It is important to understand the influence of samples on the calculation and reporting of the echo integral (NASC) and the subsequent estimation of biomass. This page discusses what is needed in order to estimate:
Currently, Echoview is designed to calculate NASC and all export variables for the area of the available samples and it does not extrapolate to the entire domain in the case that there are unknown and excluded samples within the domain.
Sv variables (visualized as echograms) contain a set of sample measurements from the pings of an echosounder. Inherent to the process of hydroacoustic sampling is that parts of water column remain unsampled or are sampled but the samples are known to be invalid. We can refer to these unsampled or unknown parts of the water column with the phrase "unknown samples".
Consider a typical hydroacoustic survey – for example, a study to estimate fish density in which ping-based sample measurements of volume backscatter from the water column are made at time intervals while moving along a transect line.
In this discussion we define unknown samples to implicitly exist:
Unknown samples will also explicitly exist:
Common causes of explicit unknown (or corrupt) samples include:
Notes:
Out-of-bounds refers to any location outside the range or depth bounds that the phenomenon of interest can be located. In a study of fish biomass the phenomenon under study is the density of a species of fish in the water column. It follows that locations outside of the water column (above the surface and below the bottom) are out of bounds. It may also be that the species is limited to (for example) a certain depth or geographic range in which case samples outside of the depth or geographic range would be out of bounds.
Currently in Echoview there is no simple way to differentiate between unknown and out-of-bounds samples. Theoretically, out of bounds samples should be treated differently when calculating and reporting NASC. There are strategies (below) that can manage data sets that contain both unknown and out-of-bounds samples and allow the user to calculate NASC (and other area density variables) based on the assumption of their choice.
Echoview NASC and other export variables are calculated over the known and within-bounds samples in a domain, rather than for the entire within-bounds area of the domain. Outside of Echoview the user then must make explicit the assumptions they wish to use when determining the NASC for the entire within-bounds area of a domain from the NASC of the known samples. It is common practice to use the known samples in the domain to estimate the NASC for the domain (equivalent to assuming that the unknown samples are equal to the mean of the known samples).
It is important to know that Echoview does not make this assumption, but reports NASC only for the known samples. It is also important to note that the validity of any assumption about unknown samples depends on a number of factors including the size of integration cells and the patchiness of the distribution of the target species. In quiet conditions where few samples are rejected as corrupt, survey results will not be strongly dependent on the assumptions made. In poor conditions with a significant percentage of corrupt or unknown samples the survey results may be highly dependent on the assumptions made about unsampled areas. The user is advised to understand this source of error and its impact on the error budget for their survey.
If Echoview NASC is used as the best estimate of the NASC for the entire in-bounds area of the domain or integration cell, then this will be equivalent to assuming unknown samples are zeros (in linear terms).
Echoview’s integration analysis estimates include:
Such estimates are calculated for an Echoview analysis domain.
As an areal density measurement, NASC (sA) is calculated in reference to an integration interval z1 to z2 (see Simmonds and MacLennan 2005), where:
and
The integration interval in effect defines the volume over which the areal density applies.
In Echoview the Thickness_mean1 is the mean thickness (height in vertical surveys) of the known samples in an analysis domain. Where an analysis is performed by cells then it is the mean thickness of the known samples in a cell or integration interval. An Echoview analysis domain is a time-depth polygon that contains the initial set of samples to be considered for analysis.
The settings on the Analysis page of the Variable Properties dialog box are used to specify samples to exclude from integration analysis calculations. When samples are excluded from integration analysis, the Thickness_mean is reduced, except in the case where Whole excluded or no-data pings do not reduce the Thickness mean is selected on the Analysis page of the Variable Properties dialog box and the conditions of the setting are met. When Thickness_mean is reduced, the original volume described by the analysis domain will not be the same as the volume the areal density is calculated for. This has important implications for subsequent biomass calculations.
