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PC-ORD TM Multivariate Analysis of Ecological Data
Version 6
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McCune, B. and M. J. Mefford. 2011. PC-ORD. Multivariate Analysis of
Ecological Data. Version 6. MjM Software, Gleneden Beach, Oregon, U.S.A. Cover: The esnce of multivariate analysis is the extraction of a small number of important relationships from a very large number of possible relationships. Waiver: Although the software has been carefully tested, the ur accepts and us the program material as it is, at the ur’s own risk, relying solely upon his/her own inspection of the program material and without reliance upon any reprentation or description concerning the program material. Neither MjM Software Design nor associated individuals make any expresd or implied warranty of any kind with regard to the program material, and shall have no liability or responsibility to any recipient with respect to any liability, loss, or damage that directly or indirectly aris out of the u of the disk and the programs and/or subroutines contained on the disk, including, but not limited to, any loss of business or loss of data or other incidental or conquential damages. By using this software you agree to this.
© 1991, 1993, 1995, 1997, 1999, 2006, 2011 MjM Software Design
© 1991, 1993, 1995, 1997, 1999, 2006, 2011 Bruce McCune
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Printed in the United States of America.
Contents
What is PC-ORD For?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4 Where is the Manual? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5 How Do I Get Started?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5 Managing Files and Projects . . . . . . . . . . . . . . . . . . . . . . . . . . . .5 System Requirements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6 Network Environments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7 Limitations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9 Technical Help. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10 Updates and Fixes . . . . . . . . . . . . . . . . . . . . . . . . . . .10
Contact Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10 Using PC-ORD: a Brief Overview . . . . . . . . . . . . . . . . . . . . . .11
1. Prepare Your Data . . . . . . . . . . . . . . . . . . . . . . . .11
2. Open Your Data Files . . . . . . . . . . . . . . . . . . . . . .14
3. Run an Analysis . . . . . . . . . . . . . . . . . . . . . . . . . .15
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4. Explore Your Results Graphically. . . . . . . . . . . . .18 Other Graph Types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .22 A Decision Tree for Beginners. . . . . . . . . . . . . . . . . . . . . . . . . .27 Batch Commands for Advanced Urs . . . . . . . . . . . . . . . . . . .28
What is PC-ORD For?
PC-ORD is a Windows program for multivariate analysis of ecological data entered in spreadsheets. The terminology in the software is tailored for ecologists. We emphasize nonparametric tools, graphical reprentation, and randomization tests for analysis of community data. In addition to utilities for transforming
data and managing fi les, PC-ORD offers many ordination and classifi cation techniques not available in major statistical packages including: CCA, DCA, MRPP, perMANOV A, two-way clustering, TWINSPAN, Beals smoothing, diversity indices, species lists, Mantel test, many ordination overlay methods (quantitative, symbol-coding, color-coding, grid, joint plot, biplot, successional vector), various rotation methods, 3D ordination graphics, indicator species analysis, Bray-Curtis ordination, city-block distance measures, species-area curves, tree data summaries, publication-quality dendrograms, and autopilot NMS.
Very large data ts can be analyzed. Most operations accept a matrix up to 32,000 rows or 32,000 columns and up to 536,848,900 matrix elements, provided that your computer has adequate memory.
Virtually any multivariate data t consisting of a t of entities, each with a number of measured attributes, is adaptable to PC-ORD. In community ecology, the fi rst matrix will often contain species abundance data in a t of samples. The possible formats for entering the data can be found in Data Preparation in the software help system. In addition to this main matrix, a cond matrix, often containing environmental data, can be entered for analysis of its relationship to
the fi rst matrix. The inclusion of this cond matrix greatly enriches the system’s analytical capabilities. Both matrices are displayed in PC-ORD in fi le viewing windows.
In studies of species traits or functional groups, one of the matrices contains traits or relative u of a t of resources by various species, subspecies, or individuals. A matrix of sites × functional groups or sites × traits can be produced by multiplying a community matrix by the functional group or trait matrix. Where is the Manual?
The full manual is built into PC-ORD, so we have not produced a paper manual. Our context-nsiti
ve Help system can be accesd at any time by pressing F1 or clicking a Help button.
How Do I Get Started?
After you install the software, click on Help | Contents in the main menu. Then navigate to Getting Started in the help system. The most important topics to read at fi rst are:
Data Preparation,
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Spreadsheet Format, and
Typical Flow of Analysis
Managing Files and Projects
Normally you will want to keep your data and results in a folder that is parate from the folder that contains PC-ORD. If you have more than one PC-ORD project, you can keep the fi les from each project in a parate folder or put them in a single folder. PC-ORD helps you resume work where you left off with the File | Open Project and File | Save Project menu items. Details of how PC-ORD manages
