Hi, okay thanks. I've attempted the commands you suggested (I have provided all of the dput results - I am not sure how to provide a "smaller" example). I hope this is ok.
> sessionInfo() R version 2.14.2 (2012-02-29) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ape_3.0-1 loaded via a namespace (and not attached): [1] gee_4.13-17 grid_2.14.2 lattice_0.20-0 nlme_3.1-103 > dput(Geo_matrix, file = "", + control = c("keepNA", "keepInteger", "showAttributes")) structure(c(0, 248.69, 248.69, 216.76, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 22.86, 234.22, 0, 210.9, 210.9, 210.9, 210.9, 152.4, 0, 0, 0, 0, 100.84, 80.53, 210.9, 0, 123.38, 292.49, 182.61, 0, 0, 234.22, 248.69, 0, 0, 34.68, 266.02, 266.02, 266.02, 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123.38, 123.38, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 22.86, 234.22, 0, 210.9, 210.9, 210.9, 210.9, 152.4, 0, 0, 0, 0, 100.84, 80.53, 210.9, 0, 123.38, 292.49, 182.61, 0, 0, 234.22, 0, 248.69, 248.69, 216.76, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 22.86, 234.22, 0, 210.9, 210.9, 210.9, 210.9, 152.4, 0, 0, 0, 0, 100.84, 80.53, 210.9, 0, 123.38, 292.49, 182.61, 0, 0, 234.22, 100.84, 349.27, 349.27, 316.9, 173.23, 173.23, 173.23, 173.23, 173.23, 173.23, 173.23, 173.23, 173.23, 173.23, 173.23, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 311.44, 122.78, 334.56, 100.84, 311.44, 311.44, 311.44, 311.44, 252.91, 100.84, 100.84, 100.84, 100.84, 0, 126.72, 311.44, 100.84, 173.23, 393.11, 283.11, 100.84, 100.84, 334.56, 80.53, 270.46, 270.46, 244.3, 48.27, 48.27, 48.27, 48.27, 48.27, 48.27, 48.27, 48.27, 48.27, 48.27, 48.27, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 221.42, 90.97, 241.33, 80.53, 221.42, 221.42, 221.42, 221.42, 167.53, 80.53, 80.53, 80.53, 80.53, 126.72, 0, 221.42, 80.53, 48.27, 312.04, 209.54, 80.53, 80.53, 241.33, 210.9, 55.48, 55.48, 50.66, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 190.14, 23.99, 210.9, 0, 0, 0, 0, 58.53, 210.9, 210.9, 210.9, 210.9, 311.44, 221.42, 0, 210.9, 212.83, 91.9, 47.72, 210.9, 210.9, 23.99, 0, 248.69, 248.69, 216.76, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 22.86, 234.22, 0, 210.9, 210.9, 210.9, 210.9, 152.4, 0, 0, 0, 0, 100.84, 80.53, 210.9, 0, 123.38, 292.49, 182.61, 0, 0, 234.22, 123.38, 266.02, 266.02, 244.59, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 212.83, 128.32, 229.52, 123.38, 212.83, 212.83, 212.83, 212.83, 166.36, 123.38, 123.38, 123.38, 123.38, 173.23, 48.27, 212.83, 123.38, 0, 304.71, 211.6, 123.38, 123.38, 229.52, 292.49, 43.84, 43.84, 77.5, 304.71, 304.71, 304.71, 304.71, 304.71, 304.71, 304.71, 304.71, 304.71, 304.71, 304.71, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 91.9, 270.33, 77.54, 292.49, 91.9, 91.9, 91.9, 91.9, 145.17, 292.49, 292.49, 292.49, 292.49, 393.11, 312.04, 91.9, 292.49, 304.71, 0, 110.04, 292.49, 292.49, 77.54, 182.61, 66.2, 66.2, 35.06, 211.6, 211.6, 211.6, 211.6, 211.6, 211.6, 211.6, 211.6, 211.6, 211.6, 211.6, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 47.72, 160.33, 68.94, 182.61, 47.72, 47.72, 47.72, 47.72, 45.73, 182.61, 182.61, 182.61, 182.61, 283.11, 209.54, 47.72, 182.61, 211.6, 110.04, 0, 182.61, 182.61, 68.94, 0, 248.69, 248.69, 