In general for biomass estimation the user will require an estimate of areal density for the entire domain, not just the part with known samples. This requires assumptions to be made about the Sv of the unknown samples. If the Echoview NASC is used without modification for domains that have a reduced Thickness_mean then this is the same as assuming a zero contribution to the areal density from the unknown samples. If another assumption is preferred then the user could for example:
Notes:
Conceptually, one would expect the following when a data set contains unknown and out-of-bounds samples:
Unknown samples whether implicit or explicit:
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When performing an integration analysis (onscreen or for export), excluded samples:
In Echoview version 4.90 and earlier, this outcome was standard for integration calculations. The reduction of the Thickness mean needs to be fully understood when calculating and reporting NASC and when subsequently estimating biomass, so that an explicit assumption can be made about how to estimate the domain average from the known samples. The reduction always means that the reported NASC (onscreen or in export data) is reported for the reduced volume. The user must decide if the NASC reported is representative of the domain or whether another assumption needs to be made.
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Analysis page settings to exclude samples and reduce the Thickness mean. One or a combination of settings can be used.
Note: When these settings are not selected, no samples are excluded. This means that the Sv mean and Thickness mean and NASC are calculated using all the samples in the analysis domain. |
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Echoview 4.90 introduced a setting to deal with the special case where an entire ping is excluded from analysis. This setting is Whole excluded or no-data pings do not reduce the Thickness mean. This setting helps you to set up the conditions where NASC can represent the water volume you intended. When performing an integration analysis using this setting, excluded samples:
The setting Whole excluded or no-data pings do not reduce the Thickness mean on the Analysis page can therefore help you to represent the water volume as intended in many cases (but refer to the Note below). It is recommended that you use this and other Exclusion settings on the Analysis page with care and ensure that you are aware of the effect a setting has on Thickness_mean. Using the Whole excluded or no-data pings do not reduce the Thickness mean setting is equivalent to removing the pings from the data set – it is as if the echosounder had not pinged at that location. The virtual variable “Reduce pings” does exactly this – it removes empty pings from the data set and can be used to visualize the effect of this Analysis setting (even if you do not own a Virtual echogram module). Be aware of the case where a whole excluded or no-data ping includes samples that are known to be out-of-bounds (e.g. samples below an exclude-below line). In this case the Thickness mean for the domain may be over or under estimated depending on whether the exclude-below-line depth in the removed pings is greater than or less than the mean exclude-below-line-depth of the domain. If it can be assumed that whole excluded pings are randomly placed with respect to the depth of exclude-lines in domains (probably a reasonable assumption in most surveys) then the error from this source will average to zero over a multiple domains. For more information contact support@echoview.com |
Analysis page settings to exclude samples and not reduce the Thickness mean.
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In Standard operating procedures for fisheries acoustic surveys in the Great Lakes: 9.1.5 Noise Removal, Parker-Setter et al (2009) discuss the assumptions about fish density in bad-data regions, impacts on Sv and sa (areal density - in Echoview this is ABC) and suggest how Echoview users may handle this with Echoview analysis export data.
The new Analysis setting in Echoview 4.90 allows you to easily achieve the desired outcome when excluded samples occupy whole pings. In addition, in many cases it is possible to apply tailored integration settings for problematic parts of an echogram using virtual variables together with the settings on the Analysis page. Operators that help you partition data and replace sample values with an estimate include:
| Operator | Action | ||||||||||
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Bitmap operators include:
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Creates data pings. It can create pings with constant SV, TS, unspecified-dB and linear values. It can also create SV and TS pings with time-varied gain (TVG), based on the SV or TS value at 1 meter and a specified absorption coefficient. |
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Provides tools to create and evaluate an arbitrary mathematical equation on a per-sample basis on the echogram data. |
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Merges the pings in two variables to create a single variable containing the pings from both the input variables. |
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Divides up echogram data according to subsets of pings. |
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Applies the line and bad data exclusion settings specified on the Analysis page of the Variable Properties dialog box for its input variable, and changes excluded sample values to 'no data' values. |
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Remove pings which meet certain criteria. |
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Fills regions with a statistical value from another echogram. |
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Resamples echogram data by ping, distance or time interval. |
For assistance with setting this up for your data, please contact the Echoview support team. Details about how to request support can be found at the Echoview website: Request software support.
The Echoview team is considering integration analysis enhancements that give you greater integration flexibility. These include (but are not limited to) the following ideas:
About analysis
About analysis variables
Samples
About integration
About no data
Thickness mean and Height mean
ABC and NASC
Sv mean
Footnotes:
1Thickness_mean or Height_mean. Where Height_mean is the projection of Thickness_mean onto the vertical axis, taking transducer geometry into account.
