Hi Dorothea,
I've copied the ape maintainer on this, because I believe you may have
found a bug.
Your analysis works without warning in ape 2.8, but gives warnings in
the current ape_3.0.1.
But what makes me think that this is a problem with the new version is
that the example given in ?mantel.test gives the same warning:
q1 <- matrix(runif(36), nrow = 6)
q2 <- matrix(runif(36), nrow = 6)
mantel.test(q1, q2, graph = TRUE,
main = "Mantel test: a random example with 6 X 6 matrices",
xlab = "z-statistic", ylab = "Density",
sub = "The vertical line shows the observed z-statistic")
Leads to many repetitions of:
[1] "Warning: non-square matrix"
[1] "Warning: non-square matrix"
Now, I find that example somewhat perplexing, because normally the
Mantel test is conducted with distance matrices which are symmetric as
well as square, but hopefully the maintainer will enlighten us.
Also note that this is a warning rather than an error, so the results
given may well be correct.
Sarah
On Thu, Mar 15, 2012 at 12:34 PM, Dorothea Hill
<dorothea.h...@zoo.ox.ac.uk> wrote:
> 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, 266.02, 266.02, 266.02,
> 266.02, 266.02, 266.02, 266.02, 266.02, 55.48, 55.48, 55.48,
> 55.48, 55.48, 55.48, 55.48, 55.48, 55.48, 55.48, 55.48, 55.48,
> 55.48, 55.48, 55.48, 55.48, 55.48, 226.49, 50.99, 248.69, 55.48,
> 55.48, 55.48, 55.48, 102.97, 248.69, 248.69, 248.69, 248.69,
> 349.27, 270.46, 55.48, 248.69, 266.02, 43.84, 66.2, 248.69, 248.69,
> 50.99, 248.69, 0, 0, 34.68, 266.02, 266.02, 266.02, 266.02, 266.02,
> 266.02, 266.02, 266.02, 266.02, 266.02, 266.02, 55.48, 55.48,
> 55.48, 55.48, 55.48, 55.48, 55.48, 55.48, 55.48, 55.48, 55.48,
> 55.48, 55.48, 55.48, 55.48, 55.48, 55.48, 226.49, 50.99, 248.69,
> 55.48, 55.48, 55.48, 55.48, 102.97, 248.69, 248.69, 248.69, 248.69,
> 349.27, 270.46, 55.48, 248.69, 266.02, 43.84, 66.2, 248.69, 248.69,
> 50.99, 216.76, 34.68, 34.68, 0, 244.59, 244.59, 244.59, 244.59,
> 244.59, 244.59, 244.59, 244.59, 244.59, 244.59, 244.59, 50.66,
> 50.66, 50.66, 50.66, 50.66, 50.66, 50.66, 50.66, 50.66, 50.66,
> 50.66, 50.66, 50.66, 50.66, 50.66, 50.66, 50.66, 194.28, 61.24,
> 216.76, 50.66, 50.66, 50.66, 50.66, 78.3, 216.76, 216.76, 216.76,
> 216.76, 316.9, 244.3, 50.66, 216.76, 244.59, 77.5, 35.06, 216.76,
> 216.76, 61.24, 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,
> 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, 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, 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, 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,
> 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, 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, 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, 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,
> 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 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, 22.86, 226.49, 226.49, 194.28, 128.32, 128.32, 128.32,
> 128.32, 128.32, 128.32, 128.32, 128.32, 128.32, 128.32, 128.32,
