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 : weeds83.DTA Covariable data : bloctime.dta Environmental data : bloctime.dta Initialization file: Forward selection of envi. variables = 0 Scaling of ordination scores = -1 Diagnostics = 1 File : weeds83.DTA Title : ploughing time experiment B. Post; weeds in 1983 Format : (I2, 10(I3,F6.0)) No. of couplets of species number and abundance per line : 10 ***WARNING*** End of file detected in species data when reading names of species and samples No samples omitted Number of samples 12 Number of species 24 Number of occurrences 288 File : bloctime.dta Title : design Format : (1X,I5,(T10,4F2.0, 2X, 3F2.0)) No. of covariables : 7 No interaction terms defined ***** WARNING ***** Missing sample names in file with covariables ************************* ****************************************************************************** Names of covariables ****************************************************************************** block 1 block 2 block 3 block 4 ****************************************************************************** File : bloctime.dta Title : design Format : (1X,I5,(T10,4F2.0, 2X, 3F2.0)) No. of environmental variables : 7 No interaction terms defined ***** WARNING ***** Missing sample names in file with environmental variables ************************* 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: 12 No. of passive samples: 0 No. of active species: 24 Total sum of squares in species data = 124.466 Total standard deviation in species data TAU = .657400 Covariable block 4 is linearly dependent, hence ignored ****** Collinearity detected when fitting variable 7 ****** 1 **** Correlation matrix **** SPEC AX1 1.0000 SPEC AX2 -.1065 1.0000 SPEC AX3 -.2481 .5203 1.0000 SPEC AX4 .0521 -.3930 .0000 1.0000 ENVI AX1 .9229 .0000 .0000 .0000 1.0000 ENVI AX2 .0000 .7273 .0000 .0000 .0000 1.0000 ENVI AX3 .0000 .0000 .0000 .0000 .0000 .0000 .0000 ENVI AX4 .0000 .0000 .0000 .0000 .0000 .0000 .0000 .0000 pltime 1 .9211 -.0442 .0000 .0000 .9981 -.0608 .0000 .0000 pltime 2 -.5092 -.6066 .0000 .0000 -.5518 -.8340 .0000 .0000 pltime 3 -.4120 .6508 .0000 .0000 -.4464 .8948 .0000 .0000 SPEC AX1 SPEC AX2 SPEC AX3 SPEC AX4 ENVI AX1 ENVI AX2 ENVI AX3 ENVI AX4 pltime 1 1.0000 pltime 2 -.5000 1.0000 pltime 3 -.5000 -.5000 1.0000 pltime 1 pltime 2 pltime 3 N name (weighted) mean stand. dev. inflation factor 1 SPEC AX1 .0000 .4365 2 SPEC AX2 .0000 .3402 3 SPEC AX3 .0000 .3814 4 SPEC AX4 .0000 .2604 5 ENVI AX1 .0000 .4028 6 ENVI AX2 .0000 .2474 7 ENVI AX3 .0000 .0000 8 ENVI AX4 .0000 .0000 5 pltime 1 .3333 .4714 1.3333 6 pltime 2 .3333 .4714 1.3333 7 pltime 3 .3333 .4714 .0000 **** Summary **** Axes 1 2 3 4 Total variance Eigenvalues : .162 .061 .145 .068 1.000 Species-environment correlations : .923 .727 .000 .000 Cumulative percentage variance of species data : 30.1 41.4 68.4 81.0 of species-environment relation: 72.6 100.0 .0 .0 Sum of all unconstrained eigenvalues .539 Sum of all canonical eigenvalues .223 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 3 covariable(s), namely: *** covariable block 1 covariable block 2 covariable block 3 *** Sample arrangement in permutation test *** Samples in block 1 : 1 2 3 The 3 plots are permuted completely at random Samples in block 2 : 5 6 7 The 3 plots are permuted completely at random Samples in block 3 : 9 10 11 The 3 plots are permuted