Ignoring imperfect detection in biological surveys is dangerous: A response to 'fitting and interpreting occupancy models'

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Guillera Arroita, Gurutzeta ^a   Lahoz Monfort, José J ^a   MacKenzie, Darryl I ^b   Wintle, Brendan A ^a   McCarthy, Michael A ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b Proteus Wildlife Research Consultants   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; MATHEMATICAL PHENOMENA; RELIABILITY; SAMPLE SIZE; SIMULATION; STATISTICAL ANALYSIS; STATISTICAL BIAS; STATISTICAL MODEL; THEORY; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; ECOLOGY; PROCEDURES;

ALGORITHMS; COMPUTER SIMULATION; ECOLOGY; MODELS, BIOLOGICAL; MODELS, STATISTICAL;

EID: 84905017777     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099571     Document Type: Article

References (39)

1. MacKenzie DI, Nichols JD, Royle JA, Pollock KH, Bailey LL, et al. (2006) Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence. New York: Academic Press.
2. MacKenzie DI, Nichols JD, Lachman GB, Droege S, Royle JA, et al. (2002) Estimating site occupancy rates when detection probabilities are less than one. Ecology 83: 2248-2255. (Pubitemid 36524763)
3. Tyre AJ, Tenhumberg B, Field SA, Niejalke D, Parris K, et al. (2003) Improving precision and reducing bias in biological surveys: estimating false-negative error rates. Ecol Appl 13: 1790-1801. (Pubitemid 38362250)
4. Bailey LL, MacKenzie DI, Nichols JD (in press) Advances and applications of occupancy models. Methods Ecol Evol doi: 10.1111/2041-210X.12100.
5. Royle JA, Dorazio RM (2008) Hierarchical Modeling and Inference in Ecology. Amsterdam: Academic Press.
6. Yoccoz NG, Nichols JD, Boulinier T (2001) Monitoring of biological diversity in space and time. Trends Ecol Evol 16: 446-453. (Pubitemid 32772596)
7. Garrard GE, Bekessy SA, McCarthy MA, Wintle BA (2008) When have we looked hard enough? A novel method for setting minimum survey effort protocols for flora surveys. Austral Ecol 33: 986-998.
8. Chen G, Kéry M, Plattner M, Ma K, Gardner B (2013) Imperfect detection is the rule rather than the exception in plant distribution studies. J Ecol 101: 183-191.
9. Gu W, Swihart RH (2004) Absent or undetected? Effects of non-detection of species occurrence on wildlife-habitat models. Biol Conserv 116: 195-203. (Pubitemid 38069867)
10. Lahoz-Monfort JJ, Guillera-Arroita G, Wintle BA (2014) Imperfect detection impacts the performance of species distribution models. Glob Ecol Biogeogr 23: 504-515.
11. Kéry M (2011) Towards the modelling of true species distributions. J Biogeogr 38: 617-618.
12. Kéry M, Guillera-Arroita G, Lahoz-Monfort JJ (2013) Analysing and mapping species range dynamics using occupancy models. J Biogeogr 40: 1463-1474.
13. Moilanen A (2002) Implications of empirical data quality to metapopulation model parameter estimation and application. Oikos 96: 516-530.
14. Welsh AH, Lindenmayer DB, Donnelly CF (2013) Fitting and Interpreting Occupancy Models. PLoS ONE 8: e52015.
15. MacKenzie DI, Royle JA (2005) Designing occupancy studies: general advice and allocating survey effort. J Appl Ecol 42: 1105-1114.
16. Bailey LL, Hines JE, Nichols JD, MacKenzie DI (2007) Sampling design trade-offs in occupancy studies with imperfect detection: examples and software. Ecol Appl 17: 281-290. (Pubitemid 46596875)
17. Guillera-Arroita G, Ridout MS, Morgan BJT (2010) Design of occupancy studies with imperfect detection. Methods Ecol Evol 1: 131-139.
18. Guillera-Arroita G, Lahoz-Monfort JJ (2012) Designing studies to detect differences in species occupancy: power analysis under imperfect detection. Methods Ecol Evol 3: 860-869.
19. Wintle BA, McCarthy MA, Parris KM, Burgman MA (2004) Precision and bias of methods for estimating point survey detection probabilities. Ecol Appl 14: 703-712 (Pubitemid 39471070)
20. Guillera-Arroita G, Ridout MS, Morgan BJT (2014) Two-stage Bayesian study design for species occupancy estimation. J Agric Biol Envir Stat 19: 278-291.
21. Royle JA (2006) Site occupancy models with heterogeneous detection probabilities. Biometrics 62: 97-102.
22. Guillera-Arroita G (2011) Impact of sampling with replacement in occupancy studies with spatial replication. Methods Ecol Evol 2: 401-406.
23. MacKenzie DI, Nichols JD, Sutton N, Kawanishi K, Bailey BL (2005) Improving inferences in population studies of rare species that are detected imperfectly. Ecology, 86(5), 2005, pp 1101-1113.
24. Williams BK, Nichols JD, Conroy MJ (2002) Analysis and Management of Animal Populations. San Diego: Academic Press.
25. Borchers DL, Buckland ST, Zucchini W (2003) Estimating Animal Abundance: Closed Populations. New York: Springer.
26. Buckland ST, Anderson DR, Burnham KP, Laake JL, Borchers DL, et al. (2001) Introduction to Distance Sampling. Oxford: Oxford University Press.
27. Fiske I, Chandler R (2011) Unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance. J Stat Softw 43: 1-23.
28. R Development Core Team (2011) R: A language and environment for statistical computing. Vienna, Austria, ISBN 3-900051-07-0, http://www.R- project.org/. R Foundation for Statistical Computing.
29. Yee TW (2010) The VGAM Package for Categorical Data Analysis. J Stat Softw 32: 1-34.
30. Hines JE (2014) PRESENCE - Software to estimate patch occupancy and related parameters. USGS-PWRC http://www.mbr-pwrc.usgs.gov/software/presence. html. Accessed 2014 May 19.
31. Guillera-Arroita G, Morgan BJT, Ridout MS, Linkie M (2011) Species occupancy modeling for detection data collected along a transect. J Agric Biol Envir Stat 16: 301-317.
32. Royle JA, Nichols JD (2003) Estimating abundance from repeated presence-absence data or point counts. Ecology 84: 777-790. (Pubitemid 36893064)
33. Laake J, Rextad E (2014) RMark - an alternative approach to building linear models in MARK. In: Cooch E, White GC, editors. Program MARK: A Gentle Introduction - Appendix C (edition 13). http://www.phidot.org/software/mark/ docs/book/ Accessed 2014 May 19.
34. White GC, Burnham KP (1999) Program MARK: Survival estimation from populations of marked animals. Bird Study 46: 120-139.
35. Lunn D, Jackson C, Best N, Thomas A, Spiegelhalter D (2012) The BUGS book - A practical introduction to Bayesian analysis: CRC Press - Chapman and Hall.
36. Plummer M (2003) JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of the 3rd International Workshop on Distributed Statistical Computing, Vienna.
37. Kéry M, Schaub M (2012) Bayesian Population Analysis using WinBUGS - A Hierarchical Perspective. Waltham: Academic Press.
38. Link WA (2003) Nonidentifiability of population size from capture-recapture data with heterogenerous detection probabilities. Biometrics 59: 1123-1130.
39. Morgan BJT, Ridout MS (2008) A new mixture model for capture heterogeneity. App Statist 57: 433-446.