garcia, R. A., Guisan, A., Maiorano, L., Naimi, B., et al. (2019) · Science Advances · doi:10.1126/sciadv.aat4858 · Cited by 1,149 · see citing works
New developments in museum-based informatics and applications in biodiversity analysis
Graham, C. H., Ferrier, S., Huettmann, F., Moritz, C. C., & Peterson, A. T. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.07.006 · Cited by 1,119 · see citing works
Self-citationElith, J., & Graham, C. H. (2009) · Ecography · doi:10.1111/j.1600-0587.2008.05505.x · Cited by 1,093 · see citing works
kuenm: an R package for detailed development of ecological niche models using Maxent
Cobos, M. E., Peterson, A. T., Barve, N., & Osorio‐Olvera, L. (2019) · PeerJ · doi:10.7717/peerj.6281 · Cited by 1,013 · see citing works
Self-citationIs my species distribution model fit for purpose? Matching data and models to applications
Guillera‐Arroita, G., Lahoz‐Monfort, J. J., Elith, J., Ascelin Gordon, A., Kujala, H., Lentini, P. E., Mccarthy, M. A., Tingley, R., & Wintle, B. A. (2015) · Global Ecology and Biogeography · doi:10.1111/geb.12268 · Cited by 969 · see citing works
Transferability and model evaluation in ecological niche modeling: a comparison of GARP and Maxent
Peterson, A. T., Papeş, M., & Eaton, M. D. (2007) · Ecography · doi:10.1111/j.0906-7590.2007.05102.x · Cited by 966 · see citing works
Self-citationBig data and the future of ecology
Hampton, S. E., Strasser, C. A., Tewksbury, J. J., Gram, W. K., Budden, A. E., Batcheller, A. L., Duke, C. S., & Porter, J. H. (2013) · Frontiers in Ecology and the Environment · doi:10.1890/120103 · Cited by 930 · see citing works
The Influence of Late Quaternary Climate-Change Velocity on Species Endemism
Sandel, B., Arge, L., Dalsgaard, B., Davies, R. G., Gaston, K. J., Sutherland, W. J., & Svenning, J. (2011) · Science · doi:10.1126/science.1210173 · Cited by 921 · see citing works
VanDerWal, J. J., Shoo, L. P., Graham, C. H., & Williams, S. E. (2009) · Ecological Modelling · doi:10.1016/j.ecolmodel.2008.11.010 · Cited by 888 · see citing works
An evaluation of methods for modelling species distributions
Segurado, P., & Araújo, M. B. (2004) · Journal of Biogeography · doi:10.1111/j.1365-2699.2004.01076.x · Cited by 875 · see citing works
Are niche‐based species distribution models transferable in space?
Randin, C. F., Dirnböck, T., Dullinger, S., Zimmermann, N. E., Zappa, M., & Guisan, A. (2006) · Journal of Biogeography · doi:10.1111/j.1365-2699.2006.01466.x · Cited by 761 · see citing works
On the selection of thresholds for predicting species occurrence with presence‐only data
Liu, C., Newell, G. R., & White, M. D. (2015) · Ecology and Evolution · doi:10.1002/ece3.1878 · Cited by 740 · see citing works
Best Practices for Scientific Computing
Wilson, G., Aruliah, D. A., Brown, C. T., Chue Hong, N. P., Davis, M., Guy, R. T., Haddock, S. H. D., Huff, K. D., Mitchell, I. M., Plumbley, M. D., et al. (2014) · PLoS Biology · doi:10.1371/journal.pbio.1001745 · Cited by 723 · see citing works
Best practices in data analysis and sharing in neuroimaging using MRI
Nichols, T. E., Das, S., Eickhoff, S. B., Evans, A. C., Glatard, T., Hanke, M., Kriegeskorte, N., Milham, M. P., Poldrack, R. A., Poline, J.-B., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4500 · Cited by 714 · see citing works
Novel competitors shape species’ responses to climate change
Alexander, J. M., Diez, J. M., & Levine, J. M. (2015) · Nature · doi:10.1038/nature14952 · Cited by 702 · see citing works
Species Distribution Modeling and Ecological Niche Modeling: Getting the Concepts Right
