When no catches matter: Coping with zeros in environmental assessments

Ecological Indicators

Volumn 10, Issue 3, 2010, Pages 572-583

  Lewin, Wolf Christian ^a,b   Freyhof, Jörg ^a   Huckstorf, Volker ^a   Mehner, Thomas ^a   Wolter, Christian ^a  

^a LEIBNIZ INSTITUTE OF FRESHWATER ECOLOGY AND INLAND FISHERIES   (Germany)

^b Institute of Inland Fisheries   (Germany)

Author keywords

Juvenile fish; Monitoring; Regression models; Species habitat relationship; Temperate rivers; Zero inflation

Indexed keywords

COMPUTATIONAL PROCEDURES; CONTINUOUS MONITORING; DATA SETS; ECOLOGICAL INTEGRITY; ECOLOGICAL PROCESS; ENVIRONMENTAL ASSESSMENT; ENVIRONMENTAL CONCERNS; ENVIRONMENTAL FACTORS; ENVIRONMENTAL LEGISLATIONS; FISH ASSEMBLAGES; FISH POPULATIONS; FURTHER DEVELOPMENT; JUVENILE FISH; LOGISTIC REGRESSION MODELS; LOGISTIC REGRESSIONS; LOW SENSITIVITY; NEGATIVE BINOMIAL DISTRIBUTION; OCCURRENCE PROBABILITY; PRESENCE/ABSENCE SAMPLINGS; RARE SPECIES; REGRESSION MODEL; REHABILITATION STRATEGY; SAMPLING POINTS; SPATIAL DISTRIBUTION; SPECIES-ENVIRONMENT RELATIONSHIPS; SPECIES-HABITAT RELATIONSHIP; SPECIES-HABITAT RELATIONSHIPS; STATISTICAL MODELS; STREAM RESTORATION;

ECOLOGY; FISH; FISHERIES; HIGH ENERGY PHYSICS; MEATS; MIXTURES; POISSON DISTRIBUTION; PROBABILITY DENSITY FUNCTION; RIVERS; SAMPLING; SIZE DISTRIBUTION;

REGRESSION ANALYSIS;

ABUNDANCE; DATA SET; ENVIRONMENTAL ASSESSMENT; ENVIRONMENTAL LEGISLATION; FISH; FRESHWATER ECOSYSTEM; JUVENILE; RESTORATION ECOLOGY; SAMPLING; SPATIAL DISTRIBUTION; TEMPERATE ENVIRONMENT;

GERMANY;

EID: 75549085815     PISSN: 1470160X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolind.2009.09.006     Document Type: Article

References (95)

