bluuebunny/crossref_metadata_2025 huggingface dataset:
A scenario‐based holistic approach to environmental flow assessments for rivers
Authors: King Jackie , Brown Cate , Sabet Hossein
Published: September 2003

An Erratum has been published for this article in River Research and Applications 21(5) 2005, 509.

Sustainable use of river ecosystems requires that they be managed holistically. This paper describes an holistic methodology, DRIFT (Downstream Response to Imposed Flow Transformation), for advising on environmental flows for rivers targetted for water‐management activities. DRIFT's basic philosophy is that all major abiotic and biotic components constitute the ecosystem to be managed; and within that, the full spectrum of flows, and their temporal and spatial variability, constitute the flows to be managed. The methodology employs experienced scientists from the following biophysical disciplines: hydrology, hydraulics, fluvial geomorphology, sedimentology, chemistry, botany and zoology. Where there are subsistence users of the river, the following socio‐economic disciplines are also employed: sociology, anthropology, water supply, public health, livestock health and resource economics.

DRIFT is a structured process for combining data and knowledge from all the disciplines to produce flow‐related scenarios for water managers to consider. It consists of four modules. In the first, or biophysical module, the river ecosystem is described and predictive capacity developed on how it would change with flow changes. In the second, or socio‐economic module, links are described between riparian people who are subsistence users of river resources, the resources they use, and their health. The objective is to develop predictive capacity of how river changes would impact their lives. In the third module, scenarios are built of potential future flows and the impacts of these on the river and the riparian people. The fourth, or economic module, lists compensation and mitigation costs.

DRIFT should run in parallel with two other exercises which are external to it: a macro‐economic assessment of the wider implications of each scenario, and a Public Participation Process whereby people other than subsistence users can indicate the level of acceptability of each scenario.

DRIFT has been developed in a semi‐arid, developing region, where water‐supply problems are pressing, and uncertainties about river‐linked ecological and social processes high. The use of DRIFT in this context is discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Interannual variation of fish assemblage structure in a Mediterranean river: implications of streamflow on the dominance of native or exotic species
Authors: Bernardo João M. , Ilhéu Maria , Matono Paula , Costa Ana M.
Published: September 2003

Streams in mediterranean‐type climate regions are shaped by predictable seasonal events of flooding and drying over an annual cycle, but also present a strong interannual flow variation.

The Guadiana River is one of the most important rivers in the Iberian Peninsula. The fish fauna presents 11 native freshwater species, including eight with high conservation status. Several exotic species are present, the most important being the American centrarchids pumpkinseed fish and largemouth bass. As a typical mediterranean‐type river, the Guadiana has an irregular hydrological regime with severe drought periods and floods; the interannual variation of discharge presents a ratio of c. 100 to 1.

From 1980 to 1995 several dry years were observed, culminating in the drought of 19910/92–19947/95. Analysing the variation of the fish assemblage structure during this period, exotic species (mostly pumpkinseed) progressively increased, strongly dominating in 1995. Indigenous populations dramatically decreased and a previously common endemic cyprinid (Anaecypris hispanica Steindachner) became endangered and one of the most threatened fishes of Europe. However, the following years presented above‐average flows with several flood events and an inverse process occurred, with native species increasing their contribution in a short period.

The importance of floods as a disturbance factor in the control of lentic or slow flowing water exotics is discussed. Native species apparently possess adaptive responses to high flows which exotics lack. This hypothesis is consistent with probability‐of‐use curves and preflood–postflood surveys. Results emphasize the importance of floods in the environmental flows of mediterranean‐type rivers. In the absence of flooding disturbance, exotic fish populations predictably grow, increasing the pressure on native species; abiotic disturbance may supersede deterministic outcomes of predation or competition and influence community structure by reducing populations of the exotic species. Copyright © 2003 John Wiley & Sons, Ltd.
Do juvenile Atlantic salmon parr track local changes in water velocity?
Authors: Kemp P. S. , Gilvear D. J. , Armstrong J. D.
Published: September 2003

When given a choice of two flows and constant food availability, salmon parr should choose the lower flow if they are to optimize their net energy gain . In a two‐choice test carried out in a recirculating flume, there was no significant selection for ranges of naturally occurring high (mean mid‐column velocities of 19.5–25.2 cm s−1) or low (7.2–10.0 cm s−1) summer flows. To test whether this result might indicate that only a proportion of the population chose optimal flows, the positions of the flows were reversed. All fish that initially chose low flow remained site‐attached when the flows were reversed. A significant proportion of the fish that initially chose high flow moved when the flows were reversed. Hence, there is no evidence that salmon can integrate energy costs and gains to optimize their feeding positions. However, the behaviour of some individual fish was consistent with a ‘rule of thumb’ of following high flows, which may improve foraging efficiency in natural streams above random in the long but not short term. The findings show that only a fraction of the parr in a population redistribute themselves in response to changes in discharge and therefore a fundamental assumption of some instream flow models is questioned. © Crown Copyright 2003. Reproduced with the permission of her majesty's stationery office. Published by John Wiley & Sons, Ltd.
Environmental flow requirements of fish in Lesotho rivers using the DRIFT methodology
Authors: Arthington Angela H. , Rall Johan L. , Kennard Mark J. , Pusey Bradley J.
Published: September 2003

