Hi every one.
I need a list of applications/soft wares which can calculate the biodiversity indices.
I would be very appreciate if you help me.
Dear Soheila
There are several software by which you are able to calculate different biodiversity parameters. For instance: Power Marker, GenAlex, Genstat, Fstat ana Past3
https://www.sams.ac.uk/science/outputs/
Check the link
Biodiversity Pro software
There are several packages (e.g., vegan, vegetarian, BiodiversityR, iNEXT, FD, and many, many more) in R that allow you to compute and/or estimate a wide suite of diversity (including functional diversity) and richness measures. You can check the documentation for each to determine what measures are available.
Species Diversity & Richness
BiodiversityR
EstimateS
Past
I agree with the comments above. However, most biodiversity indices are quite simple. I calculated a lot of them simply in EXCEL.
The free NatureServe Vista extension for ArcGIS contains this function with lots of options. It is also a full scenario-based cumulative effects assessment and planning software that can interoperate with Marxan. See www.natureserve.org/Vista.
I have used SPADE - Species Prediction and Diversity Estimation to estimate biodiversity in communities. I used an old desktop version but there is a web-based version now: https://chao.shinyapps.io/SpadeR/.
I recommend the following paper from Loiseau & Gaertner (2015) to use alternative indices that can be more appropriate or sensitive depending on your research. Functional biodiversity indices are particularly interesting for community-wide approaches. https://doi.org/10.1002/ece3.1619
R is an excellent software to perform those analysis with many packages to calculate biodiversity indices.
There are a variety of softwares/ tools that can be used to estimate biodiversity indices. for eg Estimate S is a commonly used software with which one can easily calculate/ estimate species diversity/ biodiversity indices.
Adding to an already well answered question - SPSS also has some functions
You may also use another software by name DISTANCE to calculate diversity indices. I personally do not have any such ones.
Depending on the objective of your study but I think even DISTANCE software can assist you in calculating some of these indices including biodiversity survey indices. Another softwares are PRESENCE and MARK 11 softwares.
EstimateS, the vegan package in R or PAST, all are quite useful. I think EstimateS software is very good option. Here is link
http://viceroy.eeb.uconn.edu/estimates/
Also you can use SPADE - Species Prediction and Diversity Estimation to estimate biodiversity in communities and iNEXT (iNterpolation and EXTrapolation)
http://chao.stat.nthu.edu.tw/wordpress/software_download/
I have recently used PAST and is super easy. In just one click you can obtain different indexes:
As suggested before, I think PRIMER is a very interesting option in this field.
I have recently used Past; The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheet-type data entry with univariate and multivariate statistics, curve fitting, time series analysis, data plotting, and simple phylogenetic analysis. https://folk.uio.no/ohammer/past/
This is such a wonderful thread - really helpful and inspirational - now I want to do a Ph.D. using these stats programs. It makes me so happy that all of you folks around the world are in some field that cares about biodiversity! I just cried a little - especially seeing another Armenian in the discussion, Mr. Subramanian, (I am part Armenian)...it is so important that we keep carrying out good work in this field. : )
Many colleagues already addressed good software
You can do the calculation using excel spreadsheet and also PAST that is a free and easy to use software.
In my opinion, a very good question and an interesting discussion. Best wishes
Taxonomic diversity https://cran.r-project.org/web/packages/vegan/index.html
Functional diversity https://cran.r-project.org/web/packages/FD/index.html
- Badges
- Science method