1. Aarts B.G.W., and Nienhuis P.H. Fish zonations and guilds as the basis for assessment of ecological integrity of large rivers. Hydrobiologia 500 (2003) 157-178
2. Aarts B.G.W., Van den Brink F.W.B., and Nienhuis P.H. Habitat loss as the main cause of the slow recovery of fish faunas of regulated large rivers in Europe: the transversal floodplain gradient. River Research and Application 20 (2004) 3-23
3. Akaike H. Likelihood of a model and information criteria. Journal of Econometrics 16 (1981) 2-23
4. Altman D.G., and Royston P. The cost of dichotomising continuous variables. British Medical Journal 332 (2006) 1080
5. Austin M. Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecological Modelling 200 (2007) 1-19
6. Baattrup-Pedersen A., and Riis T. Macrophyte diversity and composition in relation to substratum characteristics in regulated and unregulated Danish streams. Freshwater Biology 42 (1999) 375-385
7. Barry S.C., and Welsh A.H. Generalized additive modelling and zero inflated count data. Ecological Modelling 157 (2002) 179-188
8. Belliard J., Boët P., and Tales E. Regional and longitudinal patterns of fish community structure in the Seine River basin, France. Environmental Biology of Fishes 50 (1997) 133-147
9. Bischoff A. Juvenile Fish Recruitment in the Large Lowland River Oder: Assessing the Role of Physical Factors and Habitat Availability (2002), Shaker, Aachen
10. Brosse S., and Lek S. Modelling roach (Rutilus rutilus) microhabitat using linear and nonlinear techniques. Freshwater Biology 44 (2000) 441-452
11. Brosse S., Grossman G.D., and Lek S. Fish assemblage patterns in the littoral zone of a European reservoir. Freshwater Biology 52 (2007) 448-458
12. Cameron C., and Trivedi P.K. Regression Analysis of Count Data, Econometric Society Monograph No. 30 (1998), Cambridge University Press, UK
13. Clark A.S.S., Zydervelt E.E., and Wing S.R. Modelling count and growth data with many zeros. Journal of Experimental Marine Biology and Ecology 365 (2008) 86-95
14. Coelho M.M., and Zalewski M. Morphological variability in the ecotone-an important factor for the conservation of fish species richness in Swiss rivers. Hydrobiologia 303 (1995) 223-228
15. Cohen J. The cost of dichotomization. Applied Psychological Measurement 7 3 (1983) 249-253
16. Copp G.H. Effect of regulation on 0+ fish recruitment in the Great Ouse, a lowland river. Regulated Rivers: Research and Management 5 (1990) 251-263
17. Copp G.H., and Penaz M. Ecology of fish spawning and nursery toes in the flood plain, using a new sampling approach. Hydrobiologia 169 (1988) 209-224
18. Copp G.H., Guti G., Rovný B., and Černý J. Hierarchical analysis of habitat use by 0+ juvenile fish in Hungarian/Slovak flood plain of the Danube River. Environmental Biology of Fishes 40 (1994) 329-348
19. Cragg J.G. Some statistical models for limited dependent variables with application to the demand for durable goods. Econometrica 39 5 (1971) 829-844
20. Cunningham R.B., and Lindenmayer D.B. Modeling count data of rare species: some statistical issues. Ecology 86 5 (2005) 1135-1142
21. De Leeuw J.J., Buijse A.D., Haidvogl G., Lapinska M., Noble R., Repecka R., Virbickas T., Wisniewolski W., and Wolter C. Challenges in developing fish-based ecological assessment methods for large floodplain rivers. Fisheries Management and Ecology 14 (2007) 483-494
22. Disse M., and Engel H. Flood events in the Rhine Basin: genesis, influences and mitigation. Natural Hazards 23 (2001) 271-290
23. Duncan A., Kubecka J., Kett S., Hanna N., and Skeldon J. Habitats of 0+ fry in an English lowland river. Archiv für Hydrobiologie Suppl. 12 (2001) 153-171
24. Dynesius M., and Nilsson C. Fragmentation and flow regulation of river systems in the northern third of the world. Science 266 (1994) 762
25. Eikaas H.S., and McIntosh A.R. Habitat loss through disruption of constrained dispersal networks. Ecological Applications 16 3 (2006) 987-998
26. European Communities. Overall Approach to the Classification of Ecological Status and Ecological Potential. Common Implementation Strategy for the Water Framework Directive (2000/60/EC), WFD CIS Guidance Document No 13 (2005), Office for Official Publications of the European Communities, Luxembourg