> 190.14, 190.14, 190.14, 190.14, 190.14, 190.14, 190.14, 190.14,
> 190.14, 190.14, 190.14, 190.14, 190.14, 190.14, 190.14, 190.14,
> 190.14, 0, 213.7, 22.86, 190.14, 190.14, 190.14, 190.14, 131.84,
> 22.86, 22.86, 22.86, 22.86, 122.78, 90.97, 190.14, 22.86, 128.32,
> 270.33, 160.33, 22.86, 22.86, 213.7, 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, 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, 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, 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, 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, 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, 152.4, 102.97, 102.97, 78.3,
> 166.36, 166.36, 166.36, 166.36, 166.36, 166.36, 166.36, 166.36,
> 166.36, 166.36, 166.36, 58.53, 58.53, 58.53, 58.53, 58.53, 58.53,
> 58.53, 58.53, 58.53, 58.53, 58.53, 58.53, 58.53, 58.53, 58.53,
> 58.53, 58.53, 131.84, 81.87, 152.4, 58.53, 58.53, 58.53, 58.53,
> 0, 152.4, 152.4, 152.4, 152.4, 252.91, 167.53, 58.53, 152.4,
> 166.36, 145.17, 45.73, 152.4, 152.4, 81.87, 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, 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, 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, 559, 634,
> 593, 523, 504, 575, 513, 560, 564, 557, 532, 506, 531, 637, 497,
> 510, 545, 733, 505, 577, 627, 582, 626, 550, 507, 537, 898, 617,
> 618, 952, 971, 524, 660, 579, 512, 575, 557, 973, 558, 577, 938,
> 563, 523, 525, 534, 1293, 552, 322, 288, 293, 733, 0, 311, 455,
> 288, 375, 364, 274, 267, 338, 266, 287, 317, 319, 295, 265, 290,
> 371, 262, 271, 304, 378, 266, 332, 372, 337, 380, 310, 270, 304,
> 651, 378, 377, 699, 724, 287, 419, 336, 275, 322, 300, 696, 321,
> 316, 701, 320, 290, 288, 281, 1053, 313, 125, 134, 131, 571,
> 311, 0, 322, 135, 227, 208, 130, 113, 171, 96, 154, 121, 108,
> 137, 99, 106, 208, 94, 109, 144, 325, 110, 176, 212, 165, 203,
> 131, 107, 137, 497, 212, 217, 515, 565, 125, 259, 180, 115, 154,
> 151, 564, 157, 176, 543, 122, 117, 124, 122, 861, 161, 313, 293,
> 284, 730, 455, 322, 0, 259, 380, 371, 271, 270, 327, 277, 294,
> 320, 306, 280, 268, 281, 354, 251, 274, 311, 467, 277, 343, 387,
> 340, 383, 289, 273, 299, 662, 385, 374, 682, 735, 288, 422, 329,
> 276, 321, 319, 727, 326, 329, 702, 321, 291, 291, 282, 1056,
> 296, 134, 116, 115, 559, 288, 135, 259, 0, 203, 188, 114, 83,
> 160, 92, 135, 135, 137, 115, 87, 110, 181, 80, 97, 124, 308,
> 92, 158, 202, 159, 208, 120, 100, 126, 481, 208, 201, 531, 554,
> 113, 243, 170, 97, 134, 142, 538, 139, 156, 527, 134, 112, 110,
> 99, 879, 141, 212, 191, 188, 634, 375, 227, 380, 203, 0, 119,
> 187, 176, 103, 161, 206, 216, 191, 186, 164, 183, 285, 167, 174,
> 207, 399, 173, 243, 281, 236, 286, 186, 185, 203, 564, 269, 292,
> 604, 631, 196, 312, 233, 186, 219, 219, 621, 230, 237, 598, 217,
> 189, 187, 192, 952, 194, 189, 170, 167, 593, 364, 208, 371, 188,
> 119, 0, 152, 137, 76, 146, 195, 195, 198, 169, 139, 170, 274,
> 138, 149, 178, 352, 140, 216, 264, 217, 271, 191, 146, 178, 533,
> 252, 257, 595, 616, 159, 297, 214, 141, 212, 198, 612, 205, 210,