Peterson, A. T., & Soberón, J. (2012) · Natureza & Conservação · doi:10.4322/natcon.2012.019 · Cited by 702 · see citing works
Self-citationOwens, H., Campbell, L., Dornak, L., Saupe, E., Barve, N., Soberón, J., Ingenloff, K., Lira-Noriega, A., Hensz, C., Myers, C., et al. (2012) · Ecological Modelling · doi:10.1016/j.ecolmodel.2013.04.011 · Cited by 659 · see citing works
Self-citationHijmans, R. J. (2012) · Ecology · doi:10.1890/11-0826.1 · Cited by 639 · see citing works
Anderson, R. P., & Gonzalez, I. (2011) · Ecological Modelling · doi:10.1016/j.ecolmodel.2011.04.011 · Cited by 596 · see citing works
Integrating biodiversity distribution knowledge: toward a global map of life
Jetz, W., McPherson, J. M., & Guralnick, R. (2011) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2011.09.007 · Cited by 593 · see citing works
Multidimensional biases, gaps and uncertainties in global plant occurrence information
Meyer, C., Weigelt, P., & Kreft, H. (2016) · Ecology Letters · doi:10.1111/ele.12624 · Cited by 580 · see citing works
McPherson, J. M., Jetz, W., & Rogers, D. J. (2004) · Journal of Applied Ecology · doi:10.1111/j.0021-8901.2004.00943.x · Cited by 547 · see citing works
Sensitivity of predictive species distribution models to change in grain size
Guisan, A., Graham, C. H., Elith, J., Huettmann, F., & the NCEAS Species Distribution Modelling Group (2007) · Diversity and Distributions · doi:10.1111/j.1472-4642.2007.00342.x · Cited by 543 · see citing works
The taxonomic name resolution service: an online tool for automated standardization of plant names
Boyle, B. L., Hopkins, N., Lu, Z., Garay, J. A. R., Mozzherin, D., Rees, T., Matasci, N., Narro, M. L., Piel, W. H., McKay, S., et al. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-16 · Cited by 539 · see citing works
Equivalence of MAXENT and Poisson Point Process Models for Species Distribution Modeling in Ecology
Renner, I. W., & Warton, D. I. (2013) · Biometrics · doi:10.1111/j.1541-0420.2012.01824.x · Cited by 463 · see citing works
Measuring and comparing the accuracy of species distribution models with presence–absence data
Liu, C.-R., White, M., & Newell, G. (2011) · Ecography · doi:10.1111/j.1600-0587.2010.06354.x · Cited by 454 · see citing works
Royle, J. A., Chandler, R. B., Yackulic, C. B., & Nichols, J. D. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00182.x · Cited by 448 · see citing works
Qiao, H., Soberón, J. M., & Peterson, A. T. (2015) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12397 · Cited by 448 · see citing works
Self-citationVarela, S., Anderson, R. P., García‐Valdés, R., & Fernández‐González, F. (2014) · Ecography · doi:10.1111/j.1600-0587.2013.00441.x · Cited by 433 · see citing works
Biodiversity informatics: managing and applying primary biodiversity data
Soberón, J. M., & Peterson, A. T. (2004) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2003.1439 · Cited by 433 · see citing works
Self-citationWidespread sampling biases in herbaria revealed from large‐scale digitization
Daru, B. H., Park, D., Primack, R. B., et al. (2017) · New Phytologist · doi:10.1111/nph.14855 · Cited by 431 · see citing works
Self-citationGRASP: generalized regression analysis and spatial prediction
Lehmann, A., Overton, J. M., & Leathwick, J. R. (2002) · Ecological Modelling · doi:10.1016/s0304-3800(02)00195-3 · Cited by 422 · see citing works
The interpretation of habitat preference metrics under use–availability designs
