[Fri Jan 23 10:25:22 1998] Log file cleared [Fri Jan 23 10:25:38 1998] Settings changed [Fri Jan 23 10:25:39 1998] Running CANOCO: [Fri Jan 23 10:25:39 1998] CON file [C:\canoco\samples\BACIMSPE\logratio.con] saved [Fri Jan 23 10:25:53 1998] CON file [C:\canoco\samples\BACIMSPE\logratio.con] saved Program CANOCO Version 4.0 September 1997 - written by Cajo J.F. Ter Braak Copyright (c) 1988-1997 Centre for Biometry, 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 : TREATMNT.DTA Initialization file: Forward selection of envi. variables = 0 Scaling of ordination scores = 1 Diagnostics = 1 File : SPECIES.DTA Title : species data from 2 ponds (control, high dose) at 10 time points bassinexperime Format : (I5,6(I5,F6.0)) No. of couplets of species number and abundance per line : 6 No samples omitted Number of samples 20 Number of species 59 Number of occurrences 327 File : PONDTIME.DTA Title : covariabelen bassins 88 (voor correctie tijd- en pondeffecten) Format : (I5,8(I5,F4.0)) No. of covariables : 12 No interaction terms defined ****************************************************************************** Names of covariables ****************************************************************************** c-pond h-pond t1 t2 t3 t4 t5 t6 t7 t8 t9 t10 ****************************************************************************** File : TREATMNT.DTA Title : dummy milieuvariabelen bassins 88 Format : (I5,8(I5,F4.0)) No. of environmental variables : 2 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 = 1 No. of active samples: 20 No. of passive samples: 0 No. of active species: 57 Total sum of squares in species data = 575.959 Total standard deviation in species data TAU = .710794 (after site centering/standardization, if in force) Covariable h-pond is linearly dependent, hence ignored Covariable t10 is linearly dependent, hence ignored ****** Collinearity detected when fitting variable 2 ****** 1 **** Correlation matrix **** SPEC AX1 1.0000 SPEC AX2 -.1034 1.0000 SPEC AX3 -.2024 .0000 1.0000 SPEC AX4 -.0591 .0000 .0000 1.0000 ENVI AX1 .9580 .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 high -.9580 .0000 .0000 .0000 -1.0000 .0000 .0000 .0000 control .9580 .0000 .0000 .0000 1.0000 .0000 .0000 .0000 SPEC AX1 SPEC AX2 SPEC AX3 SPEC AX4 ENVI AX1 ENVI AX2 ENVI AX3 ENVI AX4 high 1.0000 control -1.0000 1.0000 high control N name (weighted) mean stand. dev. inflation factor 1 SPEC AX1 .0000 .3087 2 SPEC AX2 .0000 .2185 3 SPEC AX3 .0000 .1803 4 SPEC AX4 .0000 .1671 5 ENVI AX1 .0000 .2958 6 ENVI AX2 .0000 .0000 7 ENVI AX3 .0000 .0000 8 ENVI AX4 .0000 .0000 1 high .2000 .4000 2.6667 2 control .8000 .4000 .0000 **** Summary **** Axes 1 2 3 4 Total variance Eigenvalues : .087 .048 .033 .028 1.000 Species-environment correlations : .958 .000 .000 .000 Cumulative percentage variance of species data : 33.3 51.5 63.8 74.4 of species-environment relation: 100.0 .0 .0 .0 Sum of all unconstrained eigenvalues .263 Sum of all canonical eigenvalues .087 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 3 5 7 9 11 13 15 17 19 Whole plot 2 : ** Time series or line of plots ** 2 4 6 8 10 12 14 16 18 20 These 2 