Program CANOCO Version 4.0 September 1997 - written by Cajo J.F. ter Braak Copyright (c) 1988-1997 Centre for Biometry Wageningen, CPRO-DLO Box 100, 6700 AC Wageningen, the Netherlands. CANOCO performs (partial) (detrended) (canonical) correspondence analysis, principal components analysis and redundancy analysis. CANOCO is an extension of Cornell Ecology program DECORANA (Hill,1979) For explanation of the input/output see the manual or Ter Braak, C.J.F. (1995) Ordination. Chapter 5 in: Data Analysis in Community and Landscape Ecology (Jongman, R.H.G., Ter Braak, C.J.F. and Van Tongeren, O.F.R., Eds) Cambridge University Press, Cambridge, UK, 91-173 pp. *** Type of analysis *** Model Gradient analysis indirect direct hybrid linear 1=PCA 2= RDA 3 unimodal 4= CA 5= CCA 6 ,, 7=DCA 8=DCCA 9 10=non-standard analysis Type analysis number Answer = 2 *** Data files *** Species data : FUNGI.DTA Covariable data : DESIGN.DTA Environmental data : DESIGN.DTA Initialization file: Forward selection of envi. variables = 0 Scaling of ordination scores = 1 Diagnostics = 1 File : FUNGI.DTA Title : 40 64sporo carps per 225 plot TC*CED** S Format : (I5,5(I5,F10.3)) No. of couplets of species number and abundance per line : 5 Sample 9 to be omitted Sample 10 to be omitted Sample 11 to be omitted Sample 12 to be omitted Sample 21 to be omitted Sample 22 to be omitted Sample 23 to be omitted Sample 24 to be omitted Sample 33 to be omitted Sample 34 to be omitted Sample 35 to be omitted Sample 36 to be omitted Sample 45 to be omitted Sample 46 to be omitted Sample 47 to be omitted Sample 48 to be omitted Number of samples 48 Number of species 40 Number of occurrences 279 File : DESIGN.DTA Title : Baars 1995 design: stands(1-6); treatments (7-9); Age(10); soil type (11-12) Format : (I5,6(I5,F6.3)) No. of covariables : 12 No interaction terms defined ****************************************************************************** Names of covariables ****************************************************************************** Podzol Areno ****************************************************************************** File : DESIGN.DTA Title : Baars 1995 design: stands(1-6); treatments (7-9); Age(10); soil type (11-12) Format : (I5,6(I5,F6.3)) No. of environmental variables : 12 No interaction terms defined ln(Ay+B)-transformation of species data A = 1.000 B = 1.000 No species-weights specified No sample-weights specified Centring/standardization by species = 1 Centring/standardization by samples = 0 No. of active samples: 48 No. of passive samples: 0 No. of active species: 33 Total sum of squares in species data = 1288.00 Total standard deviation in species data TAU = .901738 Covariable Areno is linearly dependent, hence ignored 1 **** Correlation matrix **** SPEC AX1 1.0000 SPEC AX2 .0633 1.0000 SPEC AX3 .5858 .0000 1.0000 SPEC AX4 -.0396 .0000 .0000 1.0000 ENVI AX1 .7937 .0000 .0000 .0000 1.0000 ENVI AX2 .0000 .0000 .0000 .0000 .0000 .0000 ENVI AX3 .0000 .0000 .0000 .0000 .0000 .0000 .0000 ENVI AX4 .0000 .0000 .0000 .0000 .0000 .0000 .0000 .0000 Age -.7937 .0000 .0000 .0000 -1.0000 .0000 .0000 .0000 SPEC AX1 SPEC AX2 SPEC AX3 SPEC AX4 ENVI AX1 ENVI AX2 ENVI AX3 ENVI AX4 N name (weighted) mean stand. dev. inflation factor 1 SPEC AX1 .0000 .6010 2 SPEC AX2 .0000 .5129 3 SPEC AX3 .0000 .4063 4 SPEC AX4 .0000 .2749 5 ENVI AX1 .0000 .4771 6 ENVI AX2 .0000 .0000 7 ENVI AX3 .0000 .0000 8 ENVI AX4 .0000 .0000 10 Age 2.9288 1.0373 1.0764 **** Summary **** Axes 1 2 3 4 Total variance Eigenvalues : .228 .263 .165 .076 1.000 Species-environment correlations : .794 .000 .000 .000 Cumulative percentage variance of species data : 24.2 52.1 69.7 77.7 of species-environment relation: 100.0 .0 .0 .0 Sum of all unconstrained eigenvalues .941 Sum of all canonical eigenvalues .228 The sum of all unconstrained eigenvalues is after fitting covariables Percentages are taken with respect to residual variances i.e. variances after fitting covariables *** MESSAGE *** The fit for species is additional to the fit due to covariables. With covariables, CANOCO cannot calculate residuals for samples. 1 *** Sample arrangement in permutation test *** Whole plot 1 : 1 2 3 4 5 6 7 8 Whole plot 2 : 13 14 15 16 17 18 19 20 Whole plot 3 : 25 26 27 28 29 30 31 32 Whole plot 4 : 37 38 39 40 41 42 43 44 Whole plot 5 : 49 50 51 52 53 54 55 56 Whole plot 6 : 57 58 59 60 61 62 63 64 These 6 whole plots are permuted completely at random The 8 split plots are not permuted Seeds: 23239 945 **** Summary of Monte Carlo test **** Test of significance of all canonical axes : Trace = .228 F-ratio = 14.350 P-value = .090 ( 199 permutations under reduced model)