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 96sporo carps per 225 plot TC*CED** S Format : (I5,5(I5,F10.3)) No. of couplets of species number and abundance per line : 5 No samples omitted Number of samples 72 Number of species 40 Number of occurrences 367 File : DESIGN.DTA Title : Baars 1995 design: stands(1-6); treatments (7-9); Age(10); soil type (11-12) Format : (1X,I5,(T10,10F7.2)) No. of covariables : 12 No interaction terms defined ****************************************************************************** Names of covariables ****************************************************************************** St1_Aren St2_Podz St3_Podz St4_Aren St5_Aren St6_Aren ****************************************************************************** File : DESIGN.DTA Title : Baars 1995 design: stands(1-6); treatments (7-9); Age(10); soil type (11-12) Format : (1X,I5,(T10,10F7.2)) 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: 64 No. of passive samples: 8 No. of active species: 33 Total sum of squares in species data = 1586.86 Total standard deviation in species data TAU = .866808 Covariable St6_Aren is linearly dependent, hence ignored ****** Collinearity detected when fitting variable 9 ****** 1 **** Correlation matrix **** SPEC AX1 1.0000 SPEC AX2 .0877 1.0000 SPEC AX3 -.2824 -.3295 1.0000 SPEC AX4 .3467 .2282 .0000 1.0000 ENVI AX1 .8755 .0006 .0000 .0000 1.0000 ENVI AX2 .0000 .3842 .0000 .0000 .0000 1.0000 ENVI AX3 .0000 .0000 .0000 .0000 .0000 .0000 .0000 ENVI AX4 .0000 .0000 .0000 .0000 .0000 .0000 .0000 .0000 S .8755 .0023 .0000 .0000 1.0000 .0044 .0000 .0000 A -.3768 .3465 .0000 .0000 -.4304 .9026 .0000 .0000 C -.5541 -.2978 .0000 .0000 -.6329 -.7742 .0000 .0000 SPEC AX1 SPEC AX2 SPEC AX3 SPEC AX4 ENVI AX1 ENVI AX2 ENVI AX3 ENVI AX4 S 1.0000 A -.4264 1.0000 C -.6364 -.4264 1.0000 S A C N name (weighted) mean stand. dev. inflation factor 1 SPEC AX1 .0000 .5023 2 SPEC AX2 .0000 .2003 3 SPEC AX3 .0000 .2710 4 SPEC AX4 .0000 .2515 5 ENVI AX1 .0000 .4397 6 ENVI AX2 .0000 .0770 7 ENVI AX3 .0000 .0000 8 ENVI AX4 .0000 .0000 7 S .3750 .4841 1.2500 8 A .2500 .4330 1.3750 9 C .3750 .4841 .0000 **** Summary **** Axes 1 2 3 4 Total variance Eigenvalues : .193 .006 .073 .063 1.000 Species-environment correlations : .875 .384 .000 .000 Cumulative percentage variance of species data : 34.6 35.6 48.8 60.1 of species-environment relation: 97.0 100.0 .0 .0 Sum of all unconstrained eigenvalues .559 Sum of all canonical eigenvalues .199 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 *** Specification of blocks *** *** The permutations are conditioned on 5 covariable(s), namely: *** covariable St1_Aren covariable St2_Podz covariable St3_Podz covariable St4_Aren covariable St5_Aren *** Sample arrangement in permutation test *** Samples in block 1 : 1 2 3 4 5 6 7 8 9 10 11 12 The 12 plots are permuted completely at random Samples in block 2 : 13 14 15 16 17 18 19 20 21 22 23 24 The 12 plots are permuted completely at random Samples in block 3 : 25 26 27 28 29 30 31 32 33 34 35 36 The 12 plots are permuted completely at random Samples in block 4 : 37 38 39 40 41 42 43 44 45 46 47 48 The 12 plots are permuted completely at random Samples in block 5 : 49 50 51 52 53 54 55 56 The 8 plots are permuted completely at random Samples in block 6 : 57 58 59 60 61 62 63 64 The 8 plots are permuted completely at random Seeds: 25116 22263 **** Summary of Monte Carlo test **** Test of significance of all canonical axes : Trace = .199 F-ratio = 15.512 P-value = .005 ( 199 permutations under reduced model)