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 Number of permutations= 199 *** Permutation under reduced model *** No F-ratio F-ratio of axis 1 Data 3.991 .000 1 1.238 .000 2 1.263 .000 3 2.050 .000 4 1.263 .000 5 2.014 .000 6 3.991 .000 7 .903 .000 8 2.283 .000 9 2.283 .000 10 1.263 .000 11 1.263 .000 12 .903 .000 13 .903 .000 14 1.238 .000 15 2.013 .000 16 1.263 .000 17 .903 .000 18 2.050 .000 19 1.238 .000 20 1.263 .000 21 3.991 .000 22 2.013 .000 23 2.013 .000 24 2.014 .000 25 3.991 .000 26 1.238 .000 27 2.283 .000 28 2.050 .000 29 .903 .000 30 1.165 .000 31 1.263 .000 32 1.263 .000 33 1.263 .000 34 3.991 .000 35 2.283 .000 36 1.038 .000 37 2.283 .000 38 1.238 .000 39 1.038 .000 40 2.013 .000 41 2.050 .000 42 1.263 .000 43 1.263 .000 44 2.014 .000 45 .903 .000 46 1.165 .000 47 2.014 .000 48 2.050 .000 49 2.014 .000 50 1.165 .000 51 1.038 .000 52 2.050 .000 53 2.283 .000 54 1.038 .000 55 3.991 .000 56 1.038 .000 57 2.013 .000 58 1.038 .000 59 2.013 .000 60 1.263 .000 61 2.050 .000 62 1.165 .000 63 .903 .000 64 1.238 .000 65 1.263 .000 66 1.238 .000 67 1.263 .000 68 1.165 .000 69 2.013 .000 70 1.238 .000 71 2.013 .000 72 2.283 .000 73 2.283 .000 74 1.038 .000 75 2.283 .000 76 3.991 .000 77 2.013 .000 78 .903 .000 79 2.013 .000 80 2.013 .000 81 2.014 .000 82 1.165 .000 83 2.014 .000 84 3.991 .000 85 1.263 .000 86 2.014 .000 87 1.038 .000 88 2.013 .000 89 1.165 .000 90 2.050 .000 91 2.013 .000 92 1.238 .000 93 1.038 .000 94 2.050 .000 95 .903 .000 96 2.013 .000 97 .903 .000 98 1.238 .000 99 2.283 .000 100 2.014 .000 101 3.991 .000 102 .903 .000 103 2.283 .000 104 1.165 .000 105 2.013 .000 106 1.165 .000 107 1.165 .000 108 2.283 .000 109 2.014 .000 110 2.014 .000 111 2.014 .000 112 1.038 .000 113 2.283 .000 114 2.013 .000 115 .903 .000 116 2.013 .000 117 2.283 .000 118 2.013 .000 119 1.263 .000 120 1.165 .000 121 3.991 .000 122 2.050 .000 123 1.038 .000 124 2.283 .000 125 1.238 .000 126 3.991 .000 127 1.238 .000 128 1.238 .000 129 1.263 .000 130 1.263 .000 131 1.238 .000 132 2.014 .000 133 1.165 .000 134 3.991 .000 135 1.038 .000 136 1.263 .000 137 2.050 .000 138 1.263 .000 139 2.050 .000 140 3.991 .000 141 .903 .000 142 1.038 .000 143 .903 .000 144 2.283 .000 145 .903 .000 146 2.014 .000 147 1.165 .000 148 3.991 .000 149 2.013 .000 150 .903 .000 151 .903 .000 152 2.283 .000 153 1.238 .000 154 1.238 .000 155 1.038 .000 156 1.238 .000 157 1.165 .000 158 1.238 .000 159 3.991 .000 160 .903 .000 161 1.238 .000 162 3.991 .000 163 2.283 .000 164 3.991 .000 165 .903 .000 166 1.263 .000 167 2.013 .000 168 1.263 .000 169 2.283 .000 170 1.038 .000 171 .903 .000 172 .903 .000 173 2.050 .000 174 1.263 .000 175 2.283 .000 176 1.038 .000 177 1.263 .000 178 3.991 .000 179 1.165 .000 180 .903 .000 181 .903 .000 182 1.165 .000 183 1.165 .000 184 3.991 .000 185 1.038 .000 186 1.165 .000 187 1.038 .000 188 2.014 .000 189 2.283 .000 190 1.165 .000 191 2.014 .000 192 1.263 .000 193 2.050 .000 194 1.263 .000 195 2.014 .000 196 .903 .000 197 2.283 .000 198 2.013 .000 199 2.050 .000 P-value .095 1.000 (number of permutations= 199) **** Summary of Monte Carlo test **** Overall test : Trace = .09 F-ratio = 3.99 P-value = .09 ( 