Beyer, H. L., Haydon, D. T., Morales, J. M., Frair, J. L., Hebblewhite, M., Mitchell, M. S., & Matthiopoulos, J. (2010) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2010.0083 · Cited by 415 · see citing works
Niches and Geographic Distributions
Peterson, A. T., Soberón, J. M., Pearson, R. G., Anderson, R. P., Martínez‐Meyer, E., Nakamura, M., & Araújo, M. B. (2011) · Princeton University Press eBooks · doi:10.23943/princeton/9780691136868.003.0003 · Cited by 410 · see citing works
Self-citationWieczorek, J. R., Guo, Q., & Hijmans, R. J. (2004) · International Journal of Geographical Information Systems · doi:10.1080/13658810412331280211 · Cited by 409 · see citing works
Collinearity in ecological niche modeling: Confusions and challenges
Feng, X., Park, D. S., Liang, Y., Pandey, R., & Papeş, M. (2019) · Ecology and Evolution · doi:10.1002/ece3.5555 · Cited by 399 · see citing works
Self-citationHistorical bias in biodiversity inventories affects the observed environmental niche of the species
Hortal, J., Jiménez‐Valverde, A., Gómez, J. F., Lobo, J. M., & Baselga, A. (2008) · Oikos · doi:10.1111/j.0030-1299.2008.16434.x · Cited by 389 · see citing works
McGill, B. J. (2010) · Science · doi:10.1126/science.1188528 · Cited by 384 · see citing works
Modelling occurrence and abundance of species when detection is imperfect
Royle, J. A., Nichols, J. D., & Kéry, M. (2005) · Oikos · doi:10.1111/j.0030-1299.2005.13534.x · Cited by 375 · see citing works
Building Statistical Models To Analyze Species Distributions
Latimer, A. M., Wu, S., Gelfand, A. E., & Silander, J. A. (2006) · Ecological Applications · doi:10.1890/04-0609 · Cited by 371 · see citing works
Conjectures and Refutations: The Growth of Scientific Knowledge
Popper, K. (2014) · doi:10.4324/9780203538074 · Cited by 327 · see citing works
Next-generation sequencing data interpretation: enhancing reproducibility and accessibility
Nekrutenko, A., & Taylor, J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3305 · Cited by 317 · see citing works
Braunisch, V., Coppes, J., Arlettaz, R., Suchant, R., Schmid, H., & Bollmann, K. (2013) · Ecography · doi:10.1111/j.1600-0587.2013.00138.x · Cited by 311 · see citing works
Kass, J. M., Vilela, B., Aiello‐Lammens, M. E., Muscarella, R., Merow, C., & Anderson, R. P. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12945 · Cited by 280 · see citing works
Self-citationPetitpierre, B., Broennimann, O., Kueffer, C., Daehler, C., & Guisan, A. (2017) · Global Ecology and Biogeography · doi:10.1111/geb.12530 · Cited by 255 · see citing works
Testing the predictive performance of distribution models
Bahn, V., & McGill, B. J. (2012) · Oikos · doi:10.1111/j.1600-0706.2012.00299.x · Cited by 245 · see citing works
Saupe, E., Barve, V., Myers, C., Soberón, J., Barve, N., Hensz, C., Peterson, A., Owens, H., & Lira-Noriega, A. (2012) · Ecological Modelling · doi:10.1016/j.ecolmodel.2012.04.001 · Cited by 244 · see citing works
Self-citationNovel Three-Step Pseudo-Absence Selection Technique for Improved Species Distribution Modelling
Senay, S. D., Worner, S. P., & Ikeda, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071218 · Cited by 235 · see citing works
NicheA: creating virtual species and ecological niches in multivariate environmental scenarios
Qiao, H., Peterson, A. T., Campbell, L. P., Soberón, J. M., Ji, L., & Escobar, L. E. (2015) · Ecography · doi:10.1111/ecog.01961 · Cited by 213 · see citing works
Self-citationMechanistic and Correlative Models of Ecological Niches
Peterson, A. T., Papeş, M., & Soberón, J. M. (2015) · European Journal of Ecology · doi:10.1515/eje-2015-0014 · Cited by 206 · see citing works
