lines(absc, fish.rich.neigh, col = "red")
points(
absc,
fish.rich.neigh,
pch = 24,
cex = 2,
col = "white",
bg = "red"
)
legend(
"top",
c("Jaccard D", "Replacement", "Richness difference"),
pch = c(16, 15, 17),
col = c("black", "blue", "red")
)
points(
absc,
fish.jac.neigh,
pch = 21,
cex = 2,
col = "black",
bg = "black"
)
lines(absc, fish.repl.neigh, col = "blue")
points(
absc,
fish.repl.neigh,
pch = 22,
cex = 2,
col = "white",
bg = "blue"
)
Hint Observe how the replacement, richness and Jaccard dissimilarity indices between
neighbouring sites have been obtained: the object of class “dist” is first
transformed into a square matrix (e.g. fish.repl), its first row is removed and
the diagonal of the remaining matrix (i.e., the relevant part of the subdiagonal of
the original matrix) is extracted.
Of course, this figure is completely different from Fig. 2a of Legendre (2014).
Here we compare each site with the previous one, which gives very different
information. One can observe that from site 1 to 7, the dissimilarities are due
exclusively to richness differences. Species replacement occurs mainly between
neighbouring sites in the intermediate section of the river. Note also the large
richness difference between sites 22-23, 23-24 and 25-26, due to the drop in species
8.4 Beta Diversity
399