DOI: 10.5061/dryad.1rn8pk167
title: Echosounder derived metrics from small-scale coastal surveys

description: Echosounder surveys are appealing for monitoring benthic rocky reef fishes
 like rockfish (Sebastes spp.) as they cover large areas quickly and are
 non-destructive, but they are rarely used due to difficulties ensonifying
 benthic fish in rocky habitats.  We conducted echosounder and
 remote operated vehicle (ROV) surveys at 39 sites in Mowachaht/Muchalaht
 territory (Nootka Sound, BC, Canada) in August 2023.  We examined
 correlations between an echosounder biomass proxy (nautical area
 scattering coefficient (NASC)) and ROV benthic fish density using
 generalized linear models. Increases in the fish biomass proxy (NASC)
 within 10m of the bottom was correlated with increasing benthic fish
 density (deviance explained 52%), suggesting NASC helps predict benthic
 fish hotspot locations.  We compared echosounder and ROV habitat
 metrics using Spearman’s rank correlation tests and found rugosity and
 slope were comparable across methods with reduced analyst variability in
 echosounder metrics. This study provides a new and efficient method for
 identifying rocky reef fish hotspots in near-shore areas that can help
 fishers avoid non-target species and act as a guide for marine protected
 area (MPA) site selection.
description: # Echosounder derived metrics from small-scale coastal surveys Dataset
 DOI: [10.5061/dryad.1rn8pk167](10.5061/dryad.1rn8pk167) ## Description of
 the data and file structure The purpose of this research project was to
 develop an efficient method of identifying rocky reef fish hotspots in
 coastal regions using echosounder surveys. We focused on developing simple
 echosounder techniques that would be accessible to active acoustic novices
 to make echosounder surveys more feasible and understandable to a wider
 audience. A general understanding of active acoustic theory is still
 recommended before undertaking any echosounder surveys. We recommend the
 comprehensive active acoustic text by Simmonds et al. (2007) as a go to
 resource for gaining a basic understanding of active acoustic principles:
 Simmonds, E. John, and David N. MacLennan. *Fisheries Acoustics: Theory
 and Practice*. 2. ed., Fish and Aquatic Resources Series 10. Oxford:
 Blackwell, 2007. In this study we utilized nautical area scattering
 coefficient (NASC) as a proxy for fish biomass and investigated
 correlations between NASC and ROV detected benthic rocky reef fish
 density. We found a strong positive correlation between NASC values within
 10m of the bottom and benthic fish density in the acoustic deadzone region
 in rocky, sloping habitats preferred by rocky reef fish species.  Our
 best-fit rocky reef fish density model included NASC as a predictor and
 dramatically outperformed our other habitat-based models. This suggests
 that including NASC as a predictor of benthic rocky reef fish density can
 add substantially to regional distribution modelling. Echosounder surveys
 can quickly identify areas with high near-bottom NASC values and this
 information can be used to develop regional maps of suspected high benthic
 rocky reef fish density for use by fishers (e.g. help avoid non-target
 rockfish species) or for selecting high fish density MPA locations. 
 However, these echosounder surveys cannot identify fish species,
 diversity, abundance, or biomass and should only be used as a general
 guide for locating likely high benthic fish density areas.  Additional
 groundtruthing is required using visual methods (e.g. ROV, drop camera,
 divers, hook-and-line) to determine species composition if this data is to
 be used for more quantitative assessments of rocky reef fish abundance or
 biomass. It is our hope that the ease and efficiency of these echosounder
 surveys will allow smaller organizations to collect detailed regional data
 that is often missing from coastwide surveys and use it to inform future
 rocky reef fish survey work or local fisheries management. ### Files and
 variables #### File: Lancaster_et_al._Echoview_Templates_and_Scripts.zip
 Original data has not been provided due to the sensitive rocky reef fish
 location information it contains, however sample data files, R scripts,
 and Echoview calibration and multifrequency analysis templates are
 provided to help researchers recreate the methods we used.  Echoview or
 Visual Acquisition software is required for viewing all sample data files
 and templates.  A demonstration versions of Echoview is available at
 [https://echoview.com/support/echoview-downloads/](https://echoview.com/support/echoview-downloads/).  Original data is available upon request from Ha’oom Fisheries Society at [info@haoom.ca](mailto:info@haoom.ca) and consent of the Mowachaht/Muchalaht First Nation will be obtained before data is provided to interested parties. Step by step information on the sample files, scripts and templates and where they are located within the file Lancaster_et_al._Echoview_Templates_and_Scripts.zip are provided in the document `Lancaster_etal_Guide_for_Echosounder_and_ROV_rocky_reef_fish_surveys.pdf` (Supplemental information - Zenodo). We also provide a general description of the provided files below.  **Loading Templates and Updating Calibration files in Echoview** We have provided an Echoview multifrequency analysis template file called Nootka_multi.EV (available in folder Echoview_Analysis_Files within the provided Dryad file:  Lancaster_et_al._Echoview_Templates_and_Scripts-20250521T190818Z-1-001.zip) which will set up echograms with the same settings we used.  The template file must be saved at the following path on the computer you use for analysis: C:\Users\Public\Documents\Echoview Software\Echoview 14.0\Templates Open folder Echoview_Analysis_Files and open the file: Multifrequency_analysis_template.EV.  This template provides all the steps required for multifrequency dB differencing for fish backscatter.  Each Echoview operator (square in dataflow tab) is annotated to explain what role it plays in the overall analysis. The settings in these boxes can be adjusted by right-clicking them and selecting Variable Properties. **Calibration File Templates** We have provided completed EV calibration files as templates from before and after our survey. Files located in Lancaster_et_al._Echoview_Templates_and_Scripts-20250521T190818Z-1-001.zip\Echoview_Analysis_Files\Calibration_files. Use files: * Cal_echoview_38_startsurvey.EV * Cal_echoview_200_startsurvey.EV * Deep_Cal_echoview_38_final.EV * Deep_Cal_echoview_200_final.EV ## Code/software **R Scripts:** We performed all data cleaning and analysis operation in R version 4.3.3. We created a project within R and used github for version control and data backups.  All required scripts for data cleaning and analysis are provided in the file Lancaster_et_al._Echoview_Templates_and_Scripts-20250521T190818Z-1-001.zip\scripts. Provided scripts are numbered sequentially and running through them in order will ensure all required dataframes are loaded. Variable names are described in detail in each script. Script descriptions: 1_install_packages.R A short function used to install and load all packages. 2_depth_temp.R Clean StarOddi depth and temperature logger data. 3_Nootka_time.R Load field datasheets to calculate survey duration at each site and mean and SD. 4_cleanedcode.R Primary code for cleaning EventMeasure ROV fish annotations. Substrate and slope data from EventMeasure annotations are calculated. Field of View is calculated from ImageJ analysis results. Average depth and temperature per site is calculated (this information is useful for creating calibration files (.ecs) in Echoview before exporting line and NASC information). Fish abundance and species richness are calculated for multiple species groupings (e.g. all rockfish, all schooling fish, all soft substrate fish). We also provide code on how to bin transect data into smaller (20m) bins. We did not use binned data in our analysis but this could be helpful for performing a binned analysis on future data.  We also provide code on how to calculate abundance per subarea which was not used in the publication but is helpful for regional analyses. 5_lines_calculations.R This script processes exported bottom and deadzone buffer lines from Echoview.   All required Echoview lines must be exported before running this script and we recommend saving them in folders with the same names we used for ease of code use (e.g. odata/Transect 1/100mLines/Bottom). We calculate slope using the Great Circle Distance formula for both 20m and 5m slope bins. We also calculate both rugosity metrics (SD Slope and Ratio). We also calculate Deadzone buffer area using bottom and deadzone buffer lines. Code for binned data (20m bins) is also provided but was not used in publication. 6_SV_NASC_datapull.R This script processes exported NASC values for 5, 10, and 15m rocky reef fish zones (RFZs).  All NASC exports must be completed in Echoview before running this code.  We recommend saving exports in files with the same path we used (e.g. odata/Transect 1/100x10/1mDZ). Binned 20m code is also provided but was not used in publication. 7_analysis_GLMs_Spearmans.R This script contains the primary analysis code for figures and results reported in the publication.  We load in additional habitat variables used in our analysis (e.g. ROV rugosity).  We create a main dataframe with all important variables from both ROV and echosounder data. We examine Spearman’s correlations between all echosounder and ROV variables.  We run GLM analyses on benthic fish density data with echosounder and ROV variables as predictors. We also run GLMs for all combinations of rocky reef fish zones heights and deadzone buffer methods. We also examine NASC values across different RFZs and deadzone buffer methods and compare Pass 1 NASC values to Pass 3 NASC values. 8_ROV_fish_summary_stats.R This script creates a summary table of all fish seen with the ROV for a variety of species groupings. Final editing of this table was performed in Microsoft word. 9_Deadzone_height_calculator.R This script provides a method of calculating theoretical deadzone heights based on max, min, and mean depths, slopes and rugosity levels encountered across echosounder surveys. This formula is reproduced from the paper: Tušer, Michal, Helge Balk, Tomáš Mrkvička, Jaroslava Frouzová, Martin Čech, Milan Muška, and Jan Kubečka. “Validation of Current Acoustic Dead-Zone Estimation Methods in Lakes with Strongly Sloped Bottoms: Acoustic Dead Zones on Sloped Bottoms.” Limnology and Oceanography: Methods 9, no. 10 (October 2011): 507–14. [https://doi.org/10.4319/lom.2011.9.507](https://doi.org/10.4319/lom.2011.9.507).