Calculating Diversity

Why should we preserve biodiversity?

Biodiversity is important to preserve because it plays a crucial role in maintaining the health and balance of ecosystems. A diverse range of plant and animal species helps to ensure the continuation of vital processes such as pollination and the decomposition of organic matter. Biodiversity also provides numerous benefits to humans, such as providing food, medicine, and other resources, and it has intrinsic value as a unique and important part of our world. Additionally, preserving biodiversity helps to protect against the negative effects of climate change and other environmental challenges.

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How does biodiversity help protect against climate change?

Biodiversity plays a key role in helping to protect against climate change in several ways. For example, a diverse range of plant species can help to absorb carbon dioxide from the atmosphere, which can help to reduce the amount of greenhouse gases that contribute to global warming. Biodiversity can also help to maintain the health and resilience of ecosystems, which can make them better able to adapt to the changes brought about by climate change. In addition, the preservation of biodiversity can help to safeguard against the loss of important natural resources that are vital for human survival, such as food and water.

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How should we measure biodiversity?

There are several ways to measure biodiversity, each of which provides a different perspective on the variety and abundance of species in a given area. Some common ways to measure biodiversity include:

• The number of species in a given area: This is one of the most basic measures of biodiversity, and it can provide a general sense of the diversity of species present in an ecosystem.

• …

Overall, the best way to measure biodiversity may depend on the specific goals and circumstances of the study. It is often useful to combine multiple measures in order to get a more complete picture of the biodiversity of an ecosystem.

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Measures of Diversity

• Species richness
  • Number of species actually present
• Simpson index
  • Chance of two individuals being the same species
• Shannon entropy
  • Surprise in seeing next individual
• Berger-Parker
  • Evenness / Dominance of most abundant species

Measures of Diversity

\[D_q = \left( \sum_{i \in \{1 \dots N_S, p_i \neq 0\}} p_i^q \right)^{\frac{1}{1-q}}\]

Covers all of these measures.

Measures of Diversity

• Species richness
  • Number of species actually present
• Simpson index
  • Chance of two individuals being the same species
• Shannon entropy
  • Surprise in seeing next individual
• Berger-Parker
  • Evenness / Dominance of most abundant species

Measures of Diversity

• Species richness
  • \(D_0\)
• Simpson index
  • \(\frac{1}{D_2}\)
• Shannon entropy
  • \(log(D_1)\)
• Berger-Parker
  • \(\frac{1}{D_\infty}\)

Measures of Diversity

• Species richness
  • \(D_0\)
• Shannon entropy
  • \(log(D_1)\)
• Simpson index
  • \(\frac{1}{D_2}\)
• Berger-Parker
  • \(\frac{1}{D_\infty}\)

Measures of Diversity

• \(D_0\)
  • Species richness
• \(log(D_1)\)
  • Shannon entropy
• \(\frac{1}{D_2}\)
  • Simpson index
• \(\frac{1}{D_\infty}\)
  • Berger-Parker

Measures of Diversity

• \(D_0\)
  • Species richness
• \(D_1\)
  • exp(Shannon entropy)
• \(D_2\)
  • 1 / Simpson index
• \(D_\infty\)
  • 1 / Berger-Parker

Diversity profiles

Useful R

• sort() to sort a vector into ascending order
• rep()
• barplot()
• rmultinom() to generate multinomially distributed samples
• Inf is how we say infinity in R
• lines()

Deadlines

• Edits to GitHub repos – as soon as possible, but:
  • Practical Series 2-4: Monday 9th January, 1pm
• Project submission
  • by Monday 23rd January, 1pm
• Marks returned by Monday 13th February

Package assessment

• Does the package work (installs, docs, functions, demos and dependencies)?

    devtools::install_github("SBOHVM/pkgname")
    library(pkgname)
    library(help="pkgname")
    demo(package="pkgname")
    ?pkgname

• Can I generate reports from your demos, and how do they look?
• Is the code well structured and with clear variable names and comments?
• Is the documentation correct (for package, functions, and text in reports)?
• Does the code work correctly?