27. Ewen G.J., Cassey P., and King R.A.R. Assessment of the randomization test for binomial sex-ratio distributions in birds. The Auk 120 1 (2003) 62-68
28. Ferrier S., Drielsma M., Manion G., and Watson G. Extended statistical approaches to modelling spatial pattern in biodiversity in northeast New South Wales. II. Community-level modelling. Biodiversity and Conservation 11 (2002) 2309-2338
29. Field S.A., Tyre A.J., and Possingham H.P. Optimizing allocation of monitoring effort under economic and observational constraints. Journal of Wildlife Management 69 2 (2005) 473-482
30. Fladung E., Scholten M., and Thiel R. Modelling the habitat preferences of preadult and adult fishes on the shoreline of the large, lowland Elbe River. Journal of Applied Ichthyology 19 (2003) 303-314
31. Garner P. Suitability indices for juvenile 0+ roach (Rutilus rutilus) using point abundance sampling data. Regulated Rivers: Research and Management 10 (1995) 99-104
32. Gozlan R.E., Mastrorillo S., Dauba F., Tourenq J.-N., and Copp G.H. Multi-scale analysis of habitat use during late summer for 0+ fishes in the River Garonne (France). Aquatic Science 60 (1998) 99-117
33. Grenouillet G., Pont D., and Olivier J.M. Habitat occupancy patterns of juvenile fishes in a large lowland river: interactions with macrophytes. Archiv für Hydrobiologie 149 (2000) 307-326
34. Grenouillet G., Pont D., and Seip K.L. Abundance and species richness as a function of food resources and vegetation structure: juvenile fish assemblages in rivers. Ecography 25 (2002) 641-650
35. Gu W., and Swihert R.K. Absent or undetected? Effects of non-detection of species occurrence on wildlife-habitat models. Biological Conservation 116 (2004) 195-203
36. Guisan A., Edwards T.C., and Hastie T. Generalized linear and generalized additive models in studies of species distributions: setting the scene. Ecological Modelling 157 (2002) 89-100
37. Heilbron D.C. Zero-altered and other regression models for count data with added zeros. Biometrical Journal 36 5 (1994) 531-547
38. Herder F., and Freyhof J. Resource partitioning in a tropical stream fish assemblage. Journal of Fish Biology 69 (2006) 571-589
39. Hoeinghaus D.J., Winemiller K.O., and Birnbaum J.S. Local and regional determinants of stream fish assemblage structure: inferences based on taxonomic vs. functional groups. Journal of Biogeography 34 (2007) 324-338
40. Humpl M., and Pivnička K. Fish assemblages as influenced by environmental factors in streams in protected areas of the Czech Republic. Ecology of Freshwater Fish 15 (2006) 96-103
41. Jackman S. pscl: Classes and Methods for R Developed in the Political Science Computational Laboratory (2008), Stanford University, Department of Political Science, Stanford University, Stanford, CA R package version 1.03
42. Johnson J.B., and Omland K.S. Model selection in ecology and evolution. Trends in Ecology and Evolution 19 2 (2004) 101-108
43. Joseph L.N., Field S.A., Wilcox C., and Possingham H.P. Presence-absence versus abundance data for monitoring threatened species. Conservation Biology 20 6 (2006) 1679-1687
44. Keating K.A., and Cherry S. Use and interpretation of logistic regression in habitat-selection studies. Journal of Wildlife Management 658 4 (2004) 774-789
45. Kirchhofer A. Morphological variability in the ecotone-an important factor for the conservation of fish species richness in Swiss rivers. Hydrobiologia 303 (1995) 103-110
46. Knösche R. Organic sediment nutrient concentrations and their relationship with the hydrological connectivity of floodplain waters (River Havel, NE Germany). Hydrobiologia 560 (2006) 63-76
47. Kuhnert P.M., Martin T.G., Mengersen K., and Possingham H.P. Assessing the impacts of grazing levels on bird density in woodland habitat: a Bayesian approach using expert opinion. Environmetrics 16 (2005) 717-747
48. Kurmayer R., Keckeis H., Schrutka S., and Zweimüller I. Macro- and microhabitats used by 0+ fish in a side-arm of the River Danube. Archiv für Hydrobiologie Suppl. 113 (1996) 425-432