Self-citationExpression profiling — best practices for data generation and interpretation in clinical trials
The Tumor Analysis Best Practices Working Group (2004) · Nature Reviews Genetics · doi:10.1038/nrg1297 · Cited by 203 · see citing works
The reproducibility “crisis”: Reaction to replication crisis should not stifle innovation
Hunter, P. (2017) · The EMBO Reports · doi:10.15252/embr.201744876 · Cited by 201 · see citing works
Amat, E. M., Mateo, R. G., Nieto‐Lugilde, D., Morueta‐Holme, N., Svenning, J., & García‐Amorena, I. (2015) · Ecological Modelling · doi:10.1016/j.ecolmodel.2015.05.035 · Cited by 197 · see citing works
Prevalence, thresholds and the performance of presence–absence models
Lawson, C. R., Hodgson, J. A., Wilson, R. J., & Richards, S. A. (2014) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12123 · Cited by 194 · see citing works
Species Distribution Modelling: Contrasting presence-only models with plot abundance data
Gomes, V. H. F., Ijff, S. D., Raes, N., et al. (2018) · Scientific Reports · doi:10.1038/s41598-017-18927-1 · Cited by 191 · see citing works
A global assessment of climatic niche shifts and human influence in insect invasions
Hill, M. P., Gallardo, B., & Terblanche, J. S. (2017) · Global Ecology and Biogeography · doi:10.1111/geb.12578 · Cited by 190 · see citing works
An evaluation of transferability of ecological niche models
Qiao, H., Feng, X., Escobar, L., Peterson, A., Soberón, J., Zhu, G.-P., & Papeş, M. (2018) · Ecography · doi:10.1111/ecog.03986 · Cited by 183 · see citing works
Self-citationDelimiting the geographical background in species distribution modelling
Acevedo, P., Jiménez‐Valverde, A., Lobo, J. M., & Real, R. (2012) · Journal of Biogeography · doi:10.1111/j.1365-2699.2012.02713.x · Cited by 182 · see citing works
Zurell, D., Elith, J., & Schröder, B. (2012) · Diversity and Distributions · doi:10.1111/j.1472-4642.2012.00887.x · Cited by 181 · see citing works
A framework for species distribution modelling with improved pseudo-absence generation
Iturbide, M., Bedia, J., Herrera, S., et al. (2015) · Ecological Modelling · doi:10.1016/j.ecolmodel.2015.05.018 · Cited by 180 · see citing works
Edwards, T. C., Cutler, D. R., Zimmermann, N. E., Geiser, L. H., & Moisen, G. G. (2006) · Ecological Modelling · doi:10.1016/j.ecolmodel.2006.05.016 · Cited by 155 · see citing works
An overview of recent remote sensing and GIS based research in ecological informatics
Boyd, D. S., & Foody, G. M. (2010) · Ecological Informatics · doi:10.1016/j.ecoinf.2010.07.007 · Cited by 147 · see citing works
Kumar, S., Graham, J., West, A. M., & Evangelista, P. (2014) · Computers and Electronics in Agriculture · doi:10.1016/j.compag.2014.02.007 · Cited by 142 · see citing works
Latimer, A. M., Banerjee, S., Sang, H., Mosher, E. S., & Silander, J. A. (2009) · Ecology Letters · doi:10.1111/j.1461-0248.2008.01270.x · Cited by 141 · see citing works
Best Practices in Data Analysis and Sharing in Neuroimaging using MRIPreprint
Nichols, T. E., Das, S., Eickhoff, S. B., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/054262 · Cited by 140 · see citing works
Biogeo: an R package for assessing and improving data quality of occurrence record datasets
Robertson, M. P., Visser, V., & Hui, C. (2016) · Ecography · doi:10.1111/ecog.02118 · Cited by 138 · see citing works
Figueiredo, F. O. G., Zuquim, G., Tuomisto, H., et al. (2017) · Journal of Biogeography · doi:10.1111/jbi.13104 · Cited by 138 · see citing works
Lee, D. N., Papeş, M., & Bussche, R. A. V. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042466 · Cited by 136 · see citing works
