Computer Programs

Computer Programs
Marti Jane Anderson

Links to websites for
other useful programs

NOTE:
PC users should download the program files called "*.exe"
Mac users should download the program files called "*.mac.sit"

Mac or PC users should download the same file of user notes "*_UserNotes.pdf"

(Nb. Macintosh versions were compiled under an old Macintosh operating system (OS 8!) and are therefore not

guaranteed to work on modern Macintosh machines. If you have trouble opening or running the Mac versions,

it is advised that you use the PC versions instead, especially now that most modern Macs have this capability.)

Name of Program	Short Description	Click below to download relevant file
CAP 18/03/05	This program does canonical analysis of principal coordinates (canonical correlation analysis or canonical discriminant analysis) based on any distance measure as described by Anderson and Robinson (2003) and Anderson and Willis (2003). The test is done by permutation (using the trace and first canonical root statistics) and canonical axes for ordination are also given in the output.	CAP.exe CAP.mac.sit CAP_UserNotes.pdf
CONTROL CHART 07/09/08	This program calculates deviations of observations from centroids for multivariate control charts that can be used for ecological and environmental monitoring, as described in Anderson and Thompson (2008). Bootstrapping is used to put upper bounds on deviations, defining control chart criteria.	ControlChart.exe ControlChart_UserNotes.pdf (no Mac version is available)
DISTLM 16/06/05	This program calculates a distance-based multivariate multiple regression (e.g. dbRDA) for any linear model (environmental variables, codes for balanced or unbalanced ANOVA designs, etc.) on the basis of any distance measure, using permutation procedures, as described by McArdle and Anderson (2001). One has the option of including covariables in the model and of specifying sets of units to be permuted.	DISTLM.exe DISTLM.mac.sit DISTLM_UserNotes.pdf
DISTLM_forward 15/03/05	This program does a multivariate multiple regression on the basis of any distance measure and does a forward selection of the predictor variables, either individually or in specified sets, with tests by permutation (straightforward modification of DISTLM)	DISTLM_forward.exe DISTLM_forward.mac.sit DISTLM_forward_UserNotes.pdf
PERMANOVA 04/05/05 (note: formerly called NPMANOVA)	This program does permutational multivariate analysis of variance (McArdle and Anderson 2001, Anderson 2001) on the basis of any distance measure, using permutation procedures to obtain P-values for the tests (including interactions), for any balanced multi-factorial ANOVA design (up to nine factors). An option to include covariables and individual pair-wise multiple comparisons by permutation are also included.	PERMANOVA.exe PERMANOVA.mac.sit PERMANOVA_UserNotes.pdf
PERMDISP 15/03/05	This program compares within-group multivariate dispersions (spread or variability) among groups on the basis of any distance or dissimilarity measure using permutations.	PERMDISP.exe PERMDISP.mac.sit PERMDISP_UserNotes.pdf
PERMDISP2 11/08/06	PERMDISP2 is a modification of PERMDISP which handles unequal numbers of observations per group and which does tests based on distances to either centroids or spatial medians. For details, see: Anderson (2006) Biometrics 62: 245-253. Anderson et al. (2006) Ecology Letters 9: 683-693.	PERMDISP2.exe
PCO 15/03/05	This program calculates principal coordinates based on any distance measure of choice. The procedure is also known as metric multidimensional scaling. One can choose the number of axes to include in the output. One may also use the program to calculate distances among centroids based on principal coordinates.	PCO.exe PCO.mac.sit PCO_UserNotes.pdf
XMATRIX 15/03/06	This program calculates design matrices corresponding to factors or interaction terms in ANOVA designs. These can then be used with the DISTLM procedure to produce tests of responses of multivariate data to individual terms in complex ANOVA designs.	XMATRIX.exe XMATRIX.mac.sit XMATRIX_UserNotes.pdf

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Links to other useful programs for multivariate analysis of ecological (and other) data

Bob Clarke's PRIMER
Brian McArdle's MultivEcol for R
Cajo ter Braak's CANOCO
Dave Jones' MATLAB routines
Jari Oksanen's VEGAN for R
McCune and Mefford's PC-ORD
Pierre Legendre's software
Peter Henderson's Pisces conservation
The R project for statistical computing
Valerio De Patta Pillar's MULTIV
Brian Cade and Jon Richards' BLOSSOM

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