DRIFT (Downstream Response to Imposed Flow Transformations) is a scenario‐based environmental flow assessment methodology applied during impact studies associated with the Lesotho Highlands Water Project, Southern Africa. DRIFT offers a structured process for predicting the biophysical, social and economic consequences of altering a river's flow regime. The fish component of DRIFT provides a ten‐step protocol designed to make such predictions using field data on a river's fish fauna linked to information on flow‐related aspects of fish biology drawn from the literature and the knowledge base and professional experience of fish ecologists. A worked example of the methodology is presented based on a study site downstream from Katse Dam on the Malibamatso River, Lesotho, where the ecological consequences of four flow scenarios were evaluated. DRIFT and its fish component have emerged from studies in a semi‐arid, developing region where unpredictable hydrological regimes and data scarcity constrain the prediction of ecological responses to flow regulation. Faced with similar information constraints, scientific uncertainty and limited windows of opportunity to guide water management, other countries have employed scientific panels to recommend environmental flows. DRIFT and its fish component compare favourably with recommended best practice for Australian scientific panel assessments of the flow requirements of river ecosystems. The risks associated with use of scientific panel approaches are discussed and minimum data sets and standards are recommended for the conduct of a DRIFT fish assessment. DRIFT and related frameworks represent the second level in a three‐tiered hierarchy of environmental flow methods. They can provide environmental flow recommendations of far greater scientific resolution than hydrological methods by integrating many types of information on the responses of riverine biota to flow modifications. However, DRIFT should only be applied within an adaptive management framework where there is a genuine commitment to the generation and use of new knowledge derived from monitoring and research. Copyright © 2003 John Wiley & Sons, Ltd.
A population dynamics model and habitat simulation as a tool to predict brown trout demography in natural and bypassed stream reaches
Authors: Capra H. , Sabaton C. , Gouraud V. , Souchon Y. , Lim P.
Published: September 2003

The real impact on downstream fish populations of a change in management of a hydropower installation, in particular, the impact of an increase in instream minimum flow, can be difficult to assess. Other factors, in addition to the simple habitat limitations in low‐flow periods, can influence the evolution of a fish population over time. It has often observed in French streams that the 0+ individuals appear limited by strong discharge in the first months after their emergence (March to May). A dynamic model of a trout populations (MODYPOP) has been applied to the river Roizonne in the French Alps, upstream and downstream of a hydropower station, in order to estimate the effect of different discharge time series on trout population dynamics. Trout populations were monitored by means of annual inventories at two study sites, one with minimum flow and the other with natural flow. At each site, available habitat was described and simulated as it changed with discharge, according to the ‘microhabitat’ method (EVHA, derived from PHABSIM). Habitat time series were built on the basis of discharge time series. MODYPOP simulations, integrating habitat and discharge time series, were compared with observed fish numbers. Results indicated that fluctuations in discharge during the post‐emergence period played a major role in the dynamics of the total population. Predictions were significantly improved when the impact of strong discharge on emerging fry was integrated in the model. Copyright © 2003 John Wiley & Sons, Ltd.
Plant community responses to wetting and drying in a large arid floodplain
Authors: Capon Samantha J.
Published: September 2003

The flow regimes of large arid river catchments are amongst the most variable in the world. Plant communities which inhabit arid floodplains typically exhibit high spatial heterogeneity and are temporally dynamic in response to changing flow conditions. It has been suggested that arid floodplain ecosystems, adapted as they are to variability, will be relatively resilient to anthropogenic alterations to flow. This paper argues that floodplain plant communities in arid catchments, as in temperate and tropical regions, are primarily structured by flow regimes despite their inherent unpredictability. Consequently, changes to flood pulses through water extraction can be expected to result in changes in vegetation composition and structure which in turn may have a dramatic effect on wider ecosystem functioning. Results are presented from an ongoing study of the Cooper Creek floodplain in central Australia which illustrate the relationships between plant community dynamics and variable flood pulses. These results indicate that alterations to flow may result in a shift in community structure and an eventual loss of biodiversity. It is essential, therefore, that water resource managers in arid regions consider the requirements of floodplain plant communities when allocating environmental flows. Copyright © 2003 John Wiley & Sons, Ltd.
Effects of flow dynamics and sediment movement on microbial activity in a lowland river
Authors: Fischer Helmut , Sukhodolov Alexander , Wilczek Sabine , Engelhardt Christof
Published: September 2003