> 573, 204, 162, 154, 165, 935, 193, 111, 96, 77, 523, 274, 130,
> 271, 114, 187, 152, 0, 57, 136, 62, 97, 123, 106, 63, 63, 62,
> 192, 58, 73, 102, 290, 62, 134, 188, 131, 187, 111, 66, 100,
> 455, 178, 175, 503, 528, 83, 231, 108, 69, 128, 114, 536, 127,
> 126, 501, 124, 88, 80, 93, 855, 95, 90, 65, 70, 504, 267, 113,
> 270, 83, 176, 137, 57, 0, 115, 47, 96, 102, 99, 66, 44, 73, 175,
> 31, 34, 73, 277, 37, 111, 169, 116, 168, 88, 49, 81, 438, 155,
> 154, 496, 517, 56, 208, 115, 48, 113, 101, 515, 102, 117, 476,
> 101, 61, 57, 74, 844, 94, 158, 134, 137, 575, 338, 171, 327,
> 160, 103, 76, 136, 115, 0, 120, 165, 168, 166, 143, 109, 134,
> 244, 84, 117, 154, 332, 116, 182, 228, 181, 227, 150, 114, 142,
> 511, 222, 219, 549, 574, 139, 269, 188, 123, 170, 160, 582, 171,
> 184, 551, 171, 124, 134, 131, 909, 165, 91, 68, 73, 513, 266,
> 96, 277, 92, 161, 146, 62, 47, 120, 0, 97, 97, 94, 71, 33, 68,
> 176, 40, 43, 82, 278, 42, 112, 164, 103, 167, 91, 54, 78, 441,
> 154, 157, 501, 504, 65, 199, 120, 59, 100, 104, 504, 101, 120,
> 483, 100, 62, 60, 69, 831, 99, 147, 125, 110, 560, 287, 154,
> 294, 135, 206, 195, 97, 96, 165, 97, 0, 147, 143, 104, 92, 93,
> 215, 91, 100, 123, 309, 103, 169, 211, 176, 222, 119, 103, 131,
> 490, 211, 202, 534, 569, 122, 248, 131, 108, 155, 143, 549, 152,
> 157, 538, 152, 109, 119, 114, 894, 120, 108, 123, 128, 564, 317,
> 121, 320, 135, 216, 195, 123, 102, 168, 97, 147, 0, 95, 128,
> 94, 115, 205, 91, 90, 135, 328, 105, 160, 207, 162, 202, 102,
> 91, 131, 488, 207, 210, 520, 567, 116, 240, 177, 112, 144, 139,
> 550, 155, 157, 520, 103, 112, 111, 108, 852, 152, 99, 122, 115,
> 557, 319, 108, 306, 137, 191, 198, 106, 99, 166, 94, 143, 95,
> 0, 117, 91, 102, 192, 88, 97, 136, 325, 102, 167, 204, 153, 191,
> 101, 101, 129, 487, 198, 209, 487, 555, 115, 241, 160, 109, 137,
> 141, 549, 150, 166, 523, 110, 106, 110, 116, 851, 139, 120, 101,
> 82, 532, 295, 137, 280, 115, 186, 169, 63, 66, 143, 71, 104,
> 128, 117, 0, 68, 61, 199, 69, 78, 109, 309, 71, 137, 195, 144,
> 196, 106, 79, 103, 464, 189, 188, 512, 543, 92, 232, 131, 82,
> 137, 131, 539, 132, 143, 506, 135, 95, 89, 104, 868, 82, 88,
> 69, 72, 506, 265, 99, 268, 87, 164, 139, 63, 44, 109, 33, 92,
> 94, 91, 68, 0, 57, 175, 31, 40, 75, 277, 45, 113, 159, 106, 164,
> 88, 51, 73, 446, 149, 152, 490, 507, 66, 198, 121, 52, 97, 97,
> 509, 102, 111, 482, 93, 59, 51, 60, 832, 90, 115, 94, 87, 531,
> 290, 106, 281, 110, 183, 170, 62, 73, 134, 68, 93, 115, 102,
> 61, 57, 0, 192, 56, 73, 96, 300, 72, 132, 180, 129, 185, 91,
> 68, 92, 459, 180, 175, 503, 530, 93, 227, 120, 79, 120, 110,
> 532, 123, 144, 503, 116, 84, 84, 89, 859, 103, 185, 192, 209,
> 637, 371, 208, 354, 181, 285, 274, 192, 175, 244, 176, 215, 205,
> 192, 199, 175, 192, 0, 168, 181, 206, 389, 182, 237, 294, 243,
> 285, 199, 183, 205, 571, 290, 291, 597, 637, 201, 325, 248, 195,
> 229, 228, 640, 222, 244, 615, 194, 192, 196, 202, 951, 227, 81,
> 58, 57, 497, 262, 94, 251, 80, 167, 138, 58, 31, 84, 40, 91,
