indicators.qmd

---
title: "Indicators"
subtitle: "Calculate indicators of ecological or management interest beyond taxonomic groupings"
---

## Diversity

Here are the classic diversity indices from the R package `vegan`:

> $$
> \begin{aligned}
> H   &= - \sum_{i=1}^S p_i \log_b  p_i  &\text{Shannon-Weaver}  \\
> D_1 &= 1 - \sum_{i=1}^S p_i^2          &\text{Simpson}         \\
> D_2 &= \frac{1}{\sum_{i=1}^S p_i^2}    &\text{inverse Simpson}
> \end{aligned}
> $$
>
> where $p_i$ is the proportion of species $i$, and $S$ is the number of species so that $\sum_{i=1}^S p_i = 1$, and $b$ is the base of the logarithm.

## Endemism

Endemism could be measured as a function of the presence or average of the species range, given by either a global SDM converted to a binary range or using the existing IUCN range maps.

## Extinction Risk

This is provided by IUCN RedList, as well as sometimes at a national level, such as NatureServe's [Conservation Status Ranks](https://www.natureserve.org/conservation-status-assessment) for the U.S.

## Functional Importance

## Habitat Forming

Habitat forming species, such as coral, mangrove, seagrasses and kelp are especially important for biodiversity and ecosystem services.

## Phylogenetic Uniqueness

## Richness

## Sensitivity

Sensitivity to specific human activities, such as shipping or fishing. Some activities may have different stages of development, such as construction versus operation of offshore wind energy.

## Trophic Index