Rivers are complex linear features, (Petts, 1994). Assessing habitat quality and composition has traditionally focused on reaches of 10s metres, recently interest has moved to the mesoscale (100s of metres) e.g. Paraseiwicz (2001); Maddock and Bird (1996). Assessment at the catchment scale is the ultimate goal, e.g. European Water Framework Directive (Bragg et al, 2005) and will possibly require an element of remote sensing to be effective. In field trials, inter-operator variability of four meso-scale habitat mapping methods: MesoCaSiMiR, MesoHABSIM, Norwegian Mesohabitat Classification Method and Rapid Habitat Mapping was found to be up to 85% by area surveyed (Maddock and Hill, 2005). Further, the biological relevance of some methods, such as the weighted usable area output from PHABSIM/MesoHABSIM, has been challenged by some (Thoms, 2006) and others, whilst habitat connectivity is increasingly important (Walker, 2006)
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