[R] Problems with ecodist

Sarah Goslee
Thu, 20 Jan 2011 11:56:12 -0000

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