Fluvial systems transport sediments in suspension and in bed‐load together with bacteria adhering to the transported particles. Activity of these bacteria is assumed to be critical for processes of self‐purification of river waters. Here we present the results of multidisciplinary research designed to provide insight into how turbulent flow and movable sediments affect bacterial activity. Bacterial density and activity were investigated at 0–2, 9–11 and 18–20 cm sediment depth at three profiles longitudinally spaced along a sandy dune in the lowland River Spree in Germany. Dynamics of riverbed relief were examined via high‐resolution spatial and temporal echo‐sounding surveys. Three‐dimensional turbulent flow structure was measured at three vertical profiles, the locations of which coincided with the positions of bacterial samples. Bacterial activity was high in the upper 10 cm layer of sand which was moving relatively fast in the form of comparatively small sand waves, and significantly lower in the slow‐moving deeper layer associated with larger, slowly migrating dunes. The thickness of the upper layer tended to decrease towards the sand dune crests. A transition zone between high and low activity was found in the 9–11 cm sediment layer. The local depth of this transition zone also matched the local values of displacement heights computed from turbulent stresses profiles. We demonstrate that information on characteristic scales of sand wave motion may define regions of high bacterial activity for rivers with non‐cohesive, sandy sediment deposits. Copyright © 2003 John Wiley & Sons, Ltd.
Incorporating flow variability into environmental flow regimes using the flow events method
Authors: Stewardson Michael J. , Gippel Christopher J.
Published: September 2003

Increased understanding of the ecological importance of temporal environmental variation has led to a concern that many regulated rivers lack the natural variations in flow required to maintain pre‐regulation communities. Many of the existing environmental flow methods fail to adequately address this concern. This paper presents a new approach to characterizing flow variations for environmental flow studies using knowledge of the influence of flow events on biological and geomorphic processes. This approach has the advantage that ecological benefits of the environmental flow are clearly articulated, available knowledge is included in the development of flow recommendations and the method accounts for the natural dynamism in flow‐related ecosystem processes by using the natural flow regime as a template for the environmental flow regime. The Flow Events Method is demonstrated in an application to the Snowy River in southeast Australia. Copyright © 2003 John Wiley & Sons, Ltd.
The behavioural response of juvenile Atlantic salmon (Salmo salar) and brook trout (Salvelinus fontinalis) to experimental hydropeaking on a Newfoundland (Canada) river
Authors: Scruton D. A. , Ollerhead L. M. N. , Clarke K. D. , Pennell C. , Alfredsen K. , Harby A. , Kelley D.
Published: September 2003

Deregulation of the electric power market globally will lead to increased requirement for electricity on demand resulting in more emphasis on ‘hydropeaking’ generation. A research study was conducted on the regulated West Salmon River, Newfoundland, Canada, to examine habitat selection and movement of juvenile Atlantic salmon (Salmo salar) and brook trout (Salvelinus fontinalis) in response to flow changes related to ‘experimental’ peaking flow power generation. Fish were surgically implanted with microscale radio transmitters, released into an experimental study, and discharge was experimentally manipulated simulating two scenarios: (i) water storage during the day and generation at night, with a 2 hour transition; and (ii) night‐time storage with generation during the day. Experiments were repeated in the summer and fall. Fish were tracked throughout the diurnal cycle of each manipulation and precisely positioned in two‐dimensional space. Atlantic salmon exhibited two distinct patterns to movement: fish that showed high site fidelity and those that moved considerably during trials. Both salmon and trout were more active during fall hydropeaking experiments. Fish generally did not move long distances and moved more in a longitudinal fashion than laterally. Salmon moved greater distances, on average, than trout under all experimental conditions and during both seasons but these differences were not statistically significant. Brook trout moved more in relation to dynamic events (up‐ and down‐ramping) than at steady state flows. Trout also moved more at night during these dynamic changes and under low flow conditions. These results will assist producers of hydroelectricity to reduce the impacts of hydropeaking operations on fish and fish habitat. Copyright © 2003 John Wiley & Sons, Ltd.
Hydraulic constraints on habitat suitability for benthic invertebrates in gravel‐bed rivers
Authors: Jowett I. G.
Published: September 2003

