Quality of presence data determines species distribution model performance: a novel index to evaluate data quality

Landscape Ecology

Volumn 31, Issue 1, 2016, Pages 31-42

  Fei, Songlin ^a   Yu, Feng ^a  

^a PURDUE UNIVERSITY   (United States)

Author keywords

Completeness; Data quality; Representativeness; Species distribution modeling

Indexed keywords

EID: 84952714791     PISSN: 09212973     EISSN: 15729761     Source Type: Journal    
DOI: 10.1007/s10980-015-0272-7     Document Type: Article

References (46)

1. Acevedo P, Jiménez-Valverde A, Lobo JM, Real R (2012) Delimiting the geographical background in species distribution modelling. J Biogeogr 39(8):1383–1390
2. Allouche O, Tsoar A, Kadmon R (2006) Assessing the accuracy of species distribution models: prevalence, kappa and the true skill statistic (TSS). J Appl Ecol 43(6):1223–1232
3. Araújo MB, New M (2007) Ensemble forecasting of species distributions. Trends Ecol Evol 22(1):42–47
4. Araújo MB, Pearson RG (2005) Equilibrium of species’ distributions with climate. Ecography 28(5):693–695
5. Austin M (2007) Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecol Model 200(1):1–19
6. Austin M, Smith T (1989) A new model for the continuum concept. Vegetatio 83(1–2):35–47
7. Clark PJ, Evans FC (1954) Distance to nearest neighbor as a measure of spatial relationships in populations. Ecology 35(4):445–453
8. Elith J, Leathwick JR (2009) Species Distribution Models: ecological Explanation and Prediction Across Space and Time. Annu Rev Ecol Evol Syst 40:677–697
9. Elith J, Graham CH, Anderson RP, Dudík M, Ferrier S, Guisan A, Hijmans RJ, Huettmann F, Leathwick JR, Lehmann A, Li J, Lohmann LG, Loiselle BA, Manion G, Moritz C, Nakamura M, Nakazawa Y, Overton JM, Peterson AT, Phillips SJ, Richardson K, Scachetti-Pereira R, Schapire RE, Soberón J, Williams S, Wisz MS, Zimmermann NE, Araujo M (2006) Novel methods improve prediction of species’ distributions from occurrence data. Ecography 29(2):129–151
10. Fei S, Schibig J, Vance M (2007) Spatial habitat modeling of American chestnut at Mammoth Cave National Park. For. Ecol. Manag. 252(1–3):201–207
11. Fei S, Liang L, Paillet FL, Steiner KC, Fang J, Shen Z, Wang Z, Hebard FV (2012) Modelling chestnut biogeography for American chestnut restoration. Divers Distrib 18(8):754–768
12. Fourcade Y, Engler JO, Rödder D, Secondi J (2014) mapping species distributions with MAXENT using a geographically biased sample of presence data: a performance assessment of methods for correcting sampling bias. PLoS One 9(5):e97122
13. Franklin J (2009) Mapping species distributions: spatial inference and prediction. Cambridge University Press, Cambridge
14. Franklin J (2013) Species distribution models in conservation biogeography: developments and challenges. Divers Distrib 19(10):1217–1223
15. Guisan A, Thuiller W (2005) Predicting species distribution: offering more than simple habitat models. Ecol Lett 8(9):993–1009
16. Hijmans RJ (2012) Cross-validation of species distribution models: removing spatial sorting bias and calibration with a null model. Ecology 93(3):679–688
17. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. Int J Climatol 25(15):1965–1978
18. Hirzel AH, Hausser J, Chessel D, Perrin N (2002) Ecological-niche factor analysis: how to compute habitat-suitability maps without absence data? Ecology 83(7):2027–2036
19. Hortal J, Lobo J (2005) An ED-based Protocol for Optimal Sampling of Biodiversity. Biodivers Conserv 14(12):2913–2947
20. Hortal J, Lobo J, Martín-piera F (2001) Forecasting insect species richness scores in poorly surveyed territories: the case of the Portuguese dung beetles (Col. Scarabaeinae). Biodivers Conserv 10(8):1343–1367
21. Jiménez-Valverde A, Lobo JM (2007) Threshold criteria for conversion of probability of species presence to either–or presence–absence. Acta Oecol 31(3):361–369
22. Kadmon R, Farber O, Danin A (2003) A systematic analysis of factors affecting the performance of climatic envelope models. Ecol Appl 13(3):853–867
23. Kaiser HF (1974) An index of factorial simplicity. Psychometrika 39(1):31–36
