I have collected data on trees on farmland and i want to used the species identified to draw rarefaction curves using EstimateS. The areas sampled differ in sizes and rarefaction curves are best for comparing species diversity and richness.
Maurice,
What type of data did you collect? What type of question are you trying to address?
Dear Maurice,
I don't know how to draw rarefaction curves using EstimateS although I see many publications used. If your sampling sizes is very different across the sites, I think rarefaction is needed to compare species richness across the sites. Therefore, I recommend you to rarefy your data in R package Vegan (https://cran.r-project.org/web/packages/vegan/index.html) as well as the function “rarefy” (http://127.0.0.1:18868/library/vegan/html/rarefy.html).
hope it helps!
Wumei
Dear Maurice,
Maybe this could help you: First, you need to construct an abundance matrix for each area. In the first cell of each matrix, you should write the database name (short); then write the species number in the cell below (second row and first column) and write number of samples (months or sites, for example) in the next right cell (second row and second column). Below this, you need to add the abundance data for each species (rows) and samples (columns). Save this database in a .cvs document.
Add the database to EstimateS; modify the diversity settings as you consider; and finally compute the diversity stats. Then, EstimateS will show you many different measures, one of them is Cole Rarefaction. You can copy and paste the results in a Excel document and then construct the graphs.
I also recommend you software Past (http://folk.uio.no/ohammer/past/) or R, to obtain the curves.
:)
Best regards,
Cisteil
Hi Maurice
I attached two files that are used to make rarefaction curves with Estimates. You are in Spanish only have to translate and then apply. If you want more advice escribeme [email protected]
Thanks so much guys. I will try your recommendations and get back to you. Thanks once again.
You can use two software's of Ecological Methodology and PAST
Thanks for your resposne sir. I want to use EstimateS but i don't know how to arrange the data to reflect all the replicates. I would be more than happy if you can guide me. Thanks
I would like to recommend you to use iNext packages in R program. Here is the command. Hopefully, it can help you.
data
out
- Badges
- Science topic
- Similar topics
- Geoscience
- Asia
- India