The primary components of the physical habitat in a stream are water depth, velocity and substrate size, and these appear to be the best predictors of benthic invertebrate distribution within a stream. Substrate stability and fine sediment deposition also influence benthic invertebrate abundance, with reduced abundance where substrates are frequently disturbed or where fine sediment accumulates. Substrate stability and deposition of fine sediment provide hydraulic constraints on habitat suitability and their limits can be predicted by hydraulic formulae. Hydraulic conditions near or at the surface of the stream bed may have a more direct influence on benthic invertebrates than either water depth or mean velocity in the water column above them. If benthic invertebrates have ‘preferred’ near‐bed conditions, hydraulic considerations suggest that optimum mean water velocities for benthic invertebrates should increase with average stream depth and substrate size. Examination of three sets of field data from rivers of varying size showed that benthic invertebrate abundance was strongly related to mean velocity and substrate size, with large differences in habitat use between species. However, although there were large differences in preferred mean velocities between rivers of different size and depth, there was little evidence that this occurred within rivers of similar size and hence little support for the hypothesis that near‐bed hydraulics can provide a generalized method of predicting invertebrate habitat suitability between rivers of different size. Copyright © 2003 John Wiley & Sons, Ltd.
Improvement and optimization of fish guidance efficiency (FGE) at a behavioural fish protection system for downstream migrating Atlantic salmon (Salmo salar) smolts
Authors: Scruton D. A. , McKinley R. S. , Kouwen N. , Eddy W. , Booth R. K.
Published: September 2003

A behaviourally based fish protection system was installed in a power canal at a hydroelectric facility on the Exploits River, Grand Falls‐Windsor, Newfoundland, Canada. The river contains an anadromous wild Atlantic salmon (Salmo salar) population in the order of 30 000 returning adults annually. A floating louvre and bypass was installed to protect downstream migrating smolt from entering penstocks and turbines at the end of a power canal at the generating facility. The efficiency and effectiveness of this protection system has been evaluated since 1997 through a combination of conventional tagging (passive integrated transponder, Floy and streamer tags) and use of radio telemetry. Detailed velocity profiling was also conducted along the louvre array, bypass, and throughout the canal to assess the hydraulic performance of the protection system. Initial monitoring in 1997 and 1998 indicated low fish guidance efficiencies (FGEs) for smolt of 25 and 24.3%, respectively. In 1998, a digital spectrum processing (DSP) telemetry system, with multiple antennae, was installed along the louvre array to assist in identification of problem areas where fish were bypassing the louvre. Integration of DSP results with hydraulic monitoring suggested fish loss was associated with hydraulic turbulence and irregularities in the guidance velocities. In 1999, a ‘to scale’ physical model of the power canal, louvre and bypass system was constructed at a hydraulic laboratory to evaluate structural and operational improvements to the system. Field results and hydraulic scale modelling resulted in changes to the canal, louvre angle and bypass entrance, prior to operation in 1999 and 2000. Subsequent monitoring of smolt out‐migration in 1999, 2000 and 2001 indicated substantial improvement in unadjusted FGEs to 54.0, 65.3, and 73.3%, respectively. The paper demonstrates application of the results of detailed monitoring studies, including use of sophisticated telemetry and laboratory hydraulic modelling, for evaluation and optimization of effectiveness of a fish protection system. Copyright © 2003 John Wiley & Sons, Ltd.
A global perspective on environmental flow assessment: emerging trends in the development and application of environmental flow methodologies for rivers
Authors: Tharme R. E.
Published: September 2003

Recognition of the escalating hydrological alteration of rivers on a global scale and resultant environmental degradation, has led to the establishment of the science of environmental flow assessment whereby the quantity and quality of water required for ecosystem conservation and resource protection are determined.

A global review of the present status of environmental flow methodologies revealed the existence of some 207 individual methodologies, recorded for 44 countries within six world regions. These could be differentiated into hydrological, hydraulic rating, habitat simulation and holistic methodologies, with a further two categories representing combination‐type and other approaches.

Although historically, the United States has been at the forefront of the development and application of methodologies for prescribing environmental flows, using 37% of the global pool of techniques, parallel initiatives in other parts of the world have increasingly provided the impetus for significant advances in the field.

Application of methodologies is typically at two or more levels. (1) Reconnaissance‐level initiatives relying on hydrological methodologies are the largest group (30% of the global total), applied in all world regions. Commonly, a modified Tennant method or arbitrary low flow indices is adopted, but efforts to enhance the ecological relevance and transferability of techniques across different regions and river types are underway. (2) At more comprehensive scales of assessment, two avenues of application of methodologies exist. In developed countries of the northern hemisphere, particularly, the instream flow incremental methodology (IFIM) or other similarly structured approaches are used. As a group, these methodologies are the second most widely applied worldwide, with emphasis on complex, hydrodynamic habitat modelling. The establishment of holistic methodologies as 8% of the global total within a decade, marks an alternative route by which environmental flow assessment has advanced. Such methodologies, several of which are scenario‐based, address the flow requirements of the entire riverine ecosystem, based on explicit links between changes in flow regime and the consequences for the biophysical environment. Recent advancements include the consideration of ecosystem‐dependent livelihoods and a benchmarking process suitable for evaluating alternative water resource developments at basin scale, in relatively poorly known systems. Although centred in Australia and South Africa, holistic methodologies have stimulated considerable interest elsewhere. They may be especially appropriate in developing world regions, where environmental flow research is in its infancy and water allocations for ecosystems must, for the time being at least, be based on scant data, best professional judgement and risk assessment. Copyright © 2003 John Wiley & Sons, Ltd.
Identifying spatial and temporal patterns in the hydrological character of the Condamine–Balonne river, Australia, using multivariate statistics
Authors: Thoms Martin C. , Parsons Melissa
Published: September 2003