216.76, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 22.86, 234.22, 0, 210.9, 210.9, 210.9, 210.9, 152.4, 0, 0, 0, 0, 100.84, 80.53, 210.9, 0, 123.38, 292.49, 182.61, 0, 0, 234.22, 0, 248.69, 248.69, 216.76, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 123.38, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 210.9, 22.86, 234.22, 0, 210.9, 210.9, 210.9, 210.9, 152.4, 0, 0, 0, 0, 100.84, 80.53, 210.9, 0, 123.38, 292.49, 182.61, 0, 0, 234.22, 234.22, 50.99, 50.99, 61.24, 229.52, 229.52, 229.52, 229.52, 229.52, 229.52, 229.52, 229.52, 229.52, 229.52, 229.52, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 23.99, 213.7, 0, 234.22, 23.99, 23.99, 23.99, 23.99, 81.87, 234.22, 234.22, 234.22, 234.22, 334.56, 241.33, 23.99, 234.22, 229.52, 77.54, 68.94, 234.22, 234.22, 0), .Dim = c(54L, 54L), .Dimnames = list( c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54"), c("V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11", "V12", "V13", "V14", "V15", "V16", "V17", "V18", "V19", "V20", "V21", "V22", "V23", "V24", "V25", "V26", "V27", "V28", "V29", "V30", "V31", "V32", "V33", "V34", "V35", "V36", "V37", "V38", "V39", "V40", "V41", "V42", "V43", "V44", "V45", "V46", "V47", "V48", "V49", "V50", "V51", "V52", "V53", "V54"))) > dput(Gen_matrix, file = "", + control = c("keepNA", "keepInteger", "showAttributes")) structure(c(0, 111, 118, 552, 322, 125, 313, 134, 212, 189, 111, 90, 158, 91, 147, 108, 99, 120, 88, 115, 185, 81, 92, 131, 305, 93, 161, 207, 152, 186, 102, 96, 108, 490, 203, 206, 518, 556, 110, 240, 151, 84, 113, 128, 519, 118, 161, 502, 109, 102, 101, 91, 830, 142, 111, 0, 89, 533, 288, 134, 293, 116, 191, 170, 96, 65, 134, 68, 125, 123, 122, 101, 69, 94, 192, 58, 71, 106, 290, 72, 134, 186, 131, 189, 107, 72, 98, 463, 176, 185, 513, 532, 95, 217, 148, 83, 126, 120, 534, 121, 148, 501, 132, 86, 80, 85, 861, 123, 118, 89, 0, 532, 293, 131, 284, 115, 188, 167, 77, 70, 137, 73, 110, 128, 115, 82, 72, 87, 209, 57, 70, 117, 295, 77, 147, 187, 136, 190, 96, 65, 105, 464, 189, 178, 502, 539, 92, 226, 119, 76, 129, 123, 537, 128, 149, 508, 133, 91, 91, 84, 868, 106, 552, 533, 532, 0, 733, 571, 730, 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Sarah Goslee [mailto:sarah.gos...@gmail.com] Sent: 15 March 2012 15:48 To: Dorothea Hill; r-help Subject: Re: [R] Using the mantel test in Ape Package Hi, You didn't copy the main r-help list on this email, so I've added them back it. Beyond that, I don't see anything grossly wrong. You don't provide enough information to reproduce the problem: mantel.test() works with the 7x7 parts you provided. So you'll need to provide a small reproducible example, ideally using dput(), and also the output of sessionInfo() for your system. Sarah On Thu, Mar 15, 2012 at 11:14 AM, Dorothea Hill <dorothea.h...@zoo.ox.ac.uk> wrote: > Hello, > > Sorry for not providing sufficient information! I am an R beginner! I wonder > if it might be something to do with decimal points or if I have accidently > altered a value in one of the cells? > > The results of str() and dim() are below: > >> str(Geo_matrix) > num [1:54, 1:54] 0 249 249 217 123 ... > - attr(*, "dimnames")=List of 2 > ..$ : chr [1:54] "1" "2" "3" "4" ... > ..