elaacoustics

Analytical Tools for ILK’s ELA Acoustic Surveys

Installation

This package is not available at this time on CRAN. You can install elaacoustics from the GitHub repository using devtools::install_github().

devtools::install_github("HoldenJe/elaacoustics")

Plotting Examples

This is an example of how to use the basemaps for each lake.

library(elaacoustics)
library(ggplot2)
basemap_lake379

This is an example of how to add a point to the basemap of the lake.

basemap_lake379 + 
  geom_point(aes(x = -93.799462, y = 49.708170), pch = 13, size = 4) +
  theme_bw() +
  ylab("Latitude") + xlab("Longitude")

This is an example of how to combine multiple lake files on a single plot and add customization.

ggplot()+ 
  geom_sf(data = shape_lake379, fill = 'blue') + 
  geom_sf(data = shape_lake259, fill = 'blue') +
  geom_point(aes(x = -93.799462, y = 49.708170), pch = 13, size = 4, colour = "yellow") +
  theme_bw() +
  ylab("Latitude") + xlab("Longitude") +
  theme(axis.text.x = element_text(angle = 45, hjust = 1))

Exporting Data

Functions used for exporting data from Echoview require:

1. A valid Echoview license with automation module.
2. RDCOMClientinstalled. If RDCOMClient failed to install when erieacoustics was installed please review installation instructions on RDCOMCLient Github page.

Primary Exports for Analysis

It is expected that the survey has been processed using the appropriate file structure and analysis template and the following tasks have been completed:

1. Detected bottom line has been edited to appropriately fit bottom
2. Bad data regions have been identified (within transect as well as off-transect areas)
3. Fish track detection has been completed and manually inspected to verify that only valid fish tracks remain
4. If required, NearSurfaceExclusion and Thermocline lines have adjusted within the data file
   It is not required that the Survey analysis region be created manually as the function will automatically create the necessary line relative region prior to export.

library(elaacoustics)

# Export 1 EV file
export_ELA_data("myev.EV")

# export multiple EV files
all_ev_files <- dir(recursive = TRUE, pattern = "EV$", full.names = TRUE)
lapply(all_ev_files, export_ELA_data)

Creating *.mif files for Echoview

You can create MapInfo File format *.mif files from the shapefiles that can then be used as background maps within Echoview.

sf::st_write(shape_lake622, "L622.mif", driver = "MapInfo File")