Many environmental flow approaches calculate hydrological indicators on an annual or daily basis and do not consider the multiple scales of a rivers' hydrological character. However, hydrologic processes operate within a temporal and spatial dimension, in accordance with multidimensional and hierarchical views of river systems. This study investigates spatial and temporal patterns of the hydrological character of a large river system, and examines the impact of water‐resource development on these patterns. Over 300 regime, history and pulse‐scale flow variables have been calculated from simulated discharge data representing ‘reference’ and ‘current’ water‐resource development scenarios. Multivariate statistical analyses are used to identify measurement nodes with similar hydrological character and to determine the association between different temporal scale flow variables and groups of nodes. Six spatial hydrological zones are identified in the Condamine–Balonne River, Australia. These hydrological zones are found to have become homogenized with water‐resource development. Different temporal scales of flow variables are related to the different hydrological zones, and to water‐resource development scenarios. Thus, the temporal dimension of hydrological character is embedded within a spatial dimension of river zonation. Both dimensions should be considered in a hierarchical context, and environmental flow restoration targets may need to be set for each dimension of a river system. Copyright © 2003 John Wiley & Sons, Ltd.
Classifying the hydraulic performance of riffle–pool bedforms for habitat assessment and river rehabilitation design
Authors: Emery Joanne C. , Gurnell Angela M. , Clifford Nicholas J. , Petts Geoffrey E. , Morrissey Ian P. , Soar Philip J.
Published: September 2003

Riffle–pool sequences are the dominant bedforms in gravel and mixed bedded channels of intermediate slope. Their fundamental importance in determining the mesoscale habitat environment is demonstrated in their widespread recreation in channel restoration and rehabilitation schemes. This paper explores the hydraulic functioning of riffle–pool bedforms, particularly the variations in the hydraulic performance of different bed oscillation morphologies. It addresses the need for a quantitative means of classifying flow behaviour that can be applied in functional ecohydraulic river rehabilitation designs.

Information from reaches on two physically contrasting UK rivers with well marked riffle–pool topography are used to illustrate the approach. The reaches are mapped to obtain a detailed channel morphology. Surveys describing the streamwise depth‐averaged velocities at three flow stages are interpolated to a common regular grid, grouped using cluster analysis, and then the validity of each cluster as a distinct hydraulic patch class is assessed statistically using analysis of variance. The spatial pattern of the hydraulic patch classes is then overlain on the bed topography to link the patches to the bed morphology. The procedure groups locations along the channel which display similar suites of velocity values at different flow stages and thus differentiates between areas in the channel within which the hydraulic habitat is spatially relatively invariant from those where abrupt changes occur. It also allows the quantitative description of different hydraulic patch classes. Overlay of the hydraulic patch class boundaries on channel reach topography provides a simple but innovative method of exploring and defining the spatial hydraulic habitat implications of riffle–pools of different topographic forms. Copyright © 2003 John Wiley & Sons, Ltd.
Flow restoration and protection in Australian rivers
Authors: Arthington Angela H. , Pusey Bradley J.
Published: September 2003

Since 1857 new Australians have constructed many thousands of weirs (3600 in the Murray–Darling Basin alone) and floodplain levee banks, 446 large dams (>10 m crest height) and over 50 intra‐ and inter‐basin water transfer schemes to secure water supplies for human use. Flow regulation has changed the hydrology of major rivers on three temporal sales–the flood pulse (days to weeks), flow history (weeks to years) and the long‐term statistical pattern of flows, or flow regime (decades or longer). The regulation of river flows is widely acknowledged as a major cause of deteriorating conditions in many Australian river and floodplain ecosystems. In response to mounting environmental concerns, all states, territories and the Commonwealth Government have committed the nation to the principles of ecologically sustainable development and a process of national water reform. Rivers and wetlands are now recognized as legitimate ‘users’ of water, and jurisdictions must provide water allocations to sustain and where necessary restore ecological processes and the biodiversity of water‐dependent ecosystems. Progress in the protection and restoration of river and wetland water regimes has been significant, with over half of mainland aquatic systems designated to receive water allocations of some sort. However, exactly how much water they will receive or retain is unclear from the data available. Moreover, the ecological outcomes and benefits of water allocations are not yet apparent in most aquatic ecosystems, with the exception of certain waterbird breeding events, the disruption of algal blooms in weirs and improved fish passage. After reviewing these issues, this paper addresses two vital questions: How much water does a river need? and How can this water be clawed back from other users? Studies conducted to date in Queensland rivers suggest that around 80–92% of natural mean annual flow (and other ecologically relevant hydrological indicators) may be needed to maintain a low risk of environmental degradation. In the Top End of the Northern Territory, some rivers are maintained at 80% of their natural flow, whereas two‐thirds of various flow indicators has been proposed as the restoration target for the River Murray, and 28% of natural mean annual flow has been negotiated for the Snowy River in Victoria. To validate these estimates, ecologists are seeking opportunities to turn river restoration projects into long‐term hypothesis‐driven experiments in ecological restoration, and the funding, time and institutional support to do so. The paper ends with some suggestions to advance the water reforms and achieve higher levels of water allocation for the environment. Copyright © 2003 John Wiley & Sons, Ltd.
Links between ecotoxicology, biomonitoring and water chemistry in the integration of water quality into environmental flow assessments
Authors: Scherman P.‐A. , Muller W. J. , Palmer C. G.
Published: September 2003

