Shannon Diversity Index - Examples in R (vegan package)

What is Shannon Diversity Index:

The Shannon diversity index is a measure of biodiversity that takes into account both the richness (number of different species) and the evenness (distribution of individuals among those species) in a community. It is commonly used in ecology to quantify the diversity of species within a particular area.

Also use: Shannon Diversity Index Calculator 

The formula for Shannon diversity index (H) is given by:

'\[ H = -\sum_{i=1}^{S} p_i \cdot \ln(p_i) \]'

Where:

- '\( S \)' is the number of species in the community,

- '\( p_i \)' is the proportion of individuals belonging to the \( i \)-th species.

Example of Shannon Diversity Index in R

Now, let's go through an example in R using a hypothetical dataset. Assume you have a vector representing the abundance of different species in a community:

```R
# Example abundance data
abundance <- c(10, 5, 8, 3, 2)

# Calculate proportions
proportions <- abundance / sum(abundance)

# Calculate Shannon diversity index
shannon_index <- -sum(proportions * log(proportions))

# Print the result
cat("Shannon Diversity Index:", shannon_index, "\n")
```

In this example, the `abundance` vector represents the number of individuals for each species. The proportions are calculated by dividing each abundance value by the total abundance. The Shannon diversity index is then computed using the formula.

Example of Shannon Diversity Index in R using diversity Function - vegan package

This is a simple example, and in practice, you would often work with more complex datasets with species abundance data. You may use packages like `vegan` in R for calculating diversity indices on larger ecological datasets.

Here's an example of how you can calculate the Shannon Diversity Index in R:

```R
# Install and load the vegan package
install.packages("vegan")
library(vegan)

# Create a hypothetical community data (replace this with your own data)
# Rows represent different samples, and columns represent different species
community_data <- data.frame(
  species1 = c(5, 8, 0, 3),
  species2 = c(2, 0, 6, 4),
  species3 = c(7, 3, 1, 0)
)

# Calculate the Shannon Diversity Index
shannon_index <- diversity(community_data, index = "shannon")

# Print the result
cat("Shannon Diversity Index:", shannon_index)
```

Make sure to replace 'community_data' with your own dataset where rows represent samples and columns represent the abundance of different species in each sample.

Note: If your data is in a different format (e.g., a data frame with species in rows and samples in columns), you may need to transpose your data or adjust the function parameters accordingly.