[R] Problems with ecodist

Sarah Goslee sarah.goslee at gmail.com
Thu Jan 20 12:56:12 CET 2011


Hi,

If you read the help for mantel, it says that the data must be either
vectors of dissimilarities or objects of class dist. Since you are
reading in your data as full symmetric matrices, you have two options:
> mantel(as.dist(distancematrix) ~ as.dist(distancematrix1))
    mantelr       pval1       pval2       pval3   llim.2.5%  ulim.97.5%
 0.07596818  0.29100000  0.71000000  0.73000000 -0.02049799  0.22440245
> mantel(lower(distancematrix) ~ lower(distancematrix1))
    mantelr       pval1       pval2       pval3   llim.2.5%  ulim.97.5%
 0.07596818  0.31400000  0.68700000  0.74000000 -0.03329888  0.20299330

Sarah

On Thu, Jan 20, 2011 at 3:03 AM, deyan <gedy at ioz.ac.cn> wrote:
>
> 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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-- 
Sarah Goslee
http://www.stringpage.com
http://www.astronomicum.com
http://www.functionaldiversity.org



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