completely at random Samples in block 4 : 13 14 15 The 3 plots are permuted completely at random Seeds: 23239 945 Number of permutations= 199 *** Permutation under reduced model *** No F-ratio F-ratio of axis 1 Data 2.123 2.582 1 .549 .611 2 .483 .549 3 .652 1.089 4 1.577 1.765 5 1.022 1.066 6 .823 .824 7 .841 .921 8 1.525 1.910 9 .749 .896 10 1.185 1.855 11 1.408 1.411 12 .998 1.082 13 1.372 1.512 14 1.273 1.669 15 1.359 1.806 16 .699 .972 17 1.539 1.474 18 1.183 1.445 19 .811 .878 20 1.263 1.636 21 .913 1.008 22 .895 1.087 23 .984 1.641 24 .936 .841 25 1.253 1.531 26 .772 .884 27 .895 1.087 28 .981 1.274 29 .798 1.191 30 .972 1.003 31 .747 1.101 32 1.025 1.636 33 .852 1.339 34 .993 1.134 35 1.216 1.615 36 .633 .851 37 .699 .972 38 1.546 2.003 39 2.227 2.708 40 1.126 1.304 41 1.085 1.020 42 1.546 2.003 43 .810 .849 44 1.329 1.501 45 .749 .896 46 .864 1.423 47 1.472 1.485 48 .731 .819 49 .760 1.135 50 .801 1.103 51 .660 .705 52 1.408 1.411 53 .618 .899 54 1.508 1.686 55 1.372 1.512 56 1.275 1.642 57 .800 .793 58 .889 .998 59 1.130 1.788 60 .933 .960 61 .618 .899 62 1.087 1.232 63 .917 1.038 64 .998 1.082 65 1.253 1.531 66 1.067 1.729 67 .751 1.068 68 1.437 1.725 69 .765 .771 70 2.420 2.682 71 .760 1.135 72 .851 .988 73 .543 .603 74 1.058 1.666 75 .888 1.055 76 1.145 1.774 77 .917 1.038 78 1.036 1.566 79 .998 1.004 80 .973 1.686 81 .802 .879 82 .592 .721 83 1.036 1.566 84 1.185 1.855 85 .739 1.030 86 1.006 1.162 87 .746 1.019 88 1.130 1.788 89 1.072 1.582 90 1.487 1.525 91 .816 1.105 92 .800 .793 93 1.143 1.062 94 .618 .899 95 .818 .888 96 1.893 2.577 97 1.022 1.066 98 1.346 1.617 99 .893 .950 100 .673 .833 101 1.006 1.162 102 1.437 1.725 103 1.037 1.332 104 .889 .998 105 .816 1.105 106 1.332 1.715 107 1.220 1.257 108 1.605 1.549 109 1.253 1.929 110 .673 .833 111 1.192 1.353 112 1.038 1.578 113 1.022 1.066 114 .592 .721 115 2.420 2.682 116 1.067 1.729 117 .755 .821 118 .601 .757 119 1.008 1.026 120 .670 .823 121 .977 1.320 122 1.652 1.679 123 1.054 1.189 124 .984 1.641 125 .939 .920 126 .902 1.373 127 .543 .603 128 1.180 1.234 129 1.067 1.729 130 .749 .896 131 1.346 1.617 132 .731 .819 133 .893 .950 134 1.110 1.842 135 .998 1.082 136 .880 1.077 137 .818 .888 138 .749 .896 139 .858 1.204 140 .739 1.030 141 .699 .972 142 1.006 1.162 143 .889 .806 144 .960 1.184 145 .909 1.208 146 1.332 1.715 147 .810 .849 148 .857 .875 149 .699 .972 150 .683 .750 151 .721 .970 152 2.123 2.582 153 1.145 1.774 154 1.524 1.977 155 .858 1.204 156 .933 .960 157 1.255 1.101 158 1.329 1.501 159 .880 1.077 160 1.487 1.525 161 .893 .950 162 .777 .804 163 1.346 1.617 164 .755 .821 165 1.546 2.003 166 .951 1.258 167 1.484 1.594 168 1.546 2.003 169 .670 .823 170 1.216 1.615 171 .739 1.030 172 .972 1.003 173 1.229 1.578 174 1.216 1.615 175 .936 .841 176 .483 .549 177 .800 .793 178 .678 .694 179 2.227 2.708 180 1.185 1.855 181 .618 .899 182 .819 1.189 183 .661 .679 184 .960 1.184 185 1.253 1.531 186 1.219 1.593 187 .933 .903 188 1.220 1.257 189 .801 1.103 190 1.126 1.304 191 1.244 1.782 192 .868 1.034 193 1.216 1.615 194 .868 1.034 195 .771 .796 196 .892 1.273 197 .811 1.084 198 1.025 1.234 199 1.130 1.788 P-value .030 .030 (number of permutations= 199) **** Summary of Monte Carlo test **** Test of significance of first canonical axis: eigenvalue = .16 F-ratio = 2.58 P-value = .03 Overall test : Trace = .22 F-ratio = 2.12 P-value = .03 ( 199 permutations under reduced model)