199 permutations under reduced model) [Fri Jan 23 10:26:00 1998] CANOCO call succeeded [Fri Jan 23 10:26:01 1998] Running CANOCO: [Fri Jan 23 10:26:05 1998] CON file [C:\canoco\samples\BACIMSPE\logratio.con] saved Program CANOCO Version 4.0 September 1997 - written by Cajo J.F. Ter Braak Copyright (c) 1988-1997 Centre for Biometry, 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 : TREATMNT.DTA Initialization file: Forward selection of envi. variables = 0 Scaling of ordination scores = 1 Diagnostics = 1 File : SPECIES.DTA Title : species data from 2 ponds (control, high dose) at 10 time points bassinexperime Format : (I5,6(I5,F6.0)) No. of couplets of species number and abundance per line : 6 No samples omitted Number of samples 20 Number of species 59 Number of occurrences 327 File : PONDTIME.DTA Title : covariabelen bassins 88 (voor correctie tijd- en pondeffecten) Format : (I5,8(I5,F4.0)) No. of covariables : 12 No interaction terms defined ****************************************************************************** Names of covariables ****************************************************************************** c-pond h-pond t1 t2 t3 t4 t5 t6 t7 t8 t9 t10 ****************************************************************************** File : TREATMNT.DTA Title : dummy milieuvariabelen bassins 88 Format : (I5,8(I5,F4.0)) No. of environmental variables : 2 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 = 1 No. of active samples: 20 No. of passive samples: 0 No. of active species: 57 Total sum of squares in species data = 575.959 Total standard deviation in species data TAU = .710794 (after site centering/standardization, if in force) Covariable h-pond is linearly dependent, hence ignored Covariable t10 is linearly dependent, hence ignored ****** Collinearity detected when fitting variable 2 ****** 1 **** Correlation matrix **** SPEC AX1 1.0000 SPEC AX2 -.1034 1.0000 SPEC AX3 -.2024 .0000 1.0000 SPEC AX4 -.0591 .0000 .0000 1.0000 ENVI AX1 .9580 .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 high -.9580 .0000 .0000 .0000 -1.0000 .0000 .0000 .0000 control .9580 .0000 .0000 .0000 1.0000 .0000 .0000 .0000 SPEC AX1 SPEC AX2 SPEC AX3 SPEC AX4 ENVI AX1 ENVI AX2 ENVI AX3 ENVI AX4 high 1.0000 control -1.0000 1.0000 high control N name (weighted) mean stand. dev. inflation factor 1 SPEC AX1 .0000 .3087 2 SPEC AX2 .0000 .2185 3 SPEC AX3 .0000 .1803 4 SPEC AX4 .0000 .1671 5 ENVI AX1 .0000 .2958 6 ENVI AX2 .0000 .0000 7 ENVI AX3 .0000 .0000 8 ENVI AX4 .0000 .0000 1 high .2000 .4000 2.6667 2 control .8000 .4000 .0000 **** Summary **** Axes 1 2 3 4 Total variance Eigenvalues : .087 .048 .033 .028 1.000 Species-environment correlations : .958 .000 .000 .000 Cumulative percentage variance of species data : 33.3 51.5 63.8 74.4 of species-environment relation: 100.0 .0 .0 .0 Sum of all unconstrained eigenvalues .263 Sum of all canonical eigenvalues .087 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 3 5 7 9 11 13 15 17 19 Whole plot 2 : ** Time series or line of plots ** 2 4 6 8 10 12 14 16 18 20 These 2 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 Number of permutations= 199 *** Permutation