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rfor-loopvegan

Calculating diversity indices across sites in R

I have a dataframe(df)as follows:

Year PlotNo HabitatType Sp1 Sp2 Sp3 Sp4
2000   1       GH        0   1   2   3
1988   3       KL        2   3   4   5

where, Sp stands for Species and its columns represent abundance value.

I'm trying to find the Simpson's diversity for each row in the dataframe. I have attempted the following for loop:

require(vegan)
y <- for(i in 1:nrow(df)) {
row <- df[i,4:50] #Assuming 50 columns
diversity(row, "simp")
}

However, I keep running into an error as follows :

Error in sum(x) : invalid 'type' (character) of argument

Any ideas on how to correct this error? Or any alternate way of going about this?

Solution

  • diversity indeed needs numerical data, and this may be your problem. What do you get from sum(df[,4:50])?

    Another issue is that you do not need a for() loop: when given a data frame or a matrix, diversity will calculate the index for each row (or column if you set argument MARGIN = 2). So diversity(df[,4:50]) should do, provided that your data are numeric.