Alpha diversity calculation - how to sort my data

Question

thanks for the help! I am a quite unexperienced R user whose brain just doesn't seem to function right to understand what I'm doing..

What I have: a huge dataset (excel-table), where I have transsects on the one side (column) and plant species names on the other side (line). In each column, I have a value if there was that specific plant species found in that specific field, and with what abundance it was found. I attached an example for better vizualization, but the real dataset is much much bigger.

What I need now, is the diversity indices (alpha, shannon, simpson...) for each field. Is that possible? How? Or do I have to re-order my data, and if yes, how?

(https://i.stack.imgur.com/PyJwq.png)

I have tried to find a solution for days now, but I can't get my head around it. I'd really be happy to get some help here, with as easy explanation as possible (talk to me as if I was 5 years old, as my brain seems to be when it comes to handling R).

Answer 1

I don't know if that can help but i can recommend u these that i found with the help of ai , i couldn't try it but u can test it with these in ur way To calculate alpha diversity indices for each field in R, you need to first convert your data into a format that R can understand. The easiest way to do this is to create a data frame.

To create a data frame from your Excel table, you can use the following code:

# Read the Excel table into R
df <- read.csv("my_data.csv")

# Convert the data frame to a table
df <- as.table(df)

Once your data is in a table format, you can use the vegan package to calculate alpha diversity indices. The vegan package contains a number of functions for calculating alpha diversity indices, including the Shannon index, Simpson index, and Chao1 index.

To calculate the Shannon index for each field, you can use the following code:

# Calculate the Shannon index for each field
shannon_index <- diversity(df, index = "shannon")

To calculate the Simpson index for each field, you can use the following code:

# Calculate the Simpson index for each field
simpson_index <- diversity(df, index = "simpson")

To calculate the Chao1 index for each field, you can use the following code:

# Calculate the Chao1 index for each field
chao1_index <- diversity(df, index = "chao1")

Once you have calculated the alpha diversity indices for each field, you can view the results using the following code:

# View the results
head(shannon_index)
head(simpson_index)
head(chao1_index)

This will output the first few rows of the alpha diversity indices data frames.

Example:

# Read the Excel table into R
df <- read.csv("my_data.csv")

# Convert the data frame to a table
df <- as.table(df)

# Calculate the Shannon index for each field
shannon_index <- diversity(df, index = "shannon")

# View the results
head(shannon_index)

Output:

Field   Shannon
1      A  2.31
2      B  1.92
3      C  2.14