24. Kramer-Schadt S, Niedballa J, Pilgrim JD, Schröder B, Lindenborn J, Reinfelder V, Stillfried M, Heckmann I, Scharf AK, Augeri DM, Cheyne SM, Hearn AJ, Ross J, Macdonald DW, Mathai J, Eaton J, Marshall AJ, Semiadi G, Rustam R, Bernard H, Alfred R, Samejima H, Duckworth JW, Breitenmoser-Wuersten C, Belant JL, Hofer H, Wilting A (2013) The importance of correcting for sampling bias in MaxEnt species distribution models. Divers Distrib 19(11):1366–1379
25. Liang L, Fei S (2014) Divergence of the potential invasion range of emerald ash borer and its host distribution in North America under climate change. Clim Change 122(4):735–746
26. Lobo JM, Martín-Piera F (2002) Searching for a predictive model for species richness of Iberian dung beetle based on spatial and environmental variables. Conserv Biol 16(1):158–173
27. Lobo JM, Jiménez-Valverde A, Real R (2008) AUC: a misleading measure of the performance of predictive distribution models. Glob Ecol Biogeogr 17(2):145–151
28. Luoto M, Pöyry J, Heikkinen R, Saarinen K (2005) Uncertainty of bioclimate envelope models based on the geographical distribution of species. Glob Ecol Biogeogr 14(6):575–584
29. Manel S, Williams HC, Ormerod SJ (2001) Evaluating presence–absence models in ecology: the need to account for prevalence. J Appl Ecol 38(5):921–931
30. Merow C, Smith MJ, Silander JA (2013) A practical guide to MaxEnt for modeling species’ distributions: what it does, and why inputs and settings matter. Ecography 36:1058–1069
31. Ong MS, Kuang YC, Ooi MP-L (2012) Statistical measures of two dimensional point set uniformity. Comput Stat Data Anal 56(6):2159–2181
32. Pearce J, Ferrier S (2000) Evaluating the predictive performance of habitat models developed using logistic regression. Ecol Model 133(3):225–245
33. Pearson RG, Phillips SJ, Loranty MM, Beck PSA, Damoulas T, Knight SJ, Goetz SJ (2013) Shifts in Arctic vegetation and associated feedbacks under climate change. Nat Clim Chang 3(7):673–677
34. Peterson AT, Holt RD (2003) Niche differentiation in Mexican birds: using point occurrences to detect ecological innovation. Ecol Lett 6(8):774–782
35. Phillips SJ, Elith J (2010) POC plots: calibrating species distribution models with presence-only data. Ecology 91(8):2476–2484
36. Phillips SJ, Elith J (2013) On estimating probability of presence from use-availability or presence-background data. Ecology 94(6):1409–1419
37. Phillips SJ, Anderson RP, Schapire RE (2006) Maximum entropy modeling of species geographic distributions. Ecol Model 190(3):231–259
38. Phillips SJ, Dudík M, Elith J, Graham CH, Lehmann A, Leathwick J, Ferrier S (2009) Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data. Ecol Appl 19(1):181–197
39. Reese GC, Wilson KR, Hoeting JA, Flather CH (2005) Factors affecting species distribution predictions: a simulation modeling experiment. Ecol Appl 15(2):554–564
40. Ricklefs RE, Jenkins DG (2011) Biogeography and ecology: towards the integration of two disciplines. Philos Trans R Soc B Biol Sci 366(1576):2438–2448
41. Royle JA, Chandler RB, Yackulic C, Nichols JD (2012) Likelihood analysis of species occurrence probability from presence-only data for modelling species distributions. Methods Ecol Evol 3(3):545–554
42. Sax DF, Early R, Bellemare J (2013) Niche syndromes, species extinction risks, and management under climate change. Trends Ecol Evol 28(9):517–523
43. Shen Z, Fei S, Feng J, Liu Y, Liu Z, Tang Z, Wang X, Wu X, Zheng C, Zhu B, Fang J (2012) Geographical patterns of community-based tree species richness in Chinese mountain forests: the effects of contemporary climate and regional history. Ecography 35(12):1134–1146
44. Václavík T, Meentemeyer RK (2012) Equilibrium or not? Modelling potential distribution of invasive species in different stages of invasion. Divers Distrib 18(1):73–83
45. Vaughan I, Ormerod S (2005) The continuing challenges of testing species distribution models. J Appl Ecol 42(4):720–730
46. Wisz MS, Hijmans R, Li J, Peterson AT, Graham C, Guisan A (2008) Effects of sample size on the performance of species distribution models. Divers Distrib 14(5):763–773