COMPAS (Community Pattern Simulator) is a program that generates simulated community data based on explicit models of how species respond to environmental gradients. Simulated data of this type are useful to evaluate methods for community analysis (e.g., ordination and clustering) because the underlying gradient structure is known and can be used to specify quantitative measures of success. COMPAS has been gradually developed by Dr. Peter Minchin since the early 1980s. It was originally designed to run on mainframe systems and later adapted for personal computers. The program is not a Windows application but runs on any Windows-based PC in a command window. In the interest of stimulating research on community analysis methods, COMPAS is distributed free of charge with the expectation that any publications arising from its use will include an acknowledgement to Dr. Peter Minchin for use of the software and also cite the following paper, in which the simulation procedure implemented in COMPAS was first described:
Minchin, P.R. (1987). Simulation of multidimensional community patterns: towards a comprehensive model. Plant Ecology 71: 145-156.
COMPAS is distributed with no warranty and use of the software is totally at the user's own risk. To download a ZIP archive with the current version of COMPAS and installation instructions, click here.
DECODA (Database for Ecological Community Data) is a program written by Dr. Peter Minchin for the handling and analysis of the kinds of data often collected by community ecologists. It is both a database system and a platform for data analysis by a set of methods that were not readily available in other software when DECODA was developed. These include ordination by various forms of multidimensional scaling and vector fitting, a method for interpretation of ordinations by fitting vectors of maximum correlation with explanatory variables. DECODA includes several options for capturing data from other file types and can extract data from its databases in formats suitable for input to many other popular data analysis programs (e.g., PC-ORD, CANOCO, and Primer).
DECODA was originally created as a personal research tool and by modern standards it is not very user-friendly. Like COMPAS, it is not a Windows application but runs on any Windows-based PC in a command window. DECODA is NOT in the public domain and its use is subject to a license agreement. If you are interested in obtaining a copy of DECODA, please contact Dr. Peter Minchin. A windows application with the functionality of DECODA (and many additional capabilities) is under development but progress is slow due to other commitments and a probable release date is not yet available.
Vegan is a package in R, which is a free, open source statistical environment. The vegan package is intended to help vegetation ecologists and other community ecologists to use R. It contains all major ordination methods, ecologically meaningful dissimilarity indices, tools for analysis of diversity, species richness, and abundance models, plus numerous support functions.
The main author and developer of vegan is Dr. Jari Oksanen at the University of Oulu, Finland and several collaborators have contributed code for various procedures and methods. The code for multidimensional scaling (implemented in vegan as monoMDS) was contributed by Dr. Peter Minchin and is essentially the same as the code used in DECODA.
If you are interested in obtaining vegan, click here to visit Dr. Jari Oksanen's web page on vegan.
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