Aquatic organisms have physico‐chemical as well as flow habitat requirements. There are three main kinds of data which are useful in quantifying these requirements: chemical data which describe in‐stream chemical conditions; ecotoxicity data which describe the tolerances of organisms and their in‐stream responses to changing chemical concentrations; and biomonitoring data which describe the distribution and composition of communities. However, it is only by linking these data that organism requirements can be adequately elucidated and translated into resource quality objectives. This paper describes the methods for linking these data and their application in the integration of water quality into environmental flow assessments and the assessment of the water quality Reserve. A case study is presented to demonstrate the methodology. Copyright © 2003 John Wiley & Sons, Ltd.
Factors influencing stranding of wild juvenile brown trout (Salmo trutta) during rapid and frequent flow decreases in an artificial stream
Authors: Halleraker J. H. , Saltveit S. J. , Harby A. , Arnekleiv J. V. , Fjeldstad H.‐P. , Kohler B.
Published: September 2003

To provide environmental guidelines for operation of peaking hydropower plants, stranding experiments with juvenile brown trout (Salmo trutta) were conducted in a 3.8 m wide and 19.2 m long artificial stream. We found a significant decrease in stranding of trout fry by reducing the dewatering speed from >60 cm h−1 to <10 cm h−1. At water temperatures around 11°C we found that less than 8% of the trout stranded during night experiments (on average for all subsets at dewatering rate >60 cm h−1). However, the highest stranding rate occurred at water temperatures around 7°C during rapid dewatering at night (mean=22% stranding). Significantly more fry were stranded in the first versus the second to fifth dewatering episode (mean=22% versus 10% stranding) at rapid daytime dewatering in 11°C water. Stranding of larger fry (>0+) was negligible at water temperatures around 11°C, except at rapid dewatering during daylight. Further, twice as many 0+trout as larger fry (>70 mm in June, >60 mm in late summer) stranded during rapid dewatering during daytime, and almost three times as many 0+stranded during rapid dewatering when they were mixed with trout parr compared to homogeneous 0+experiments. Our study showed a tendency towards an increased stranding of fry with long habituation time (<30 hours versus >30 hours with stable flow). We recommend dewatering in darkness at all times of year to reduce stranding of salmonids, and to use slow ramping rates <10 cm h−1. After longer periods with stable flows, a gentle drop in discharge is recommended, which might also reduce stress and possible sub‐lethal effects. Copyright © 2003 John Wiley & Sons, Ltd.
Evolving policy reforms and experiences for addressing downstream impacts in World Bank water resources projects
Authors: Hirji Rafik , Panella Thomas
Published: September 2003

The systematic integration of environmental flow requirements (EFR) in water resources management decision‐making and policy reforms is a complex task and still a developing field, on which agreement does not yet exist, even in industrialized countries. The complexity is compounded by lack of data and weak institutional capacity. In addition, environmental flow assessments, i.e. the process of determining EFR, can be costly and may yield uncertain results with limited utility to decision‐makers.

