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WISER Deliverable D6.1-3: WISERBUGS (WISER Bioassessment Uncertainty Guidance Software) tool for assessing confidence of WFD ecological status class User Manual and software: Release 1.1 (Sept 2010).

Clarke, R. T., 2010. WISER Deliverable D6.1-3: WISERBUGS (WISER Bioassessment Uncertainty Guidance Software) tool for assessing confidence of WFD ecological status class User Manual and software: Release 1.1 (Sept 2010). Technical Report. European Union FP7 Project WISER on-line .

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WISERBUGS_(Release_1_1)_User_Manual_(WISER_Deliverable_D6_1_3)_v3.pdf - Published Version


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The aim of the software program WISERBUGS is to assist in quantifying uncertainty in the assessment of the ecological status of lakes, rivers, transitional (estuarine) and coastal waters. WISERBUGS (WISER Bioassessment Uncertainty Guidance Software) is a product of the WISER (Water bodies in Europe: Integrative Systems to assess Ecological status and Recovery) research project (Grant 226273 - WISER) supported by the European Commission under the Seventh Framework Programme ( The WISER project aim was to assist in developing methods for calibrating different biological survey results for lakes, transitional and coastal waters against ecological quality classifications to be developed for the Water Framework Directive (WFD). The WFD requires Member States to assess, monitor, and where inadequate, improve the ecological status of water bodies (rivers, lakes, transitional and coastal waters). All such water bodies are to be classified to one of five ecological status classes (high, good, moderate, poor and bad) with the aim of eventually achieving or maintaining good or better status for all water bodies. The ecological status (i.e. condition) of a water body is often measured using one or more metrics derived from the taxonomic composition and/or abundance obtained from field samples/surveys and/or habitat surveys. The term metric here usually refers to any biological index or other single-valued measure which is designed to measure some aspect of the biological community and its taxonomic composition at a site or water body. The Articles of the Water Framework Directive (Annex V, section 1.3) require that “Estimates of the level of confidence and precision of the results provided by the monitoring programmes shall be given in the (monitoring) Plan”. Thus, water body monitoring and management organisations need to have some understanding and estimates of the confidence to which an individual water body can be assigned to an ecological status class. In addition the WFD requires that the Ecological Status of surface waters of Member States are maintained or improved. However, because of the uncertainties associated with biological monitoring, waterbodies may appear to change Ecological Status over time when, in reality, this is only an artefact due to the uncertainty resulting from the whole bioassessment process and sampling procedures. A core part of the WISER project was to collect standardised field sample and survey information on phytoplankton, aquatic macrophytes, macroinvertebrates, fish and aquatic habitats at each of a wide range of lake, transitional and coastal water body sites across Europe. One important reason for this was to improve understanding and provide estimates of the sampling uncertainty (replicate, sub-sample, spatial and temporal) associated with specific sampling/surveying methods, individual metrics and multi-metric classification rules. The WISERBUGS software program has been written to provide a general means of using simulations to assess uncertainty in estimates of ecological status class for water bodies based on either single metrics or a combination of metrics, multi-metric indices (MMIs) and multi-metric rules. The User provides prior estimates of the relevant sampling uncertainty for each metric and metric value to be involved in the water body assessments, together with metric status class limits and the rules for combining metrics into an overall water body assessment. WISERBUGS can also be used just to test the effect of new status class limits and multi-metric rules on site/waterbody status assessments, without any uncertainty assessment (by setting all uncertainty components to zero). Although initially designed for use with river macroinvertebrate data and metrics, program WISERBUGS is designed to be as generic as possible, so that it can be used with a wide range of metrics derived from field site sampling and survey data for any single or combination of biological quality elements (BQEs, namely phytoplankton, aquatic flora, macroinvertebrates and/or fish) and any type of water body (rivers, lakes, transitional or coastal waters). The program requires the User to provide a ‘Metric Specification File’ in EXCEL format, in which they specify which metrics are to be used to determine the site or waterbody bioassessments, the individual metric uncertainty estimates and the multi-metric rules for combining information from individual metrics. The uncertainty in the estimate of the (usually) mean value of a metric for a water body depends on the level of sampling replication on which it was based in terms of replicate sampling, spatial and temporal sampling coverage over the area of the water body to be assessed and the period of time for which the water body assessment is to apply. The estimates of uncertainty in individual metric values can include the sampling standard deviation (SD) due to sampling/sub-sampling variation and (optionally) the SD and bias due to sample sorting and identification. In practice the uncertainty SD estimates for each metric for each water body or site to be assessed within WISERBUGS must be based on best-available information from replicated sampling studies on this or environmentally-similar water bodies. The ecological status class assessment for individual metrics can be based on just the observed (O) values of metrics or on normalised Ecological Quality Ratios (EQRs) involving the ratio of the observed metric values to the Reference Condition values (E1) of the metric.The EQR could be a RIVPACS-type O/E ratio where E1 is set a RIVPACS model-based site-specific expected value and E0 is set to zero When several EQRs are used to create a Multi-Metric Index (MMI) by averaging their values, each EQR is forced into the range 0-1 by setting any EQR values greater than 1 to 1. If EQRs are used, then the User can provide an estimate of the error SD for the Reference Condition values (E1) of each metric for the group of sites or water bodies to be assessed. The same User-specified ‘Metric Specification File’ must also give the ecological status class (‘High’ to ‘Poor’) limits for each metric or EQR. Program WISERBUGS allows the User to specify a wide range of rules for combining individual metrics into multi-metric indices (MMI) or for combining individual metric classes into a metric group class and thus in deriving an overall site/waterbody assessment. For example, it can cope with combining status classes for macro-invertebrate metrics designed to measure one type of stress (e.g. eutrophication, diversity or acidification) and then combine (using the same or a different rule) the classes from these individual stress types into an overall class for macro-invertebrates, and then combine (using the same or a different rule) the overall class for macroinvertebrates with that for one or more other biological quality elements (macrophytes, diatoms or fish). For each set of sites/waterbodies to be assessed, the program reads the observed values of each metric to be used from a User-specified ‘Observed metric values’ EXCEL file. The observed values of the metrics must have been calculated previously, outside of program WISERBUGS. The layout of this input file was designed to provide immediate compatibility with the metric values EXCEL files derived and output from the freshwater macroinvertebrate sample software known as ‘AQEMrap’ or ‘ASTERICS’ (obtainable from the EU Fifth Framework Programme river classification project STAR Web site at The AQEMrap software could be used to calculate and export observed metric values for freshwater macroinvertebrate samples for input to the WISERBUGS program. The content and format of the User-specified EXCEL input files are explained in detail in Section 4. WISERBUGS uses the uncertainty estimates for each metric to simulate a large number of other possible observed metric or EQR values which could have been obtained for the site/waterbody. If the sampling SD is considered to be constant on a specified transformed scale, then, in each simulation the observed value (x) is first transformed, then a random sampling error (z) added and the result back-transformed to obtain a simulated observed value. Each simulation leads to a status class based on each individual metric and then groups of metrics in the specified multi-metric rules for site/waterbody bioassessment. From the statistical distribution of simulated values and classes, estimates of the probability of belonging to each status class are obtained. The content and format of the EXCEL output file give the ecological status assessment and the associated uncertainty for each site/waterbody is explained in Section 5 WISERBUGS software and User Manaual was written and produced by Ralph Clarke of Bournemouth University (BourneU) in the UK.

Item Type:Monograph (Technical Report)
Group:Faculty of Science & Technology
ID Code:18232
Deposited By: Professor Ralph Clarke
Deposited On:28 Jun 2011 15:48
Last Modified:14 Mar 2022 13:39


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