Self-citationEnquist, B. J., Condit, R., Peet, R. K., et al. (2016) · doi:10.7287/peerj.preprints.2615v2 · Cited by 132 · see citing works
Michener, W. K., Allard, S. L., Budden, A. E., Cook, R. B., Douglass, K., Frame, M., Kelling, S., Koskela, R. J., Tenopir, C., & Vieglais, D. (2011) · Ecological Informatics · doi:10.1016/j.ecoinf.2011.08.007 · Cited by 130 · see citing works
Effects of grain size and niche breadth on species distribution modeling
Connor, T., Hull, V., Viña, A., Shortridge, A. M., Tang, Y., Zhang, J.-D., Wang, F., & Liu, J.-G. (2018) · Ecography · doi:10.1111/ecog.03416 · Cited by 121 · see citing works
MODELING SPECIES–HABITAT RELATIONSHIPS WITH SPATIALLY AUTOCORRELATED OBSERVATION DATA
Wintle, B. A., & Bardos, D. C. (2006) · Ecological Applications · doi:10.1890/1051-0761(2006)016[1945:msrwsa]2.0.co;2 · Cited by 120 · see citing works
Bradter, U., Kunin, W., Altringham, J., Thom, T., & Benton, T. (2013) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2012.00253.x · Cited by 120 · see citing works
BioGeomancer: Automated Georeferencing to Map the World's Biodiversity Data
Guralnick, R., Wieczorek, J. R., Beaman, R. S., et al. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040381 · Cited by 115 · see citing works
Big data for forecasting the impacts of global change on plant communities
Franklin, J., Serra-Diaz, J. M., Syphard, A. D., & Regan, H. M. (2016) · Global Ecology and Biogeography · doi:10.1111/geb.12501 · Cited by 113 · see citing works
Cooper, J. C., & Soberón, J. M. (2017) · Global Ecology and Biogeography · doi:10.1111/geb.12678 · Cited by 105 · see citing works
Reliability of 'new drug target' claims called into question
Mullard, A. (2011) · Nature Reviews Drug Discovery · doi:10.1038/nrd3545 · Cited by 98 · see citing works
Smeraldo, S., Febbraro, M. D., Bosso, L., et al. (2018) · Biodiversity and Conservation · doi:10.1007/s10531-018-1545-7 · Cited by 92 · see citing works
Derville, S., Torres, L. G., Iovan, C., & Garrigue, C. (2018) · Diversity and Distributions · doi:10.1111/ddi.12782 · Cited by 92 · see citing works
Guralnick, R., Walls, R., & Jetz, W. (2017) · Ecography · doi:10.1111/ecog.02942 · Cited by 83 · see citing works
Bosch, S., Tyberghein, L., Deneudt, K., Hernández, F., & Clerck, O. D. (2017) · Diversity and Distributions · doi:10.1111/ddi.12668 · Cited by 83 · see citing works
Merow, C., Allen, J. M., Aiello‐Lammens, M. E., & Silander, J. A. (2016) · Global Ecology and Biogeography · doi:10.1111/geb.12453 · Cited by 81 · see citing works
Self-citationQiao, H., Escobar, L. E., & Peterson, A. T. (2017) · Scientific Reports · doi:10.1038/s41598-017-01313-2 · Cited by 80 · see citing works
Self-citationRecord, S., Fitzpatrick, M. C., Finley, A. O., Veloz, S., & Ellison, A. M. (2013) · Global Ecology and Biogeography · doi:10.1111/geb.12017 · Cited by 79 · see citing works
Reproducibility and Repeatability in Ecology
Cassey, P., & Blackburn, T. M. (2006) · BioScience · doi:10.1641/0006-3568(2006)56[958:rarie]2.0.co;2 · Cited by 76 · see citing works
Fitzpatrick, M. C., Blois, J. L., Williams, J. W., Nieto‐Lugilde, D., Maguire, K. C., & Lorenz, D. J. (2018) · Global Change Biology · doi:10.1111/gcb.14138 · Cited by 69 · see citing works
Implications and alternatives of assigning climate data to geographical centroids
Park, D., & Davis, C. “. (2017) · Journal of Biogeography · doi:10.1111/jbi.13029 · Cited by 67 · see citing works
Self-citationTaulman, J. F., & Robbins, L. W. (2014) · Journal of Biogeography · doi:10.1111/jbi.12319 · Cited by 64 · see citing works
