Chapter 2 Preparing for the workshop

To prepare for this workshop, you must do the following steps:

Download the data required for this workshop:

Their data can also be retrieved from the ade4 package:

library(ade4)
data(doubs)

spe <- doubs$fish
env <- doubs$env

Alternatively, from the codep package:

library(codep)
data(Doubs)

spe <- Doubs.fish
env <- Doubs.env

Download the script containing the coldiss() function:

You must also use these packages:

list.of.packages <- c("ape", "ade4", "codep", "gclus", "vegan",
    "GGally", "PlaneGeometry", "remotes", "matlib", "MASS")

new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,
    "Package"])]

if (length(new.packages) > 0) {
    install.packages(new.packages, dependencies = TRUE)
    print(paste0("The following package was installed:", new.packages))
} else if (length(new.packages) == 0) {
    print("All packages were already installed previously")
}

## [1] "The following package was installed:ape"          
## [2] "The following package was installed:ade4"         
## [3] "The following package was installed:codep"        
## [4] "The following package was installed:gclus"        
## [5] "The following package was installed:vegan"        
## [6] "The following package was installed:GGally"       
## [7] "The following package was installed:PlaneGeometry"
## [8] "The following package was installed:remotes"      
## [9] "The following package was installed:matlib"

# Load all required libraries at once
invisible(lapply(list.of.packages, library, character.only = TRUE,
    quietly = TRUE))

# source(file.choose()) # use coldiss.R which you have
# downloaded to your own directory