probably folowing reference will help

Austin PC, Hux JE (2002) A brief note on overlapping confi-

dence intervals. J Vasc Surg 36:194–195

If you have got the abundance based sampling data as instructed by Estimates user manual (should prepared in .txt file), then load data in estimates software after running it, than calculate diversity statts. Export the result to excel file. Now by using the result, place Sample in X axis and Mau Tau in Y axis, its sample based rarefaction, if individuals is placed in X axis, than its individual based rarefaction.

Thanks Yagya, Katharina and Animesh for your suggestions.

How to figure out which one is Mau Tau values from output (result) of EstimateS 9.1. Is it S Mean(run) which we put along Y-axis?

Actually I want to plot sample based species rarefaction curve for two different habitats to compare species richness. For this I generated a species x samples matrix on the bases of species presence (1) and absence (0) and converted it into .txt file from excel. Form this matrices, 500 resamples with replacement should be randomly drawn for each sample size. I need to plot the average value of species richness from 500 resamples against the respective sample size. To my understanding this curve should reach asymptote which indicates the number of samples required for sampling species richness. 

Can I have further explanation on understanding the output result of EstimateS 9.1 or I need to choose some specific Diversity Settings?

I am not sure I understand the problem. After all, EstimateS explains how to organize the data, and once you have the data set correctly organized, you just run it and you will get the numbers for the curves. You then save the output, and plot them in your favorite program.

Also, you might need a good text editor, to edit the output of EstimateS - notepad++ is really good. Basically, you must remove the header and understand the organization, and then import your data into a graphing program.

Also, in the program R, there is a package called BiodiversityR which also does similar analysis, with many more options, and graphics along the way. I highly recommend it to use, perhaps in conjunction with EstimateS which is also good.

JJR

Hi Rita,

You are right. The MAO TAO values is the S(mean). The sequential columns gives you the 95% CI (one column for the lower bound and the other for the upper bound), which is very useful if you want to compare sites. You can easily create a plot in R using the results of EstimateS, as James stated. Are you familiar with R? I can send you a small script to plot your curves in R if you want.

James, the BiodiversityR is a great package. The only problem is it only calculates rarefactions using samples, not individuals, like EstimateS does.

Fabricio,

Could you also share with me scripts for curve plotting in R? 

Thanks 

Thanks James and Fabricio for your suggestions. Yes, I heard a lot about R but haven't used it yet. I'm really interested to learn it too. 

Hey Fabricio!  It would be a great help for me  if you could send  the script to plot curves in R. I tried to plot the graph in SPSS but couldn't get a nice one. Yes the 95% Cl is there in the output and I'm thinking to include it in my curve to compare species richness of two sites. Thanks for assuring about MAO TAO values. Do you have any idea of the terms Singleton Mean and Doubleton Mean and also Unique Mean that come along with the output result of EstimateS? In fact I got too many output coulmns in the result of EstimateS from my input data and it is taking too long for me to select the one which I need for plotting my sample based species rarefaction curve.

Fabrício, I am afraid you are incorrect. You CAN plot by individuals as well as by samples. It only depends on how you organize your data. http://www.worldagroforestry.org/resources/databases/tree-diversity-analysis

At any rate, I suppose it might be a lot to ask to have any one program do everything we want, the way we want it...

As far as curve fitting goes, if you know a little R, then you can just grab the output of BiodiversityR and plot it in R (better than BiodiversityR does, perhaps), or you can use it in your favorite graphing program - I use CoPlot.

Hi guys,

Really sorry for the delay. I was in the field with no internet access.

James, I made a mistake about the packages in the first reply. I meant VEGAN, not BiodiversityR. Sorry for the confusion. I don't know why, but the argument "xvar=individuals" in the function "vegan::specaccum" doesn't work... Anyways, this is another history. Good to know that BiodiversityR do that. I use this package very little.

Rita and Geraud, I attached a simple script to plot the curves in R. But if you are not familiar with R, maybe you will have problems. 

Hey Fabricio!

Thanks for the attachment file. Yes, you are right. Since I'm not used to with R, it is quite difficult for me to understand it. So I have thought to plot my curve in Origin software.

Further suggestions regarding using EstimateS and plotting curves are most welcome!

I found R statistics a bit complex language than Python. 

Thanks Fabricio sharing this!

Thanks Fabrico for the R script. I did a google search for the diversity data to plot my rarefaction curve and it brought me here. I know a little bit of R from the cousera online course. I am glad you can share it Fabrico. Thanks much. I was thinking of plotting the graph in excel but noe I can do it in R, Vagan. Also, I read that there is a new package 'iNEXT' they say it has very good graphics but its hard to put your legends in.

Thanks everyone for the discussions. Sorry I didn't contribute anything, but would like to if any thing pops up.

Regards,

Elizah