Dear colleagues
Do you have formulas for calculating Alpha-Beta-Gamma Diversity in Excel?
It could be Hurlbert’s PIE (Olszewski 2004) or other type of abundance based Beta diversity. In the worst case it could also be incidence based Beta diversity.
Thank you in advance
http://bpmsg.com/diversity-as-business-kpi-alpha-and-beta-diversity/
Check this out. I think it might do what you need it to do. It is Shannon's version of diversity. I am not in ecology, but it certainly uses an alpha and a beta diversity and of course the sum of which is gamma.
Mattew it is approximately 15-50 islands, and 15-300 species depending on variant. If you could extend this software it would be very useful, not just for me but for other ecologists
Can I clarify which is the 15-50 and which is the 300 regarding the current instantiation of the file? Again, I am not an ecologist, so I just want to be certain what I am looking at.
My assumption is the the islands are the samples and the species are the categories. Please confirm that.
Actually, I just had a better idea (and I should have thought of this earlier) that wil get a solution from an ecologist's perspective (as these libraries are typically designed by the people who use them):
There are two R libraries:
vegan
entropart
that should be able to do what you need. All you need to do is input a matrix (which is what you would input into Excel anyway). You could literally load a .CSV into that or a .TXT into that without problem.
Those libraries are designed specifically to handle that task.
A quick search for R package vegan or R package entropart should give you enough information to do what you need to do.
If you install library vegan (including its dependencies), run the command library(vegan), and then load the data set using data=read.csv(directory,header=FALSE), you can analyze it.
I just experimented with it and using the function adipart(data,"shannon") produced the exact same result as the Excel sheet I referenced before on the same data.
I also spoofed it with a 50 x 312 data set and it functioned (I cannot verify the accuracy of its measurements mind you, but it produces alpha, beta, and gamma diversities with statistical significance). Given that it worked for the smaller set, it should work for the larger one.
Hope that helps.
Hi Marcin,
I have developed a software that works directly with data from Excel worksheets. It is very convenient. The software calculates the main diversity index: Shanon, Shanon equity, Simpson, Brillouin, Berger-Parker, McIntosh, Margalef, Menhinick, Gleason.
You can download the software and view the instructions on our faculty webpage:
http://www.silvic.usv.ro/software.php
More details in:
https://www.researchgate.net/publication/270616537_A_tool_for_computing_diversity_and_consideration_on_differences_between_diversity_indices
Article A tool for computing diversity and consideration on differen...
Matthew
Well I still haven’t learnt R, shame on me; but that is the reason I use excel. So as I understand your suggestion is learn R and apply vegan?
If I have no choice, well I will think about or use PAST that has some functions for calculating Beta div; but based on incidences.
Dear Ciprian
Thanks for the paper, but apparently it doesn’t deal with beta div.
Sincerely
In trying to modify the Excel sheet, it becomes inordinately massive. R is so much easier. I will put together a document to get you started. It will easily be your best bet for something that large (and it might help you with other things you encounter down the road).
Dear Marcin,
it seems that you want to use a free software such as the marvelous PAST. It is straightforward and similar to Excel. I assume you will like it as most of my students.
http://folk.uio.no/ohammer/past/
Klaus, I do like PAST, as your students. The only problem is the way it calculates Beta diversity - just incidence based indices. Anyhow, I will have to start to like it or learn a bit of R. Thanks to all of you
- Badges
- Science method
- Similar topics
- Biological Science
- Ecology