under reduced model *** No F-ratio F-ratio of axis 1 Data 3.991 .000 1 1.238 .000 2 1.263 .000 3 2.050 .000 4 1.263 .000 5 2.014 .000 6 3.991 .000 7 .903 .000 8 2.283 .000 9 2.283 .000 10 1.263 .000 11 1.263 .000 12 .903 .000 13 .903 .000 14 1.238 .000 15 2.013 .000 16 1.263 .000 17 .903 .000 18 2.050 .000 19 1.238 .000 20 1.263 .000 21 3.991 .000 22 2.013 .000 23 2.013 .000 24 2.014 .000 25 3.991 .000 26 1.238 .000 27 2.283 .000 28 2.050 .000 29 .903 .000 30 1.165 .000 31 1.263 .000 32 1.263 .000 33 1.263 .000 34 3.991 .000 35 2.283 .000 36 1.038 .000 37 2.283 .000 38 1.238 .000 39 1.038 .000 40 2.013 .000 41 2.050 .000 42 1.263 .000 43 1.263 .000 44 2.014 .000 45 .903 .000 46 1.165 .000 47 2.014 .000 48 2.050 .000 49 2.014 .000 50 1.165 .000 51 1.038 .000 52 2.050 .000 53 2.283 .000 54 1.038 .000 55 3.991 .000 56 1.038 .000 57 2.013 .000 58 1.038 .000 59 2.013 .000 60 1.263 .000 61 2.050 .000 62 1.165 .000 63 .903 .000 64 1.238 .000 65 1.263 .000 66 1.238 .000 67 1.263 .000 68 1.165 .000 69 2.013 .000 70 1.238 .000 71 2.013 .000 72 2.283 .000 73 2.283 .000 74 1.038 .000 75 2.283 .000 76 3.991 .000 77 2.013 .000 78 .903 .000 79 2.013 .000 80 2.013 .000 81 2.014 .000 82 1.165 .000 83 2.014 .000 84 3.991 .000 85 1.263 .000 86 2.014 .000 87 1.038 .000 88 2.013 .000 89 1.165 .000 90 2.050 .000 91 2.013 .000 92 1.238 .000 93 1.038 .000 94 2.050 .000 95 .903 .000 96 2.013 .000 97 .903 .000 98 1.238 .000 99 2.283 .000 100 2.014 .000 101 3.991 .000 102 .903 .000 103 2.283 .000 104 1.165 .000 105 2.013 .000 106 1.165 .000 107 1.165 .000 108 2.283 .000 109 2.014 .000 110 2.014 .000 111 2.014 .000 112 1.038 .000 113 2.283 .000 114 2.013 .000 115 .903 .000 116 2.013 .000 117 2.283 .000 118 2.013 .000 119 1.263 .000 120 1.165 .000 121 3.991 .000 122 2.050 .000 123 1.038 .000 124 2.283 .000 125 1.238 .000 126 3.991 .000 127 1.238 .000 128 1.238 .000 129 1.263 .000 130 1.263 .000 131 1.238 .000 132 2.014 .000 133 1.165 .000 134 3.991 .000 135 1.038 .000 136 1.263 .000 137 2.050 .000 138 1.263 .000 139 2.050 .000 140 3.991 .000 141 .903 .000 142 1.038 .000 143 .903 .000 144 2.283 .000 145 .903 .000 146 2.014 .000 147 1.165 .000 148 3.991 .000 149 2.013 .000 150 .903 .000 151 .903 .000 152 2.283 .000 153 1.238 .000 154 1.238 .000 155 1.038 .000 156 1.238 .000 157 1.165 .000 158 1.238 .000 159 3.991 .000 160 .903 .000 161 1.238 .000 162 3.991 .000 163 2.283 .000 164 3.991 .000 165 .903 .000 166 1.263 .000 167 2.013 .000 168 1.263 .000 169 2.283 .000 170 1.038 .000 171 .903 .000 172 .903 .000 173 2.050 .000 174 1.263 .000 175 2.283 .000 176 1.038 .000 177 1.263 .000 178 3.991 .000 179 1.165 .000 180 .903 .000 181 .903 .000 182 1.165 .000 183 1.165 .000 184 3.991 .000 185 1.038 .000 186 1.165 .000 187 1.038 .000 188 2.014 .000 189 2.283 .000 190 1.165 .000 191 2.014 .000 192 1.263 .000 193 2.050 .000 194 1.263 .000 195 2.014 .000 196 .903 .000 197 2.283 .000 198 2.013 .000 199 2.050 .000 P-value .095 1.000 (number of permutations= 199) **** Summary of Monte Carlo test **** Overall test : Trace = .09 F-ratio = 3.99 P-value = .09 ( 199 permutations under reduced model) [Fri Jan 23 10:26:12 1998] CANOCO call succeeded