[R] Using the mantel test in Ape Package
Dorothea Hill
dorothea.hill at zoo.ox.ac.uk
Thu Mar 15 17:34:30 CET 2012
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,
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661, 224, 0, 279, 218, 225, 257, 637, 242, 257, 624, 243, 213,
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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,
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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,
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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,
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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,
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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,
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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,
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861, 746, 897, 904, 768, 821, 828, 954, 909, 838, 851, 872, 1271,
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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.goslee at 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.hill at 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.goslee at gmail.com]
> Sent: 14 March 2012 23:33
> To: Dorothea Hill
> Cc: r-help at 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.hill at 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
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