Prior to that, we compute some statistics about the observed species richness and
number of individuals.
# Number of species in the 70 moss or soil cores
(mite.nbsp <- specnumber(mite))
# Cores with minimum and maximum observed species richness
mite.nbsp[mite.nbsp == min(mite.nbsp)]
mite.nbsp[mite.nbsp == max(mite.nbsp)]
range(mite.nbsp)
# Total abundance in the 70 cores
(mite.abund <- rowSums(mite))
range(mite.abund)
# Abundance in the cores with smallest number of species
mite.abund[mite.nbsp == min(mite.nbsp)]
# Abundance in the core with largest number of species
mite.abund[mite.nbsp == max(mite.nbsp)]
# Number of species in the core with smallest abundance
mite.nbsp[mite.abund == min(mite.abund)]
# Number of species in the core with largest abundance
mite.nbsp[mite.abund == max(mite.abund)]
# Rarefaction to 80 individuals
mite.rare80 <- rarefy(mite, sample = 80)
# Compare ranking of observed and rarefied cores
sort(mite.nbsp)
sort(round(mite.rare80))
# Cores with minimum and maximum estimated species richness
mite.rare80[mite.rare80 == min(mite.rare80)]
mite.rare80[mite.rare80 == max(mite.rare80)]
# Observed core with smallest predicted species richness
mite[which(mite.rare80 == min(mite.rare80)),]
# Observed core with largest predicted species richness
mite[which(mite.rare80 == max(mite.rare80)),]
As revealed by the first lines of code, the actual numbers of species in the data set
range from 5 to 25. Also, observe that one of the two cores with the smallest
observed number of individuals (core #57) is also the one with the smallest number
of species; however, the core with the largest abundance (core #67) also contains
very few species (only 6). The core with the highest observed species richness is core
#11 (25 species).
Now, these comparisons are made on unstandardized samples. The rarefaction to
80 individuals modifies the ranking of the core. The core with the smallest estimated
number of species is core #67. As seen above, it is the core with the largest observed
abundance. A look at the observed abundance profile explains this feature: of the
781 individuals observed in that core, 723 belong to a single species (Limncfci).
With 6 observed species for a total of 783 individuals, the estimation for 80 individuals drops to 3.8 species. At the other extreme, the core with the highest estimated
species richness is core #30 with 19.1 species for 80 individuals. The actual numbers
8.2 The Multiple Facets of Diversity
377
number of individuals.
# Number of species in the 70 moss or soil cores
(mite.nbsp <- specnumber(mite))
# Cores with minimum and maximum observed species richness
mite.nbsp[mite.nbsp == min(mite.nbsp)]
mite.nbsp[mite.nbsp == max(mite.nbsp)]
range(mite.nbsp)
# Total abundance in the 70 cores
(mite.abund <- rowSums(mite))
range(mite.abund)
# Abundance in the cores with smallest number of species
mite.abund[mite.nbsp == min(mite.nbsp)]
# Abundance in the core with largest number of species
mite.abund[mite.nbsp == max(mite.nbsp)]
# Number of species in the core with smallest abundance
mite.nbsp[mite.abund == min(mite.abund)]
# Number of species in the core with largest abundance
mite.nbsp[mite.abund == max(mite.abund)]
# Rarefaction to 80 individuals
mite.rare80 <- rarefy(mite, sample = 80)
# Compare ranking of observed and rarefied cores
sort(mite.nbsp)
sort(round(mite.rare80))
# Cores with minimum and maximum estimated species richness
mite.rare80[mite.rare80 == min(mite.rare80)]
mite.rare80[mite.rare80 == max(mite.rare80)]
# Observed core with smallest predicted species richness
mite[which(mite.rare80 == min(mite.rare80)),]
# Observed core with largest predicted species richness
mite[which(mite.rare80 == max(mite.rare80)),]
As revealed by the first lines of code, the actual numbers of species in the data set
range from 5 to 25. Also, observe that one of the two cores with the smallest
observed number of individuals (core #57) is also the one with the smallest number
of species; however, the core with the largest abundance (core #67) also contains
very few species (only 6). The core with the highest observed species richness is core
#11 (25 species).
Now, these comparisons are made on unstandardized samples. The rarefaction to
80 individuals modifies the ranking of the core. The core with the smallest estimated
number of species is core #67. As seen above, it is the core with the largest observed
abundance. A look at the observed abundance profile explains this feature: of the
781 individuals observed in that core, 723 belong to a single species (Limncfci).
With 6 observed species for a total of 783 individuals, the estimation for 80 individuals drops to 3.8 species. At the other extreme, the core with the highest estimated
species richness is core #30 with 19.1 species for 80 individuals. The actual numbers
8.2 The Multiple Facets of Diversity
377