Community Ecology: Analytical Methods Using R and Excel (Data in the Wild) by Mark Gardener

Author:Mark Gardener [Gardener, Mark]
Language: eng
Format: azw3
ISBN: 9781907807633
Publisher: Pelagic Publishing
Published: 2014-03-28T04:00:00+00:00

So, using Excel to determine beta diversity is fairly straightforward but, of course, the more samples you have the more ‘individual’ your formulae will become. Using R gives a bit more flexibility because you do not have to create formulae for individual groups of samples. In the following exercise you can have a go at calculating the beta diversity using the same ground beetle data.

Have a Go: Use R to calculate beta diversity for species richness using replicated habitat data

You will need the CERE.RData file for this exercise; you’ll be looking at the ground beetle data. There are two data items gb.biol contains the community data and gb.site contains the habitat information. You’ll also need the vegan package.

1. Start by making sure that the vegan package is loaded and ready:

> library(vegan)

2. The gamma diversity can be found for the habitats by with the specnumber() command, which allows a grouping variable to be used:

> gamma <- specnumber(gb.biol, gb.site$Habitat)

> gamma

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