The importance of temporal resolution for niche modelling in dynamic marine environments
Fernández, M., Yesson, C., Gannier, A., Miller, P. I., & Azevedo, J. M. N. (2017) · Journal of Biogeography · doi:10.1111/jbi.13080 · Cited by 64 · see citing works
Misleading prioritizations from modelling range shifts under climate change
Sofaer, H. R., Jarnevich, C. S., & Flather, C. H. (2018) · Global Ecology and Biogeography · doi:10.1111/geb.12726 · Cited by 62 · see citing works
Hertzog, L. R., Besnard, A. G., & Jay‐Robert, P. (2014) · Diversity and Distributions · doi:10.1111/ddi.12249 · Cited by 60 · see citing works
Genotypic variability enhances the reproducibility of an ecological study
Milcu, A., Freitas, R. P., Ellison, A. M., Blouin, M., Scheu, S., Freschet, G. T., Rose, L., Barot, S., Cesarz, S., Eisenhauer, N., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0434-x · Cited by 57 · see citing works
Rapid range expansion of the Brazilian free-tailed bat in the southeastern United States, 2008–2016
McCracken, G. F., Bernard, R. F., Gamba‐Rios, M., et al. (2017) · Journal of Mammalogy · doi:10.1093/jmammal/gyx188 · Cited by 53 · see citing works
Suzuki, N., Olson, D. H., & Reilly, E. C. (2007) · Biodiversity and Conservation · doi:10.1007/s10531-007-9281-4 · Cited by 50 · see citing works
Towards a more reproducible ecology
Borregaard, M. K., & Hart, E. (2016) · Ecography · doi:10.1111/ecog.02493 · Cited by 49 · see citing works
Bartoleti, L. F. D. M., Peres, E. A., Sobral‐Souza, T., et al. (2017) · Journal of Biogeography · doi:10.1111/jbi.12998 · Cited by 48 · see citing works
Mammola, S., & Isaia, M. (2017) · Journal of Biogeography · doi:10.1111/jbi.13087 · Cited by 43 · see citing works
Species' range model metadata standards: RMMS
Merow, C., Maitner, B., Owens, H. L., Kass, J. M., Enquist, B. J., Jetz, W., & Guralnick, R. (2019) · Global Ecology and Biogeography · doi:10.1111/geb.12993 · Cited by 42 · see citing works
Self-citationThe effect of spatially marginal localities in modelling species niches and distributions
Soley‐Guardia, M., Radosavljević, A., Rivera, J. L., & Anderson, R. P. (2014) · Journal of Biogeography · doi:10.1111/jbi.12297 · Cited by 41 · see citing works
Publish or Perish—An Ailing Enterprise?
Gad‐el‐Hak, M. (2004) · Physics Today · doi:10.1063/1.1712503 · Cited by 41 · see citing works
Boria, R. A., Olson, L. E., Goodman, S. M., et al. (2016) · Diversity and Distributions · doi:10.1111/ddi.12510 · Cited by 41 · see citing works
Williams, H. M., Willemoes, M., & Thorup, K. (2017) · Journal of Avian Biology · doi:10.1111/jav.01476 · Cited by 41 · see citing works
Applying species distribution modelling to a data poor, pelagic fish complex: the ocean sunfishes
Phillips, N. D., Reid, N., Thys, T. M., Harrod, C., Payne, N. L., Morgan, C. A., White, H. J., Porter, S., & Houghton, J. D. R. (2017) · Journal of Biogeography · doi:10.1111/jbi.13033 · Cited by 39 · see citing works
Does the jack of all trades fare best? Survival and niche width in Late Pleistocene megafauna
Febbraro, M. D., Carotenuto, F., Castiglione, S., et al. (2017) · Journal of Biogeography · doi:10.1111/jbi.13078 · Cited by 39 · see citing works
Feng, X., & Papeş, M. (2014) · Journal of Biogeography · doi:10.1111/jbi.12427 · Cited by 37 · see citing works
Self-citationMartínez-Gutiérrez, P. G., Martínez‐Meyer, E., Palomares, F., & Fernández, N. (2017) · Diversity and Distributions · doi:10.1111/ddi.12662 · Cited by 37 · see citing works
Would Ecology Fail the Repeatability Test?
