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 : SPECIES.DTA Covariable data : PONDTIME.DTA Environmental data : toxicant.DTA Initialization file: Forward selection of envi. variables = 0 Scaling of ordination scores = 1 Diagnostics = 1 File : SPECIES.DTA Title : species data of BACI basin experiment 88 NET (van Wijngaarden, SC-DLO) Format : (I7,17F4.0/7X,17F4.0/7X,17F4.0/43X,8F4.0) No. of couplets of species number and abundance per line : 0 No samples omitted Number of samples 30 Number of species 59 Number of occurrences 456 File : PONDTIME.DTA Title : covariables basins 88 (for correction for pond and time differences) Format : (I2,1X,14(F2.0)) No. of covariables : 13 No interaction terms defined ****************************************************************************** Names of covariables ****************************************************************************** c-pond l-pond h-pond t1 t2 t3 t4 t5 t6 t7 t8 t9 t10 ****************************************************************************** File : toxicant.DTA Title : treatment dummy variables with toxlevel (0,1,2) for control low,high basins Format : (1X,I5,(T10,17F4.0)) No. of environmental variables : 4 No interaction terms defined ln(Ay+B)-transformation of species data A = 1.000 B = 1.000 Weight .00 is given to species 8 No sample-weights specified Centring/standardization by species = 1 Centring/standardization by samples = 0 No. of active samples: 30 No. of passive samples: 0 No. of active species: 58 Total sum of squares in species data = 646.971 Total standard deviation in species data TAU = .609773 Covariable h-pond is linearly dependent, hence ignored Covariable t10 is linearly dependent, hence ignored 1 **** Correlation matrix **** SPEC AX1 1.0000 SPEC AX2 .2778 1.0000 SPEC AX3 .1895 .0000 1.0000 SPEC AX4 -.1775 .0000 .0000 1.0000 ENVI AX1 .8935 .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 toxlevel .8935 .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 .2426 2 SPEC AX2 .0000 .2373 3 SPEC AX3 .0000 .1890 4 SPEC AX4 .0000 .1707 5 ENVI AX1 .0000 .2168 6 ENVI AX2 .0000 .0000 7 ENVI AX3 .0000 .0000 8 ENVI AX4 .0000 .0000 4 toxlevel .4000 .7118 3.1667 **** Summary **** Axes 1 2 3 4 Total variance Eigenvalues : .047 .056 .036 .029 1.000 Species-environment correlations : .893 .000 .000 .000 Cumulative percentage variance of species data : 14.7 32.3 43.5 52.6 of species-environment relation: 100.0 .0 .0 .0 Sum of all unconstrained eigenvalues .320 Sum of all canonical eigenvalues .047 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 : ** Time series or line of plots ** 1 4 7 10 13 16 19 22 25 28 Whole plot 2 : ** Time series or line of plots ** 2 5 8 11 14 17 20 23 26 29 Whole plot 3 : ** Time series or line of plots ** 3 6 9 12 15 18 21 24 27 30 These 3 whole plots are permuted completely at random The 10 split plots are permuted using cyclic shifts using the same permutation in each whole plot Seeds: 23239 945 **** Summary of Monte Carlo test **** Test of significance of all canonical axes : Trace = .047 F-ratio = 2.931 P-value = .045 ( 199 permutations under reduced model)