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.