Schnitzer, S. A., & Carson, W. P. (2016) · BioScience · doi:10.1093/biosci/biv176 · Cited by 35 · see citing works
The zoon r package for reproducible and shareable species distribution modelling
Golding, N., August, T., Lucas, T. C. D., Gavaghan, D. J., van Loon, E. E., & McInerny, G. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12858 · Cited by 35 · see citing works
The sensitivity of species distribution modeling to scale differences
Song, W., Kim, E., Lee, D. K., et al. (2012) · Ecological Modelling · doi:10.1016/j.ecolmodel.2012.09.012 · Cited by 34 · see citing works
geoknife: reproducible web‐processing of large gridded datasets
Read, J. S., Walker, J. I., Appling, A., et al. (2015) · Ecography · doi:10.1111/ecog.01880 · Cited by 34 · see citing works
The origin and phylogenetic relationships of the New Zealand ravens
Scofield, R. P., Mitchell, K. J., Wood, J. R., Pietri, V. L. D., Jarvie, S., Llamas, B., & Cooper, A. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.09.022 · Cited by 27 · see citing works
Castro, M. C., Ciancio, M. R., Pacheco, V., et al. (2015) · Zootaxa · doi:10.11646/zootaxa.3947.1.2 · Cited by 25 · see citing works
A reciprocal test of D arwin's naturalization hypothesis in two mediterranean‐climate regions
Park, D., & Potter, D. (2015) · Global Ecology and Biogeography · doi:10.1111/geb.12352 · Cited by 25 · see citing works
Self-citationThe role of physiological optima in shaping the geographic distribution of S panish moss
Barve, N. V., Martin, C. E., Brunsell, N. A., et al. (2014) · Global Ecology and Biogeography · doi:10.1111/geb.12150 · Cited by 21 · see citing works
Lost locations and the (ir)repeatability of ecological studies
Shapiro, J. T., & Báldí, A. (2012) · Frontiers in Ecology and the Environment · doi:10.1890/12.wb.015 · Cited by 17 · see citing works
Assessment of climatically suitable area for Syrmaticus reevesii under climate change
Feng, X., Lin, C., Qiao, H., & Ji, L. (2015) · Endangered Species Research · doi:10.3354/esr00668 · Cited by 17 · see citing works
Self-citationFeng, X., & Papeş, M. (2017) · Diversity and Distributions · doi:10.1111/ddi.12606 · Cited by 16 · see citing works
Self-citationEstimating the population size of lemurs based on their mutualistic food trees
Herrera, J. P., Borgerson, C., Lydia, T., Andriamahazoarivosoa, P., Rasolofoniaina, B. J. R., Rakotondrafarasata, E. R., Randrianasolo, J. L. R. R., Johnson, S. E., Wright, P. C., & Golden, C. D. W. (2018) · Journal of Biogeography · doi:10.1111/jbi.13409 · Cited by 16 · see citing works
Lee, T., Evans, T. A., Cameron, S. L., Hochuli, D. F., Ho, S. Y. W., & Lo, N. C. (2017) · Journal of Biogeography · doi:10.1111/jbi.12878 · Cited by 15 · see citing works
Best practices for reporting climate data in ecology
Morueta‐Holme, N., Oldfather, M. F., Olliff‐Yang, R. L., et al. (2018) · Nature Climate Change · doi:10.1038/s41558-017-0060-2 · Cited by 15 · see citing works
Sochor, M., Šarhanová, P., Pfanzelt, S., et al. (2017) · Journal of Biogeography · doi:10.1111/jbi.13084 · Cited by 13 · see citing works
A little bit everyday: range size determinants inArachis(Fabaceae), a dispersal‐limited group
Ceolin, G. B., & Giehl, E. L. H. (2017) · Journal of Biogeography · doi:10.1111/jbi.13082 · Cited by 11 · see citing works
McMinn, R. L., Russell, F., & Beck, J. B. (2016) · Journal of Biogeography · doi:10.1111/jbi.12879 · Cited by 10 · see citing works
