# Beta functional diversity expressed as percentage of gamma
spe.rao$FD$Beta_prop
spe.rao$FD$Beta_add / spe.rao$FD$Gamma
# Multiplicative beta Rao functional diversity
spe.rao$FD$Gamma / spe.rao$FD$Mean_Alpha
# Variation of alpha TD, FD and PD along the Doubs river
spe.rao$TD$Alpha
spe.rao$PD$Alpha
spe.rao$FD$Alpha
# Add Rao-based diversity indices to the div data frame
div$alphaTD <- spe.rao$TD$Alpha
div$alphaPD <- spe.rao$PD$Alpha
div$alphaFD <- spe.rao$FD$Alpha
# Save the div data frame as a CSV file
write.csv(div, file = "diversity.csv", quote = FALSE)
# Phylogenetic diversity (Rao)
names(spe.rao$PD)
# Mean alpha Rao phylogenetic diversity
spe.rao$PD$Mean_Alpha
# Gamma Rao phylogenetic diversity
spe.rao$PD$Gamma
# Additive beta Rao phylogenetic diversity
spe.rao$PD$Beta_add
spe.rao$PD$Gamma - spe.rao$PD$Mean_Alpha
# Beta phylogenetic diversity expressed as percentage of gamma
spe.rao$PD$Beta_prop
spe.rao$PD$Beta_add / spe.rao$PD$Gamma
# Multiplicative beta Rao phylogenetic diversity
spe.rao$PD$Gamma / spe.rao$PD$Mean_Alpha
# Functional diversity (Rao)
names(spe.rao$FD)
# Mean alpha Rao functional diversity
spe.rao$FD$Mean_Alpha
# Gamma Rao functional diversity
spe.rao$FD$Gamma
# Additive beta Rao functional diversity
spe.rao$FD$Beta_add
spe.rao$FD$Gamma - spe.rao$FD$Mean_Alpha
In addition, we can plot the alpha diversity indices of each site on the map of the
Doubs River (Fig. 8.12; see the code in the accompanying R script):
Compare these spatial patterns with those of Figure 8.10. How do you interpret
the difference between taxonomic and phylogenetic diversity patterns?
8.5 Functional Diversity, Functional Composition and Phylogenetic. . .
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