The function getAlphaMetrics computes nine alpha diversity metrics for
a given community data frame, where measure is a character input
specifying the abundance or biomass field used for the calculations. For each
row of the data frame with data, getAlphaMetrics calculates
the following metrics:
- Species richness (S) as the total number of species in each year with
currency > 0.
- Numerical abundance (N) as the total currency (sum) in each year
(either total abundance or total biomass).
- Maximum Numerical abundance (maxN) as the highest currency value reported
in each year.
- Shannon or Shannon–Weaver index is calculated as \(\sum_{i}p_{i}log_{b}p_{i}\),
where \(p_{i}\) is the proportional abundance of species i and b is the base
of the logarithm (natural logarithms), while exponential Shannon is given by
exp(Shannon).
- Simpson's index is calculated as \(1-sum(p_{i}^{2})\), while Inverse
Simpson as \(1/sum(p_{i}^{2})\).
- McNaughton's Dominance is calculated as the sum of the pi of the two most
abundant species.
- Probability of intraspecific encounter or PIE is calculated as
\(\left(\frac{N}{N-1}\right)\left(1-\sum_{i=1}^{S}\pi_{i}^{2}\right)\).
Note that the input data frame needs to be in the format of the output of the
gridding function and/or resampling functions,
which includes keeping the default BioTIME data column names. If such columns
are not found an error is issued and the computations are halted.