```
#' Matrix of contrast weights
#'
#' This function assembles multiple vectors of contrasts weights into a matrix. All pairwise contrasts between habitats on each island are computed separately. Contrasts between habitats across islands are not considered.
#'
#' @param specdata A data frame containing at least columns for the dependent variables, as well as a column "island" and a column "habitat".
#' @return A matrix of contrast weights. Each row is a contrast. Each column is a habitat on a given island. Each row is filled with zeros, except the two habitats to compare, which are given values 1 and -1.
#' @author Raphael Scherrer
#' @export
# Function to create a matrix of contrast weights between habitats on each island
matrix_contrasts <- function(specdata) {
# What are the groups?
grouping <- with(specdata, island:habitat)
groups <- levels(as.factor(grouping))
# Matrix of contrast weights between habitats within islands
W <- lapply(levels(specdata$island), function(curr.island) {
# What habitats are on this island?
curr.habitats <- levels(droplevels(with(specdata, habitat[island == curr.island])))
# All pairwise comparisons
contrasts <- combn(curr.habitats, 2)
# For each contrast (column)...
W <- apply(contrasts, 2, function(curr.contrast) {
# Locate first habitat
i <- grep(paste0(curr.island, ".*", curr.contrast[1]), groups)
# Locate second habitat
j <- grep(paste0(curr.island, ".*", curr.contrast[2]), groups)
# Create a vector of contrast weights
W <- rep(0, length(groups))
W[i] <- 1
W[j] <- -1
return(W)
})
# Transpose to have each row corresponding to one contrast
W <- t(W)
return(W)
})
# Merge all vectors of contrast weights into a single matrix
W <- do.call("rbind", W)
return(W)
}
```

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