In HoldenJe/erieacoustics: Analysis Tools For Erie Acoustic Surveys

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>", 
  eval = FALSE
)

library(erieacoustics)

Introduction

The package erieacoustics provides tools to standardize the analysis of Lake Erie acoustic survey data across the three surveys (WB, CB, EB). Historically the surveys have followed similar analytical approaches as described in the Standard Operating Procedures this effort aims to provide a common suite of R tools to improve standardization as well as provide better documentation of the survey.

Project Set Up

An RStudio project template has been created establish a common directory structure and necessary README files for the surveys. The common project directory structure is an important guiding principle as many of the functions expect data to be stored in a specific directory tree and common naming conventions.

Directory Structure

Folder | Description ---------- | -------------------------------------------------- 1_Annual_Protocol | contains Rmarkdown scripts and products for annual survey protocol 2_EVTemplate | Echoview processing template should be stored here to be available to set_up_transect 3_Ping_Data | contains the acoustic data for each transect 3_Ping_Data/TransectName | each transect should be uniquely named and all data stored within a single directory 4_Trawl_Data | contains the paired trawl data 5_Enviro_Data | contains environmental measurements 6_Misc | contains miscellaneous files associated with survey 7_Annual_Summary | contains Rmarkdown scripts and products for annual summary

Processing Steps

1. Check that a template exists

evtemplate <- file.path(getwd(), '2_EVTemplate/ErieHacTemplate_2021.EV')
dir.exists("3_Ping_Data") 
file.exists(evtemplate)

1. Use COM scripting to open new file using the template, import all acoustic files (i.e. *.raw, *.dt4) and perform tasks within the Echoview Template.

set_up_transect(evtemplate, projecthome = getwd(),
                sonartype = "BIOSONICS", tranname = "G_315_07062021")

1. View files with in EV and make necessary adjustments

2. Define line relative regions Important to follow the established naming convention. Provide a description and example here. Include a screen capture.

3. Export transect data

export_transect_evdata(getwd(),"G_315_07062021",1000)

1. Run analysis scripts.

HoldenJe/erieacoustics documentation built on Jan. 29, 2024, 12:32 a.m.