> 91, 88, 69, 31, 56, 168, 0, 35, 76, 256, 38, 108, 152, 103, 149,
> 71, 36, 64, 433, 144, 139, 473, 498, 61, 193, 110, 45, 94, 84,
> 506, 95, 108, 473, 90, 50, 56, 53, 831, 89, 92, 71, 70, 510,
> 271, 109, 274, 97, 174, 149, 73, 34, 117, 43, 100, 90, 97, 78,
> 40, 73, 181, 35, 0, 83, 283, 53, 115, 161, 110, 168, 86, 53,
> 79, 440, 153, 154, 500, 519, 60, 198, 119, 54, 105, 103, 511,
> 104, 121, 480, 95, 59, 51, 66, 836, 94, 131, 106, 117, 545, 304,
> 144, 311, 124, 207, 178, 102, 73, 154, 82, 123, 135, 136, 109,
> 75, 96, 206, 76, 83, 0, 300, 70, 148, 198, 151, 205, 123, 92,
> 114, 473, 194, 189, 535, 548, 107, 239, 156, 95, 146, 124, 550,
> 141, 152, 517, 136, 100, 96, 109, 883, 133, 305, 290, 295, 733,
> 378, 325, 467, 308, 399, 352, 290, 277, 332, 278, 309, 328, 325,
> 309, 277, 300, 389, 256, 283, 300, 0, 276, 346, 394, 349, 388,
> 303, 276, 306, 671, 388, 385, 707, 736, 301, 427, 338, 287, 328,
> 316, 738, 305, 338, 707, 339, 296, 298, 287, 1069, 325, 93, 72,
> 77, 505, 266, 110, 277, 92, 173, 140, 62, 37, 116, 42, 103, 105,
> 102, 71, 45, 72, 182, 38, 53, 70, 276, 0, 120, 160, 115, 163,
> 95, 50, 80, 439, 158, 155, 499, 508, 75, 207, 118, 53, 110, 96,
> 504, 97, 110, 481, 112, 70, 66, 73, 841, 97, 161, 134, 147, 577,
> 332, 176, 343, 158, 243, 216, 134, 111, 182, 112, 169, 160, 167,
> 137, 113, 132, 237, 108, 115, 148, 346, 120, 0, 232, 179, 238,
> 151, 122, 144, 503, 216, 219, 567, 578, 133, 259, 194, 131, 170,
> 172, 580, 167, 188, 551, 163, 130, 132, 133, 887, 161, 207, 186,
> 187, 627, 372, 212, 387, 202, 281, 264, 188, 169, 228, 164, 211,
> 207, 204, 195, 159, 180, 294, 152, 161, 198, 394, 160, 232, 0,
> 221, 97, 193, 160, 190, 549, 266, 269, 595, 620, 189, 275, 234,
> 171, 202, 208, 594, 205, 226, 591, 214, 172, 176, 153, 927, 215,
> 152, 131, 136, 582, 337, 165, 340, 159, 236, 217, 131, 116, 181,
> 103, 176, 162, 153, 144, 106, 129, 243, 103, 110, 151, 349, 115,
> 179, 221, 0, 228, 148, 115, 145, 498, 217, 222, 558, 573, 132,
> 262, 193, 124, 155, 159, 563, 160, 185, 544, 171, 131, 119, 136,
> 890, 170, 186, 189, 190, 626, 380, 203, 383, 208, 286, 271, 187,
> 168, 227, 167, 222, 202, 191, 196, 164, 185, 285, 149, 168, 205,
> 388, 163, 238, 97, 228, 0, 180, 162, 194, 558, 271, 272, 588,
> 622, 188, 320, 241, 174, 200, 205, 616, 199, 231, 592, 215, 185,
> 181, 177, 922, 216, 102, 107, 96, 550, 310, 131, 289, 120, 186,
> 191, 111, 88, 150, 91, 119, 102, 101, 106, 88, 91, 199, 71, 86,
> 123, 303, 95, 151, 193, 148, 180, 0, 86, 118, 476, 195, 194,
> 500, 556, 112, 224, 153, 100, 133, 131, 537, 136, 159, 516, 105,
> 102, 103, 101, 850, 120, 96, 72, 65, 507, 270, 107, 273, 100,
> 185, 146, 66, 49, 114, 54, 103, 91, 101, 79, 51, 68, 183, 36,
> 53, 92, 276, 50, 122, 160, 115, 162, 86, 0, 78, 437, 162, 149,
> 491, 514, 75, 205, 124, 59, 104, 82, 514, 99, 104, 479, 112,
> 72, 68, 67, 837, 99, 108, 98, 105, 537, 304, 137, 299, 126, 203,
> 178, 100, 81, 142, 78, 131, 131, 129, 103, 73, 92, 205, 64, 79,
> 114, 306, 80, 144, 190, 145, 194, 118, 78, 0, 477, 190, 191,
