Requirements
R version: 3.6.x or newer 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.
install.packages("devtools")
# Tidyverse (data cleaning and arrangement)
install.packages('tidyverse')
# Mapping spatial data
install.packages('plotly')
# VTrack - Tools for Telemetry Analysis
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/-/archive/master/glatos-master.zip",
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('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')
#Install ffmpeg, which we use for the GLATOS-derived animations.
library(glatos) # once you have your GLATOS installed properly
install_ffmpeg()
install.packages("TMB")
install.packages("rgdal")
install.packages("moveHMM")
devtools::install_github("lawlerem/markmodmover", build_vignettes=TRUE)
install.packages('circular')
install.packages('gridExtra')
Once the packages are installed, set your working directory using setwd('<path-to-folder>')
We have provided R Markdown files for each lesson which can be downloaded here.