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Problems with ecodist
2 messages · deyan, Sarah Goslee
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. -- View this message in context: http://r.789695.n4.nabble.com/Problems-with-ecodist-tp3225480p3225480.html Sent from the R help mailing list archive at Nabble.com. ? ? ? ?[[alternative HTML version deleted]]
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