[R] Problems with ecodist

deyan
Thu, 20 Jan 2011 08:03:10 -0000

Dear Dr.Goslee and anyone may intrested in matrix manipulate,
I am using your ecodist to do mantel and partial mantel test, I have
locality data and shape variation data, and the two distance matrixs are
given as belowings. When I run the analysis, it is always report that the
matrix is not square, but I didn't know what's wrong with my data. Would
you
please help me on this. I am quite new to R.

Thanks.

> distancematrix <- as.matrix(read.table("test1.txt"))
> distancematrix1 <- as.matrix(read.table("test2.txt"))
> distancematrix1
          Loc1      Loc2      Loc3      Loc4       Loc5       Loc6     Loc7
Loc8     Loc9    Loc10     Loc11      Loc12
Loc1     0.000 2293.8671 2180.7127  7563.934  2494.5049  2522.3946 5953.609
2511.5994 2047.683 4448.721  3180.844  3112.6798
Loc2  2293.867    0.0000  443.2497  9831.220   472.2009   397.4316 8213.580
1114.9120 2087.877 6723.807  2407.192  1314.6927
Loc3  2180.713  443.2497    0.0000  9620.263   915.4497   836.5849 8001.565
708.1212 2377.024 6627.808  2818.822  1063.8092
Loc4  7563.934 9831.2199 9620.2627     0.000 10057.8311 10085.8054 1619.041
9639.4505 8967.156 3482.672 10046.113 10253.9565
Loc5  2494.505  472.2009  915.4497 10057.831     0.0000   112.6242 8448.063
1569.7006 1846.755 6845.471  1983.525  1670.4862
Loc6  2522.395  397.4316  836.5849 10085.805   112.6242     0.0000 8473.279
1473.1610 1951.517 6897.051  2092.925  1558.8962
Loc7  5953.609 8213.5803 8001.5652  1619.041  8448.0626  8473.2789    0.000
8034.9093 7447.264 2171.838  8568.467  8654.3923
Loc8  2511.599 1114.9120  708.1212  9639.451  1569.7006  1473.1610 8034.909
0.0000 3064.747 6870.287  3518.951   631.5406
Loc9  2047.683 2087.8774 2377.0240  8967.156  1846.7549  1951.5175 7447.264
3064.7466    0.000 5528.956  1182.826  3397.4896
Loc10 4448.721 6723.8068 6627.8081  3482.672  6845.4709  6897.0513 2171.838
6870.2865 5528.956    0.000  6572.264  7497.8614
Loc11 3180.844 2407.1921 2818.8222 10046.113  1983.5246  2092.9254 8568.467
3518.9508 1182.826 6572.264     0.000  3647.8307
Loc12 3112.680 1314.6927 1063.8092 10253.957  1670.4862  1558.8962 8654.392
631.5406 3397.490 7497.861  3647.831     0.0000
> distancematrix
         sample1 sample2 sample3 sample4 sample5 sample6 sample7 sample8
sample9 sample10 sample11 sample12
sample1   0.0000  0.0229  0.0258  0.0394  0.0295  0.0337  0.0269  0.0345
0.0314   0.0418   0.0577   0.0853
sample2   0.0229  0.0000  0.0219  0.0373  0.0337  0.0352  0.0320  0.0310
0.0275   0.0508   0.0533   0.0739
sample3   0.0258  0.0219  0.0000  0.0349  0.0375  0.0332  0.0309  0.0233
0.0246   0.0522   0.0539   0.0748
sample4   0.0394  0.0373  0.0349  0.0000  0.0590  0.0514  0.0356  0.0321
0.0354   0.0737   0.0365   0.0652
sample5   0.0295  0.0337  0.0375  0.0590  0.0000  0.0311  0.0482  0.0474
0.0401   0.0331   0.0726   0.0931
sample6   0.0337  0.0352  0.0332  0.0514  0.0311  0.0000  0.0406  0.0362
0.0363   0.0429   0.0708   0.0903
sample7   0.0269  0.0320  0.0309  0.0356  0.0482  0.0406  0.0000  0.0359
0.0370   0.0536   0.0625   0.0888
sample8   0.0345  0.0310  0.0233  0.0321  0.0474  0.0362  0.0359  0.0000
0.0267   0.0649   0.0498   0.0662
sample9   0.0314  0.0275  0.0246  0.0354  0.0401  0.0363  0.0370  0.0267
0.0000   0.0569   0.0583   0.0693
sample10  0.0418  0.0508  0.0522  0.0737  0.0331  0.0429  0.0536  0.0649
0.0569   0.0000   0.0919   0.1150
sample11  0.0577  0.0533  0.0539  0.0365  0.0726  0.0708  0.0625  0.0498
0.0583   0.0919   0.0000   0.0601
sample12  0.0853  0.0739  0.0748  0.0652  0.0931  0.0903  0.0888  0.0662
0.0693   0.1150   0.0601   0.0000
> mantel(distancematrix~distancematrix1)
error mantel(distancematrix ~ distancematrix1) : Matrix not square.
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