Dear Tristan,
Thanks alot for spotting this. This is fixed now. The new version is
available here:
https://svn.mpl.ird.fr/ape/dev/ape/R/drop.tip.R
More tests will be welcome.
Cheers,
Emmanuel
Tristan Lefebure wrote on 15/11/2012 18:09:
Dear all,
I am puzzled with the following dropt.tip behaviour:
######
require(ape)
tr<-
read.tree(text='(((t1:1.047859182,t2:1.047859182):0.2756716989,t3:1.323530881):0.9374413868,(((((t4:1.004540609,(t5:0.825851211,t6:0.825851211):0.1786893979):0.2456960053,((t7:1.056756599,t8:1.056756599):0.06431900218,t9:1.121075601):0.1291610131):0.3349743758,t10:1.58521099):0.2527177518,((t11:0.7045266296,t12:0.7045266296):0.9569230276,(t13:1.434588187,t14:1.434588187):0.2268614706):0.1764790846):0.08226490869,((((t15:1.279204276,((t16:1.114074687,t17:1.114074687):0.1122507672,t18:1.226325454):0.05287882165):0.1013794601,((((t19:0.9955287763,t20:0.9955287763):0.1328862159,(((t21:0.5523867955,t22:0.5523867955):0.2108511243,t23:0.7632379198):0.1651743381,((t24:0.6573230631,t25:0.6573230631):0.1870302034,(t26:0.7107704271,t27:0.7107704271):0.1335828394):0.08405899131):0.2000027343):0.1056949204,(t28:1.153531955,t29:1.153531955):0.08057795766):0.05156567335,((t30:0.7944490533,t31:0.7944490533):0.3247998092,(((t32:0.6657996502,t33:0.6657996502):0.1778661928,((t34:0.1423836508!
,t!
35:0.1423836508):0.5359910966,t36:0.6783747474):0.1652910955):0.08026277837,t37:0.9239286214):0.1953202411):0.1664267234):0.0949081502):0.06478712445,(((t38:0.7909217241,(t39:0.404267298,t40:0.404267298):0.3866544261):0.4221751735,((t41:0.9390399711,t42:0.9390399711):0.1900443404,(((((t43:0.7331382087,(t44:0.5724991151,(t45:0.4288431567,t46:0.4288431567):0.1436559584):0.1606390935):0.0802190135,t47:0.8133572222):0.09505692675,t48:0.9084141489):0.1203866568,(((t49:0.7400008033,t50:0.7400008033):0.081110064,(t51:0.4635806844,t52:0.4635806844):0.3575301829):0.09861132464,t53:0.9197221919):0.1090786138):0.03016346022,(t54:0.7468362228,t55:0.7468362228):0.3121280432):0.07012004561):0.08401258605):0.1109195687,t56:1.324016466):0.1213543942):0.1153375546,((t57:1.136226544,t58:1.136226544):0.2488130821,(t59:0.493435228,t60:0.493435228):0.8916043976):0.1756687895):0.3594852354):0.3407786169);')
torm<- paste('t',
c(2,3,4,6,10,11,12,17,18,26,29,33,37,38,41,45,46,51,52,53,55), sep='')
tr$node.label<- paste('n', 1:Nnode(tr), sep='')
x11(); plot(tr, cex=0.7); nodelabels(tr$node.label, cex=0.7);
tr2<- drop.tip(tr, torm)
x11(); plot(tr2, cex=0.7); nodelabels(tr2$node.label, cex=0.7);
#####
Just look at the top clade made of t60, t59, t57 and t57. This clade is not
impacted by the tree pruning; but look at the node labels, they have been
badly reassigned... I've tried to replicate the problem on a smaller data
set, but did not succeed.
Thanks!
--
Tristan Lefebure
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--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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