Dataset DOI: 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/. 

Original data is available upon request from Ha’oom Fisheries Society at 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.