> 525, 530, 101, 233, 134, 77, 124, 104, 534, 119, 156, 493, 136,
> 86, 92, 85, 861, 121, 490, 463, 464, 898, 651, 497, 662, 481,
> 564, 533, 455, 438, 511, 441, 490, 488, 487, 464, 446, 459, 571,
> 433, 440, 473, 671, 439, 503, 549, 498, 558, 476, 437, 477, 0,
> 545, 540, 106, 125, 450, 582, 509, 442, 495, 483, 897, 492, 501,
> 864, 501, 465, 447, 456, 746, 494, 203, 176, 189, 617, 378, 212,
> 385, 208, 269, 252, 178, 155, 222, 154, 211, 207, 198, 189, 149,
> 180, 290, 144, 153, 194, 388, 158, 216, 266, 217, 271, 195, 162,
> 190, 545, 0, 45, 603, 620, 163, 301, 232, 167, 206, 206, 616,
> 209, 224, 585, 218, 170, 168, 179, 897, 205, 206, 185, 178, 618,
> 377, 217, 374, 201, 292, 257, 175, 154, 219, 157, 202, 210, 209,
> 188, 152, 175, 291, 139, 154, 189, 385, 155, 219, 269, 222, 272,
> 194, 149, 191, 540, 45, 0, 596, 623, 164, 312, 229, 162, 217,
> 197, 623, 212, 219, 600, 209, 173, 177, 172, 904, 210, 518, 513,
> 502, 952, 699, 515, 682, 531, 604, 595, 503, 496, 549, 501, 534,
> 520, 487, 512, 490, 503, 597, 473, 500, 535, 707, 499, 567, 595,
> 558, 588, 500, 491, 525, 106, 603, 596, 0, 175, 518, 630, 557,
> 496, 541, 538, 959, 554, 561, 922, 523, 511, 511, 498, 768, 524,
> 556, 532, 539, 971, 724, 565, 735, 554, 631, 616, 528, 517, 574,
> 504, 569, 567, 555, 543, 507, 530, 637, 498, 519, 548, 736, 508,
> 578, 620, 573, 622, 556, 514, 530, 125, 620, 623, 175, 0, 535,
> 661, 582, 525, 562, 562, 974, 565, 580, 951, 570, 520, 524, 531,
> 821, 561, 110, 95, 92, 524, 287, 125, 288, 113, 196, 159, 83,
> 56, 139, 65, 122, 116, 115, 92, 66, 93, 201, 61, 60, 107, 301,
> 75, 133, 189, 132, 188, 112, 75, 101, 450, 163, 164, 518, 535,
> 0, 224, 149, 76, 127, 123, 537, 126, 139, 498, 129, 85, 71, 94,
> 828, 120, 240, 217, 226, 660, 419, 259, 422, 243, 312, 297, 231,
> 208, 269, 199, 248, 240, 241, 232, 198, 227, 325, 193, 198, 239,
> 427, 207, 259, 275, 262, 320, 224, 205, 233, 582, 301, 312, 630,
> 661, 224, 0, 279, 218, 225, 257, 637, 242, 257, 624, 243, 213,
> 211, 198, 954, 248, 151, 148, 119, 579, 336, 180, 329, 170, 233,
> 214, 108, 115, 188, 120, 131, 177, 160, 131, 121, 120, 248, 110,
> 119, 156, 338, 118, 194, 234, 193, 241, 153, 124, 134, 509, 232,
> 229, 557, 582, 149, 279, 0, 91, 168, 154, 564, 157, 188, 529,
> 174, 138, 140, 119, 909, 139, 84, 83, 76, 512, 275, 115, 276,
> 97, 186, 141, 69, 48, 123, 59, 108, 112, 109, 82, 52, 79, 195,
> 45, 54, 95, 287, 53, 131, 171, 124, 174, 100, 59, 77, 442, 167,
> 162, 496, 525, 76, 218, 91, 0, 99, 85, 493, 92, 123, 464, 121,
> 75, 65, 48, 838, 104, 113, 126, 129, 575, 322, 154, 321, 134,
> 219, 212, 128, 113, 170, 100, 155, 144, 137, 137, 97, 120, 229,
> 94, 105, 146, 328, 110, 170, 202, 155, 200, 133, 104, 124, 495,
> 206, 217, 541, 562, 127, 225, 168, 99, 0, 136, 526, 109, 172,
> 513, 161, 118, 114, 93, 851, 159, 128, 120, 123, 557, 300, 151,
> 319, 142, 219, 198, 114, 101, 160, 104, 143, 139, 141, 131, 97,
> 110, 228, 84, 103, 124, 316, 96, 172, 208, 159, 205, 131, 82,
> 104, 483, 206, 197, 538, 562, 123, 257, 154, 85, 136, 0, 542,