Field‐measured variables outperform derived alternatives in Maryland stream biodiversity models
Johnston, M. R., Elmore, A. J., Mokany, K., et al. (2017) · Diversity and Distributions · doi:10.1111/ddi.12598 · Cited by 10 · see citing works
Genotypic variability enhances the reproducibility of an ecological studyPreprint
Milcu, A., Freitas, R. P., Ellison, A. M., Blouin, M., Scheu, S., Girin, T., Freschet, G. T., Rose, L., Scherer‐Lorenzen, M., Barot, S., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/080119 · Cited by 6 · see citing works
Project Data Management Planning
Michener, W. K. (2017) · Springer eBooks · doi:10.1007/978-3-319-59928-1_2 · Cited by 5 · see citing works
Data Quality Task Group 2: Tests and Assertions
Belbin, L., Chapman, A. D., Wieczorek, J. R., et al. (2018) · Biodiversity Information Science and Standards · doi:10.3897/biss.2.25608 · Cited by 3 · see citing works
Flagged first, then by citations
Research works printed but not linked: 3
- QA Note: Case #PM_MOD16_17166 (LAADS and DAAC, 2017); https:// go.nature.com/2lu5NCw
- Mahammad, S. S. & Ramakrishnan, R. GeoTIFF: a standard image file format for GIS applications. In Map India Conf. 2003 28-31 (2003).
- iNaturalist Research-grade Observations (iNaturalist.org, 2018); https://doi. org/10.15468/ab3s5x · DOI
Cited by
Sorted by citations
Data integration enables global biodiversity synthesis
Heberling, J. M., Miller, J. T., Noesgaard, D., Weingart, S. B., & Schigel, D. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2018093118 · Cited by 380 · see citing works
Borges, F. O., Guerreiro, M., Santos, C. P., Paula, J. R., & Rosa, R. (2022) · Frontiers in Marine Science · doi:10.3389/fmars.2022.1018766 · Cited by 28 · see citing works
“This method also has a predictive performance that is consistently competitive with other high-performing methods (Elith et al., 2006; Feng et al., 2019).”
MethodMedina Madariaga, G., Nguyen, H. H., Kiesel, J., Peters, K., Feld, C. K., Jaehnig, S. C., & Cambas, Y. T. (2024) · doi:10.1101/2024.05.28.596146 · Cited by 1 · see citing works
- Authors
- Feng, X., Park, D. S., Walker, C., Peterson, A. T., Merow, C., & Papeş, M.
- Affiliations
- University of Arizona (US)
- Harvard University (US)
- Oklahoma State University (US)
- University of Kansas (US)
- University of Connecticut (US)
- University of Tennessee at Knoxville (US)
- Corresponding author
- Feng, Xiao
- Venue
- Nature Ecology & Evolution
- Published
- 2019-09-23
- Volume
- 3
- Issue
- 10
- Pages
- 1382-1395
- ISSN
- 2397-334X (ISSN-L)
- OpenAlex
- W2974478553
- Cited by
- 323
- References
- 178
- Citations by year
- 2026: 37 · 2025: 55 · 2024: 66 · 2023: 65 · 2022: 47 · 2021: 30 · 2020: 22 · 2019: 1
- FWCI
- 1.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Ecology & Evolution (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (1661510, 1913673)
- University of Arizona
- National Institute for Mathematical and Biological Synthesis
- Topics
- Physical Sciences › Environmental Science › Ecological Modeling › Species Distribution and Climate Change
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- ecological niche modeling, species distribution modeling, reproducibility, reporting guidelines, reporting checklist, model parameters, data provenance, metadata, biodiversity data, journal peer review
- MeSH terms
- Ecology, Reproducibility of Results, Ecosystem, Biodiversity, Checklist
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