This paper focuses on the evolving policy reforms and operational experiences within the World Bank to mainstream EFR into water resources management. It includes a brief discussion of the context of environmental flows in the World Bank's work, and looks at the evolution of the World Bank's policies related to the integration of environmental flow considerations in its activities. Five case studies illustrate the World Bank's varied involvement in environmental flow issues. The paper concludes with recommendations for improving the integration of environmental flow considerations into water resource development and management. Copyright © 2003 John Wiley & Sons, Ltd.
A score test for binary data with patient non‐compliance
Authors: Branson Michael , Whitehead John
Published: September 2003

A score test is developed for binary clinical trial data, which incorporates patient non‐compliance while respecting randomization. It is assumed in this paper that compliance is ‘all‐or‐nothing’, in the sense that a patient either accepts all of the treatment assigned as specified in the protocol, or none of it. Direct analytic comparisons of the adjusted test statistic for both the score test and the likelihood ratio test are made with the corresponding test statistics that adhere to the intention‐to‐treat principle. It is shown that no gain in power is possible over the intention‐to‐treat analysis, by adjusting for patient non‐compliance. Sample size formulae are derived and simulation studies are used to demonstrate that the sample size approximation holds. Copyright © 2003 John Wiley & Sons, Ltd.
Full‐likelihood approaches to misclassification of a binary exposure in matched case‐control studies
Authors: Rice Kenneth
Published: September 2003

We consider analysis of matched case‐control studies where a binary exposure is potentially misclassified, and there may be a variety of matching ratios. The parameter of interest is the ratio of odds of case exposure to control exposure. By extending the conditional model for perfectly classified data via a random effects or Bayesian formulation, we obtain estimates and confidence intervals for the misclassified case which reduce back to standard analytic forms as the error probabilities reduce to zero. Several examples are given, highlighting different analytic phenomena. In a simulation study, using mixed matching ratios, the coverage of the intervals are found to be good, although point estimates are slightly biased on the log scale. Extensions of the basic model are given allowing for uncertainty in the knowledge of misclassification rates, and the inclusion of prior information about the parameter of interest. Copyright © 2003 John Wiley & Sons, Ltd.
A comparison of two methods for the estimation of precision with incomplete longitudinal data, jointly modelled with a time‐to‐event outcome
Authors: Touloumi G. , Babiker A. G. , Kenward M. G. , Pocock S. J. , Darbyshire J. H.
Published: September 2003

Several methods for the estimation and comparison of rates of change in longitudinal studies with staggered entry and informative drop‐outs have been recently proposed. For multivariate normal linear models, REML estimation is used. There are various approaches to maximizing the corresponding log‐likelihood; in this paper we use a restricted iterative generalized least squares method (RIGLS) combined with a nested EM algorithm. An important statistical problem in such approaches is the estimation of the standard errors adjusted for the missing data (observed data information matrix). Louis has provided a general technique for computing the observed data information in terms of completed data quantities within the EM framework. The multiple imputation (MI) method for obtaining variances can be regarded as an alternative to this. The aim of this paper is to develop, apply and compare the Louis and a modified MI method in the setting of longitudinal studies where the source of missing data is either death or disease progression (informative) or end of the study (assumed non‐informative). Longitudinal data are simultaneously modelled with the missingness process. The methods are illustrated by modelling CD4 count data from an HIV‐1 clinical trial and evaluated through simulation studies. Both methods, Louis and MI, are used with Monte Carlo simulations of the missing data using the appropriate conditional distributions, the former with 100 simulations, the latter with 5 and 10. It is seen that naive SEs based on the completed data likelihood can be seriously biased. This bias was largely corrected by Louis and modified MI methods, which gave broadly similar estimates. Given the relative simplicity of the modified MI method, it may be preferable. Copyright © 2003 John Wiley & Sons, Ltd.
Efficacy endpoint selection and multiplicity adjustment methods in clinical trials with inherent multiple endpoint issues
Authors: Sankoh Abdul J. , D'Agostino Ralph B. , Huque Mohammad F.
Published: September 2003

The ideal approach for the design and analysis of clinical trials is to select a single primary endpoint that provides a complete characterization of the disease under study and permits an efficient evaluation of the effect of a test drug. However, this is often not possible for a number of diseases or clinical trials. This paper examines some practical clinical decision‐making scenarios for the selection and analysis of efficacy outcome measures in clinical trials with inherent multiplicity components. Copyright © 2003 John Wiley & Sons, Ltd.
Robust asymptotic sampling theory for correlations in pedigrees
Authors: Keen K. J. , Elston Robert C.
Published: September 2003

Methods to unravel the genetic determinants of non‐Mendelian diseases lie at the next frontier of statistical approaches for human genetics. It is generally agreed that, before proceeding with segregation or linkage analysis, the trait under study ought to be shown to exhibit familial correlation. By coding dichotomous traits as binary variables, a single robust approach in the estimation of pedigree correlations, rather than two distinct approaches, can be used to assess the potential heritability of a trait, and, latterly, to examine the mode of inheritance. The asymptotic theory to conduct hypothesis tests and confidence intervals for correlations among different members of nuclear families is well established but is applicable only if the nuclear families are independent. As a further contribution to the literature, we derive the asymptotic sampling distribution of correlations between random variables among arbitrary pairs of members in extended families for the Pearson product‐moment estimator with generalized weights. This derivation is done without assuming normality of the traits. The sampling distribution is shown to be asymptotically normal to first order, and hence large‐sample hypothesis tests and confidence intervals with estimates of the variances and correlation coefficients are proposed. Discussion concludes with an example and a suggestion for future research. Copyright © 2003 John Wiley & Sons, Ltd.
Comparing linear and nonlinear mixed model approaches to cosinor analysis
Authors: Mikulich Susan K. , Zerbe Gary O. , Jones Richard H. , Crowley Thomas J.
Published: September 2003

