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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