This lesson is being piloted (Beta version)

OTN R - Acoustic Telemetry Workshop: Setup

Requirements

R version: 3.6.x or newer (recommend 4.0.x) and RStudio

Open RStudio and run this install script. It’s best to run it line by line instead of all at once in case there are errors.

Note: When running through the installs, you may encounter a prompt asking you to upgrade dependent packages. Choosing Option 3: None, works in most situations and will prevent upgrades of packages you weren’t explicitly looking to upgrade.


# Tidyverse (data cleaning and arrangement)
install.packages('tidyverse')

# VTrack - Tools for Telemetry Analysis
install.packages("devtools")
library(devtools)
devtools::install_github("rossdwyer/VTrack")

# GLATOS - acoustic telemetry package that does filtering, vis, array simulation, etc.
install.packages('remotes')
library(remotes)
install_url("https://gitlab.oceantrack.org/GreatLakes/glatos/-/raw/spg-workshop-2020/glatos_0.4.2.1.tar.gz",
            build_opts = c("--no-resave-data", "--no-manual"))  

# Marmap - library that allows non-straight-line interpolation between two points.
# Useful for avoiding land masses when interpolating fish positions.
install.packages('marmap')

# Lubridate - part of Tidyverse, improves the process of creating date objects
install.packages('lubridate')

# gganimate and gifski help you animate ggplot objects
install.packages('gganimate')
install.packages('gifski')

# R language Bindings for the GEOS library, a pre-compiled, open source geometry engine for fast spatial calculation
install.packages('rgeos')
install.packages('rgdal')
install.packages('mapproj')

# Package for dealing with argos data, some useful functions for working with a series of geospatial data points
install.packages('argosfilter')

# SP and Raster packages for mapping.
install.packages('sp')
install.packages('raster')

# spdplyr - use dplyr's subsetting/grouping/selection syntax on spatial data frames.
install.packages('spdplyr')

# mapview - generate a local webservice that shows you a map representation of your
# spatial dataframe.
install.packages('mapview')

# Install ffmpeg, which we use for the GLATOS-derived animations.
library(glatos) # once you have your GLATOS installed properly
install_ffmpeg()

Dataset and Code

Once the packages are installed, you can download the datasets and code for this workshop from this link.

  1. Select the GREEN “Code” button at the top and choose “Download ZIP”
  2. Unzip the folder and move to secure location on your computer (Documents, Desktop etc.)
  3. Copy the folder’s path and use it to set your working directly in R using setwd('<path-to-folder>').

If you are familiar with Git and Github, feel free to clone this repository as you normally would, by running git clone https://github.com/ocean-tracking-network/2020-07-16-OTNSPG-R-workshop.git in a terminal program and following from step 3 above.