49. Lambert D.L. Zero-inflated Poisson regression, with an application to defects in manufacturing. Technometrics 34 1 (1992) 1-14
50. Land K.C., McCall P.L., and Nagin D.S. A comparison of Poisson, negative binomial, and semiparametric mixed Poisson regression models: with empirical applications to criminal careers data. Sociological Methods Research 24 (1996) 387-442
51. Langler G.J., and Smith C. Effects of habitat enhancement on 0-group fishes in a lowland river. Regulated Rivers: Research and Management 17 (2001) 677-686
52. Lapointe N.W.R., Corkum L.D., and Mandrak N.E. Point sampling by boat electrofishing: a test of the effort required to assess fish communities. North American Journal of Fisheries Management 26 (2006) 793-799
53. Lasne E., and Laffaille P. Analysis of distribution patterns of yellow European eels in the Loire catchment using logistic models based on presence-absence of different size-classes. Ecology of Freshwater Fish 17 (2008) 30-37
54. Lawler J.J., White D., Sifneos J.C., and Master L.L. Rare species and the use of indicator groups for conservation planning. Conservation Biology 17 3 (2003) 875-882
55. Lazzari M.A. Habitat variability in young-of-the-year winter flounder, Pseudopleuronectes americanus, in Maine estuaries. Fisheries Research 90 (2008) 296-304
56. Lewin W.-C., Okun N., and Mehner T. Determinants of the distribution of juvenile fish in the littoral area of a shallow lake. Freshwater Biology 49 (2004) 410-424
57. Lindsey J.K. On the use of corrections for overdispersion. Journal of the Royal Statistical Society: Series C 48 4 (1999) 553-561
58. MacKenzie D.I., and Royle J.A. Designing occupancy studies: general advice and allocating survey effort. Journal of Applied Ecology 42 (2005) 1105-1114
59. Martin T.G., Wintle B.A., Rhodes J.R., Kuhnert P.M., Field S.A., Low-Choy S.J., Tyre A.J., and Possingham H.P. Zero tolerance ecology: improving ecological inference by modelling the source of zero observations. Ecology Letters 8 (2005) 1235-1246
60. Matthews W.J. Fish faunal structure in an Ozark stream: stability, persistence and a catastrophic flood. Copeia 1986 (1986) 388-397
61. Minami M., Lennert-Cody C.E., Gaoc W., and Verdesoto M.R. Modeling shark bycatch: the zero-inflated negative binomial regression model with smoothing. Fisheries Research 84 (2007) 210-221
62. Mullahy J. Specification and testing of some modified count data models. Journal of Econometrics 33 (1986) 341-365
63. Nielsen S.E., Johnson C.J., Heard D.C., and Boyce M.S. Can models of presence/absence be used to scale abundance? Two case studies considering extremes in life history. Ecography 28 (2005) 197-208
64. Noble R.R.A., Cowx I.G., and Starkie A. Development of fish-based methods for the assessment of ecological status in English and Welsh rivers. Fisheries Management and Ecology 14 (2007) 495-508
65. O'Neill M.F., and Faddy M.J. Use of binary and truncated negative binomial modelling in the analysis of recreational catch data. Fisheries Research 60 (2003) 471-477
66. Olden J.D., and Jackson D.A. A comparison of statistical approaches for modelling fish species distributions. Freshwater Biology 47 (2002) 1976-1995
67. Persat H., and Copp G.H. Electric fishing and point abundance sampling for the ichthyology of large rivers. In: Cowx I.G. (Ed). Developments in Electric Fishing (1990), Blackwell Scientific Publications Ltd. 197-209
68. Pinder L.C.V., Marker A.F.H., Mann H.K., Bassi J.A.B., and Copp G.H. The River Great Ouse, a highly eutrophic, slow-flowing, regulated lowland river in Eastern England. Regulated Rivers: Research and Management 13 (1997) 203-219
69. Poff N.L., Olden J.D., Merritt D.M., and Pepin D.M. Homogenization of regional river dynamics by dams and global biodiversity implications. Proceedings of the National Academy of Sciences 104 14 (2007) 5732-5737
70. Pont D., Hugueny B., and Oberdorff T. Modelling habitat requirement of European fishes: do species have similar responses to local and regional environmental constraints?. Canadian Journal of Fisheries and Aquatic Sciences 62 (2005) 163-173
71. Potts J.M., and Elith J. Comparing species abundance models. Ecological Modelling 199 (2006) 153-163