The cosinor model, used for variables governed by circadian and other biological rhythms, is a nonlinear model in the amplitude and acrophase parameters that has a linear representation upon transformation. With linear cosinor analysis, amplitude and acrophase for each harmonic can be computed as nonlinear functions of the estimated linear regression coefficients. Here a flexible mixed model approach to cosinor analysis is considered, where the fixed effect parameters may enter nonlinearly as acrophase and amplitude for each harmonic or linearly after transformation to regression coefficients. In addition, the random effects may enter nonlinearly as subject‐specific deviations from the acrophases and amplitudes or linearly as subject‐specific deviations from the regression coefficients. It is also possible for the fixed effects to enter nonlinearly while the random effects enter linearly. Additionally, we evaluate whether including higher order linear harmonic terms as random effects, that is, Rao–Khatri ‘covariance adjustment’, improves precision. Applying the delta method to nonlinear functions of the parameters from linear mixed cosinor models to obtain approximate variances produces results that are often identical to results from nonlinear mixed models. Consequently, traditional linear cosinor analysis can often be used to estimate and compare the nonlinear parameters of interest, that is, amplitudes and acrophases, via the delta method. This is advantageous since the nonlinear mixed model may have convergence difficulties for more complex models. However, for some multiple‐group analyses, the linear cosinor transformation should not be used and we clarify when the two methods are equivalent and when they differ. Copyright © 2003 John Wiley & Sons, Ltd.
Modelling the relationship between continuous covariates and clinical events using isotonic regression
Authors: Ancukiewicz Marek , Finkelstein Dianne M. , Schoenfeld David A.
Published: September 2003

In a medical study we are often interested in graphically displaying the relationship between continuous variables and clinical events indicating disease progression. Often, it is reasonable to make the minimal assumption that the risk of progression is an arbitrary monotone function of the continuous variable. Sometimes the continuous variable is a disease marker which is recorded longitudinally, and so the goal is to provide a graphical display of the relationship between the hazard for progression and the most recent measurement of the longitudinal marker. For example, we know that for a patient with HIV infection, declining CD4 count is associated with an increased risk of opportunistic infection. The goal of this paper is to extend isotonic regression techniques to failure time data with a continuous covariate, to obtain a non‐parametric estimate for the hazard of disease progression as a monotonic function of the continuous variable. We propose two methods for modelling the relationship of the hazard and covariate: the first assumes that the hazard is constant over time, and the second allows the hazard to be an arbitrary function of time. These methods will be applied to graphically display the risk for an AIDS patient of an opportunistic infection as a function of CD4 count. Copyright © 2003 John Wiley & Sons, Ltd.
The analysis of survival data with a non‐susceptible fraction and dual censoring mechanisms
Authors: Gagnon David R. , Glickman Mark E. , Myers Richard H. , Cupples L. Adrienne
Published: September 2003

It is known that the ages of onset of many diseases are determined by both a genetic predisposition to disease as well as environmental risk factors that are capable of either triggering or hastening the onset of disease. Difficulties in modelling onset ages arise when a large fraction fail to inherit the disease‐causing gene, and multiple reasons for censoring result in unobserved onset ages. We present a parametric Bayesian model that includes subjects with missing age information, non‐susceptible subjects and allows for regression on risk factor information. The model is fit using Markov chain Monte Carlo simulation from the posterior distribution, and allows the simultaneous estimation of the proportion of the population at risk of disease, the mean onset age of disease, survival after disease onset, and the association of risk factors with susceptibility, onset age and survival after onset. An example employing Huntington's disease data is presented. Copyright © 2003 John Wiley & Sons, Ltd.
A hierarchical model for spatially clustered disease rates
Authors: Gangnon Ronald E. , Clayton Murray K.
Published: September 2003

Maps of regional disease rates are potentially useful tools in examining spatial patterns of disease and for identifying clusters. Bayes and empirical Bayes approaches to this problem have proven useful in smoothing crude maps of disease rates. In recent years, models including both spatially correlated random effects and spatially unstructured random effects have been very popular. The spatially correlated random effects have been proposed in an attempt to capture a general clustering in the data. As an alternative, we propose replacing the spatially structured random effect with fixed clustering effects associated with particular areas. A reversible jump Markov chain Monte Carlo (RJMCMC) algorithm for posterior inference is described. We illustrate the model using the well‐known New York leukaemia data. Copyright © 2003 John Wiley & Sons, Ltd.