### Installation instruction resistance GA for the Thursday morning session on resistance surfaces.
## Written by Joscha Beninde & Isolde van Riemsdijk. 
## With questions for installation, email: isolde.van_riemsdijk@biol.lu.se, j.beninde@vu.nl or send a message on Slack
## There will also be trouble-shooting opportunities in breaks on Wednesday, so we can ensure everyone has a running installation on Thursday.

## Installing packages ResistanceGA and dependencies 
# We assume that you have installed R and R studio. If not, please use this website to install them following instructions for your running system: https://rstudio-education.github.io/hopr/starting.html

# in Rstudio (or R) install the packages "devtools", "tinytex", "terra", and "ResistanceGA" by typing the following in the command line and hitting enter after each line:
# Install 'devtools' package, if needed
if(!("devtools" %in% list.files(.libPaths()))) {
    install.packages("devtools", repo = "http://cran.rstudio.com", dep = TRUE)}

# tinytex;
install.packages("tinytex") 
library("tinytex")
tinytex::install_tinytex()
# terra;
install.packages("terra")
library("terra")

# ResistanceGA
devtools::install_github("wpeterman/ResistanceGA", build_vignettes = TRUE) # Download package
library("ResistanceGA")
## if you get errors during the installation of this package, try and see if you can get it to work by installing the packages as follows:
install.packages("<name of the package>")
library("<name of the package>")
# and rerunning the devtools command until you are successfull or run out of patience. In the latter case, do not hesitate to contact us!

# If installation ran without any errors, do a small test-run to see if the installation was indeed successfull. The following line of code will generate an error regardless:
Frag.tran <- Resistance.tran(transformation = "Monomolecular", 
                          shape = 0.3, 
                          max = 150, 
                          r = Frag)
						  
# If the error reports that it cannot find "Frag", then your installation was sucessfull and you can continue with the installtion of Julia
# If the error reports that it cannot find the function "Resistance.tran" then contact us to further trouble-shoot your installation! 

## Installing coding software Julia, and Circuitscape for fast optimization
# Install Julia for your system with the installation wizzard that you can download here: https://julialang.org/downloads/

# Install the Julia package Circuitscape (following under the header "Installation" here: https://github.com/Circuitscape/Circuitscape.jl)
# Start Julia, and in the command line of Julia, type (hit "enter" after every line):

# Load the package functions:
using Pkg
# Add the package "Circuitscape":
Pkg.add("Circuitscape")
# Test your newly installed package:
Pkg.test("Circuitscape")
# The test was successfull if the final line reports "Testing Circuitscape tests passed"

# Now we need to get the path where Julia is by running (for instructions for MAC, see below):
ENV["PATH"]
# Your computer probably answers with a long string with several paths to different locations on your computer, separated by semi-colons (;)
# You need to look for the path ending with "Julia", the version number, and "bin". For me it was:
C:\\Users\\Isolde\\AppData\\Local\\Programs\\Julia-1.9.3\\bin
# Save this path somewhere so you can use it for the tutorial

# And the path where Julia is for MAC users (thanks to Ernst Jonsson for solving this one):
# use the shell (the mac terminal)
sudo mkdir -p /usr/local/bin
sudo rm -f /usr/local/bin/julia
sudo ln -s /Applications/Julia-1.9.app/Contents/Resources/julia /usr/local/bin/julia
# Use this first path here (/Applications/ ... /julia) for the optional test below and the tutorial!

## OPTIONAL: to test if your Julia installation was sucessfull, restart your computer, and run the following code in the R studio or the R terminal:
# Replace the path here to the path you saved above, remember to replace the double backward slashes with single forward slashes
JULIA_HOME <- "C:/Users/Isolde/AppData/Local/Programs/Julia-1.9.3/bin"
JuliaCall::julia_setup(JULIA_HOME)

## You are all prepared now, we look forward to meeting you all!