$ : chr [1:54] "V1" "V2" "V3" "V4" ... >> str(Gen_matrix) > num [1:54, 1:54] 0 111 118 552 322 125 313 134 212 189 ... > - attr(*, "dimnames")=List of 2 > ..$ : chr [1:54] "1" "2" "3" "4" ... > ..$ : chr [1:54] "V1" "V2" "V3" "V4" ... >> dim(Gen_matrix) > [1] 54 54 >> dim(Geo_matrix) > [1] 54 54 > > The geo_dist csv looks like this before import (this is only the first 7x7): > > 0 248.69 248.69 216.76 123.38 123.38 123.38 > 248.69 0 0 34.68 266.02 266.02 266.02 > 248.69 0 0 34.68 266.02 266.02 266.02 > 216.76 34.68 34.68 0 244.59 244.59 244.59 > 123.38 266.02 266.02 244.59 0 0 0 > 123.38 266.02 266.02 244.59 0 0 0 > 123.38 266.02 266.02 244.59 0 0 0 > > And the gen_dist csv looks like this before import (again first 7x7) > 0 111 118 552 322 125 313 > 111 0 89 533 288 134 293 > 118 89 0 532 293 131 284 > 552 533 532 0 733 571 730 > 322 288 293 733 0 311 455 > 125 134 131 571 311 0 322 > 313 293 284 730 455 322 0 > > After import and converting to a matrix, geo_matrix looks like this: > > V1 V2 V3 V4 V5 V6 V7 V8 V9 > V10 V11 V12 V13 V14 > 1 0.00 248.69 248.69 216.76 123.38 123.38 123.38 123.38 123.38 > 123.38 123.38 123.38 123.38 123.38 > 2 248.69 0.00 0.00 34.68 266.02 266.02 266.02 266.02 266.02 > 266.02 266.02 266.02 266.02 266.02 > 3 248.69 0.00 0.00 34.68 266.02 266.02 266.02 266.02 266.02 > 266.02 266.02 266.02 266.02 266.02 > 4 216.76 34.68 34.68 0.00 244.59 244.59 244.59 244.59 244.59 > 244.59 244.59 244.59 244.59 244.59 > > And gen_matrix looks like this: > > V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 > V17 V18 V19 V20 V21 V22 V23 V24 > 1 0 111 118 552 322 125 313 134 212 189 111 90 158 91 147 108 > 99 120 88 115 185 81 92 131 > 2 111 0 89 533 288 134 293 116 191 170 96 65 134 68 125 123 > 122 101 69 94 192 58 71 106 > 3 118 89 0 532 293 131 284 115 188 167 77 70 137 73 110 128 > 115 82 72 87 209 57 70 117 > 4 552 533 532 0 733 571 730 559 634 593 523 504 575 513 560 564 > 557 532 506 531 637 497 510 545 > 5 322 288 293 733 0 311 455 288 375 364 274 267 338 266 287 317 > 319 295 265 290 371 262 271 304 > > Many thanks. > > > > -----Original Message----- > From: Sarah Goslee [mailto:sarah.gos...@gmail.com] > Sent: 14 March 2012 23:33 > To: Dorothea Hill > Cc: r-help@r-project.org > Subject: Re: [R] Using the mantel test in Ape Package > > Hi, > > On Wed, Mar 14, 2012 at 2:21 PM, Dorothea Hill <dorothea.h...@zoo.ox.ac.uk> > wrote: >> Hi, >> >> I am trying to use a mantel test on two distance matrices. The code I have >> entered for each is: >> >> Gen_dists <- read.csv(file.choose(), >> stringsAsFactors = >> FALSE, >> na.strings = c(" "), >> fill = T, >> header = FALSE, >> blank.lines.skip = FALSE) >> >> Gen_matrix <- as.matrix(Gen_dists) >> >> mantel.test(Geo_matrix, Gen_matrix, nperm = 999, graph = T, >> alternative = "great") >> >> I am getting a result but with lots of warning messages : >> "Warning: non-square matrix" >> >> However, my matrices are square! > > Not according to R. Somewhere in the import or modification steps they have > become unsquare. Since you provide neither a reproducible example nor any > description of your matrices -- str() and dim() seem particularly relevant -- > we can't possibly tell you where. > > Sarah > -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.