72. Pretty J.L., Harrison S.S.C., Shepherd D.J., Smith C., Hildrew A.G., and Hey R.D. River rehabilitation and fish populations: assessing the benefit of instream structures. Journal of Applied Ecology 40 (2003) 251-265
73. Ragland D.R. Dichotomizing continuous outcome variables: dependence of the magnitude of association and statistical power on the cutpoint. Epidemiology 3 5 (1992) 434-440
74. Rahel F.J. The hierarchical nature of community persistence: a problem of scale. The American Naturalist 136 (1990) 328-344
75. Rosenfeld J. Assessing the habitat requirements of stream fishes: an overview and evaluation of different approaches. Transactions of the American Fisheries Society 132 (2003) 953-968
76. Scardi M., Cataudella S., Di Dato P., Fresia E., and Tancionia L. An expert system based on fish assemblages for evaluating the ecological quality of streams and rivers. Ecological Informatics 3 (2008) 55-63
77. Schiemer F., and Waidbacher H. Strategies for conservation of a Danubian fish fauna. In: Boon P.J., Calow P., and Petts G.E. (Eds). River Conservation and Management (1992), John Wiley Ltd. 363-382
78. Schiemer F., Keckeis H., Reckendorfer W., and Winkler G. The "inshore retention concept" and its significance for large rivers. Archiv für Hydrobiologie 135 Suppl. 2-4 (2001) 509-516
79. Simberloff D., and Dayan T. The guild concept and the structure of ecological communities. Annual Review of Ecology and Systematics 22 (1991) 115-143
80. Stefansson G. Analysis of ground fish survey abundance data: combining the GLM and delta approaches. ICES Journal of Marine Science 53 (1996) 577-588
81. Tiffan K.F., Clark L.O., Garland R.D., and Rondorf D.W. Variables influencing the presence of subyearling fall chinook salmon in shoreline habitats of the Hanford Reach, Columbia River. North American Journal of Fisheries Management 26 (2006) 351-360
82. Turgeon K., and Rodriguez M.A. Predicting microhabitat selection in juvenile Atlantic salmon Salmo salar by the use of logistic regression and classification trees. Freshwater Biology 50 (2005) 539-551
83. Tyre A.J., Tenhumberg B., Field S.A., Niejalke D., Parris K., and Possingham H.P. Improving precision and reducing bias in biological surveys: estimating false-negative error rates. Ecological Applications 13 6 (2003) 1790-1801 2003
84. Vadas R.L., and Orth D.J. Formulation of habitat suitability models for stream fish guilds: do the standard methods work?. Transactions of the American Fisheries Society 130 (2001) 217-235
85. Valova Z., Jurajda P., and Janáč M. Spatial distribution of 0+ juvenile fish in differently modified lowland rivers. Folia Zoologica 55 3 (2006) 293-308
86. Venables W.N., and Ripley B.D. Modern Applied Statistics with S (2002), Springer, London
87. Vuong Q.H. Likelihood ratio tests for model selection and non-nested hypotheses. Econometrica 57 (1989) 307-333
88. Welcomme R.L., Winemiller K.O., and Cowx I.G. Fish environmental guilds as a tool for assessment of ecological condition of rivers. River Research and Applications 22 (2006) 377-396
89. Welsh A.H., Cunningham R.B., Donnelly C.F., and Lindenmayer D.B. Modelling the abundance of rare species: statistical models for counts with extra zeros. Ecological Modelling 88 (1996) 297-308
90. Welsh A.H., Cunningham R.B., and Chambers R.L. Methodology for estimating the abundance of rare animals: seabird nesting on north east Herald Cay. Biometrics 56 (2000) 22-30
91. Wintle B.A., Kavanagh R.P., McCarthy M.A., and Burgman M.A. Estimating and dealing with detectability in occupance surveys for forest owls and arboreal marsupials. Journal of Wildlife Management 69 3 (2005) 905-917
92. Wolda H., and Marek J. Measuring variation in abundance, the problem with zeros. European Journal of Entomology 91 (1994) 145-161
93. Zeileis A., and Hothorn T. Diagnostic checking in regression relationships. R News 2 3 (2002) 7-10
94. Zeileis A., Kleiber C., and Jackman S. Regression models for count data in R. Journal of Statistical Software 27 8 (2008) 1-25
95. Zorn C.J.W. An analytic and empirical examination of zero-inflated and hurdle Poisson specifications. Sociological Methods Research 26 (1996) 368-400