> 139, 148, 509, 158, 114, 112, 105, 872, 147, 519, 534, 537, 973,
> 696, 564, 727, 538, 621, 612, 536, 515, 582, 504, 549, 550, 549,
> 539, 509, 532, 640, 506, 511, 550, 738, 504, 580, 594, 563, 616,
> 537, 514, 534, 897, 616, 623, 959, 974, 537, 637, 564, 493, 526,
> 542, 0, 523, 574, 915, 559, 528, 526, 491, 1271, 559, 118, 121,
> 128, 558, 321, 157, 326, 139, 230, 205, 127, 102, 171, 101, 152,
> 155, 150, 132, 102, 123, 222, 95, 104, 141, 305, 97, 167, 205,
> 160, 199, 136, 99, 119, 492, 209, 212, 554, 565, 126, 242, 157,
> 92, 109, 139, 523, 0, 169, 510, 160, 121, 121, 92, 876, 158,
> 161, 148, 149, 577, 316, 176, 329, 156, 237, 210, 126, 117, 184,
> 120, 157, 157, 166, 143, 111, 144, 244, 108, 121, 152, 338, 110,
> 188, 226, 185, 231, 159, 104, 156, 501, 224, 219, 561, 580, 139,
> 257, 188, 123, 172, 148, 574, 169, 0, 539, 170, 136, 132, 135,
> 897, 157, 502, 501, 508, 938, 701, 543, 702, 527, 598, 573, 501,
> 476, 551, 483, 538, 520, 523, 506, 482, 503, 615, 473, 480, 517,
> 707, 481, 551, 591, 544, 592, 516, 479, 493, 864, 585, 600, 922,
> 951, 498, 624, 529, 464, 513, 509, 915, 510, 539, 0, 543, 501,
> 487, 478, 1256, 538, 109, 132, 133, 563, 320, 122, 321, 134,
> 217, 204, 124, 101, 171, 100, 152, 103, 110, 135, 93, 116, 194,
> 90, 95, 136, 339, 112, 163, 214, 171, 215, 105, 112, 136, 501,
> 218, 209, 523, 570, 129, 243, 174, 121, 161, 158, 559, 160, 170,
> 543, 0, 115, 120, 121, 847, 153, 102, 86, 91, 523, 290, 117,
> 291, 112, 189, 162, 88, 61, 124, 62, 109, 112, 106, 95, 59, 84,
> 192, 50, 59, 100, 296, 70, 130, 172, 131, 185, 102, 72, 86, 465,
> 170, 173, 511, 520, 85, 213, 138, 75, 118, 114, 528, 121, 136,
> 501, 115, 0, 80, 85, 853, 113, 101, 80, 91, 525, 288, 124, 291,
> 110, 187, 154, 80, 57, 134, 60, 119, 111, 110, 89, 51, 84, 196,
> 56, 51, 96, 298, 66, 132, 176, 119, 181, 103, 68, 92, 447, 168,
> 177, 511, 524, 71, 211, 140, 65, 114, 112, 526, 121, 132, 487,
> 120, 80, 0, 83, 845, 111, 91, 85, 84, 534, 281, 122, 282, 99,
> 192, 165, 93, 74, 131, 69, 114, 108, 116, 104, 60, 89, 202, 53,
> 66, 109, 287, 73, 133, 153, 136, 177, 101, 67, 85, 456, 179,
> 172, 498, 531, 94, 198, 119, 48, 93, 105, 491, 92, 135, 478,
> 121, 85, 83, 0, 826, 120, 830, 861, 868, 1293, 1053, 861, 1056,
> 879, 952, 935, 855, 844, 909, 831, 894, 852, 851, 868, 832, 859,
> 951, 831, 836, 883, 1069, 841, 887, 927, 890, 922, 850, 837,
> 861, 746, 897, 904, 768, 821, 828, 954, 909, 838, 851, 872, 1271,
> 876, 897, 1256, 847, 853, 845, 826, 0, 886, 142, 123, 106, 552,
> 313, 161, 296, 141, 194, 193, 95, 94, 165, 99, 120, 152, 139,
> 82, 90, 103, 227, 89, 94, 133, 325, 97, 161, 215, 170, 216, 120,
> 99, 121, 494, 205, 210, 524, 561, 120, 248, 139, 104, 159, 147,
> 559, 158, 157, 538, 153, 113, 111, 120, 886, 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")))
>
>
> -----Original Message-----
> From: 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
--
Sarah Goslee
http://www.stringpage.com
http://www.sarahgoslee.com
http://www.functionaldiversity.org
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