Hi Krzysztof,
The composition of the splits are obtained with bitsplits(phy). You can
print them with more details after converting in the class "prop.part"
with as.prop.part(). The development version of ape (3.2-0.2) has an
improved plot() method for this class.
HTH
Best,
Emmanuel
Le 29/01/2015 18:47, Krzysztof Kozak a écrit :
Hello,
I have an unrooted reference tree phy and a distribution of other trees X.
I want to know how often certain bipartitions from phy are found among
trees in X.
In ape I can use countBipartitions(phy,X) to do this. However, the returned
vector refers to bipartitions by number.
[1] 1255 1291 679 455 1300 831 600 433 1339 814 1403 1321 551 614
224 335 1386 833 568 102 1384 884 1439 1457 957 632 428 142 138
55 1493 941 1524 1527 559 390 1531 1551 1014 552 1583 384 186 980
1497 1013
[47] 571 139 1569 1066 1571 1538 1078 369 182 92 1649 1155 79 73
1583 1078 1596 1060 531 1527 1513 1090 1492 357 1562 1061 599 291 1453
970 577 159 76 1068 88 185 25 43 1555 1532 976 1041 1509 317
165 105
[93] 37 31 363 39 606 100 26 1457 989 1444 926 626 633 1406
889 1435 448 1353 329 185 140 119 1364 857 582 91 54 190 26
52 1367 858 661 448 359 237 71 87 367 171 175 1115 1188 500
391 346
[139] 251 198 209 1881
How do i know which number is which split in the tree? (I am interested in
a question about specific splits, not some sort of summary.)
Many thanks,
__
Krzysztof "Chris" Kozak
PhD Candidate, Department of Zoology
University of Cambridge, CB2 3EJ
http://heliconius.zoo.cam.ac.uk/people/krzysztof-kozak/
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