Re: [R-sig-phylo] Mixup with plotted bootstrap values
The bug reported by Alastair is now fixed. This required to change some
C code, and so the whole package needs to be recompiled (this will be in
the next release of ape). The svn has been updated.
For developers, the code in src/tree_build.c has been slightly improved
at this occasion and it may be generalized further to decode Newick
strings in an efficient and fast way.
Emmanuel
Emmanuel Paradis wrote on 24/02/2011 16:14:
Alastair,
That's indeed the correct work-around. The is because a different code
is used whether the NEXUS file has a TRANSLATE block or not. I'll fix
the bug very soon.
Cheers,
Emmanuel
PS: thanks for the tip on using Figtree.
Alastair Potts wrote on 24/02/2011 14:57:
Hi All,
I think I have located the problem. As usual I had experienced it
before and I found (or someone else found) a workaround - but I
couldn't remember it.
The bootstrap values ($node.label) is mixed up when I save the
bootstrap tree as a nexus file with a translation table in PAUP (this
is the default by the way). If I save the bootstrap tree without a
translation table (i.e. FORMAT=ALTNEX), then the BS values are in
their correct places.
If I open both saved bootstrap trees (i.e. with and without
translation tables) in FigTree, I get identical trees with the
bootstrap labels in the correct places. Obviously this has not been
the case in R. I think that there may be a problem when reading in the
translation table when there are values included with each node. I've
included examples of both saved files from PAUP if anyone wishes to
play around with the problem.
So, for those of you using PAUP, the quick work-around to avoid this
problem in future is to use SAVETREES ... FORMAT=ALTNEX ...
Cheers,
Alastair
-
Alastair Potts
PhD candidate
Botany Department
University of Cape Town
alastair.po...@uct.ac.za or pott...@gmail.com
University Private Bag, Rondebosch 7700, South Africa
or
PO Box 115, Loxton 6985, South Africa
Cell: 082 491-7275
-
Emmanuel Paradis wrote:
Hi Alastair,
I copied the Newick string below into R, read it with read.tree, and
this seems to work as normal.
I also tried to do the same with Figtree: the tree and its tip labels
are OK, but the node labels are not (eg, it displays 377 for the
root instead of 100). My guess is that it's a problem when decoding
the strings (maybe specific to Linux).
Best,
Emmanuel
Alastair Potts wrote on 23/02/2011 21:09:
Hi All,
I'm sure I've had this problem before and found a way to fix it.
I've spent an hour looking for the solution, but can't seem to find it.
In short, I've run a bootstrap analysis in PAUP* which provided a
consensus tree with bootstrap values. This tree opens fine in
FigTree. I read it in using ape's read.nexus and plot the node using
nodelabel and the $node.label property of the imported tree. I've
done nothing else to the tree (e.g. ladderize which I know sometimes
causes problems), yet my node label bootstrap values are all
shuffled around in some way and I can't figure out why.
My code is simply:
pt - read.nexus('dataset1.bootstrap.swap.NNI.tree')
plot(pt,cex=0.7)
nodelabels(pt$node.label)
Possibly the problem lies with the nexus tree, so here it is for
what it's worth:
tree PAUP_1 = [U]
(1:0,((2:100,(3:100,4:100)80:80,5:100,6:100,(7:100,10:100)60:60,8:100,9:100,(11:100,34:100)60:60,15:100,(16:100,37:100,54:100,56:100,57:100,71:100,72:100)70:70,18:100,(23:100,25:100,30:100,31:100,35:100,116:100,117:100)59:59,26:100,27:100,32:100,33:100,39:100,48:100,58:100,59:100,60:100,64:100,69:100,70:100,78:100,79:100,80:100,82:100,(83:100,84:100,85:100)52:52,94:100,99:100,101:100,102:100,107:100,119:100)70:70,(12:100,(13:100,14:100,53:100,90:100)69:69,28:100,(62:100,63:100)96:96,(66:100,67:100)69:69,68:100,91:100,92:100,93:100,97:100,98:100,100:100)81:81,(17:100,19:100,21:100,24:100,38:100,42:100,43:100,(44:100,45:100)67:67,47:100,49:100,50:100,61:100)82:82,(20:100,40:100,41:100,51:100,52:100,73:100,74:100,108:100,109:100,110:100,118:100)65:65,(22:100,29:100,36:100,46:100,75:100,76:100,105:100,111:100,112:100,113:100,114:100,115:100)97:97,55:100,(65:100,86:100,89:100,96:100)68:68,(77:100,(81:100,95:100,103:100,104:100)68:68,106:100)65:65,(87:100,88:100)98:98)100:100)
1
00
;
My apologies for not setting up a standard replication of the error
- but I'm not really sure how to go about it with this example.
Thanks in advance for your help.
Cheers,
Alastair
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--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
___
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R-sig-phylo@r-project.org
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Re: [R-sig-phylo] Mixup with plotted bootstrap values
Alastair,
That's indeed the correct work-around. The is because a different code
is used whether the NEXUS file has a TRANSLATE block or not. I'll fix
the bug very soon.
Cheers,
Emmanuel
PS: thanks for the tip on using Figtree.
Alastair Potts wrote on 24/02/2011 14:57:
Hi All,
I think I have located the problem. As usual I had experienced it before
and I found (or someone else found) a workaround - but I couldn't
remember it.
The bootstrap values ($node.label) is mixed up when I save the bootstrap
tree as a nexus file with a translation table in PAUP (this is the
default by the way). If I save the bootstrap tree without a translation
table (i.e. FORMAT=ALTNEX), then the BS values are in their correct places.
If I open both saved bootstrap trees (i.e. with and without translation
tables) in FigTree, I get identical trees with the bootstrap labels in
the correct places. Obviously this has not been the case in R. I think
that there may be a problem when reading in the translation table when
there are values included with each node. I've included examples of both
saved files from PAUP if anyone wishes to play around with the problem.
So, for those of you using PAUP, the quick work-around to avoid this
problem in future is to use SAVETREES ... FORMAT=ALTNEX ...
Cheers,
Alastair
-
Alastair Potts
PhD candidate
Botany Department
University of Cape Town
alastair.po...@uct.ac.za or pott...@gmail.com
University Private Bag, Rondebosch 7700, South Africa
or
PO Box 115, Loxton 6985, South Africa
Cell: 082 491-7275
-
Emmanuel Paradis wrote:
Hi Alastair,
I copied the Newick string below into R, read it with read.tree, and
this seems to work as normal.
I also tried to do the same with Figtree: the tree and its tip labels
are OK, but the node labels are not (eg, it displays 377 for the
root instead of 100). My guess is that it's a problem when decoding
the strings (maybe specific to Linux).
Best,
Emmanuel
Alastair Potts wrote on 23/02/2011 21:09:
Hi All,
I'm sure I've had this problem before and found a way to fix it. I've
spent an hour looking for the solution, but can't seem to find it.
In short, I've run a bootstrap analysis in PAUP* which provided a
consensus tree with bootstrap values. This tree opens fine in
FigTree. I read it in using ape's read.nexus and plot the node using
nodelabel and the $node.label property of the imported tree. I've
done nothing else to the tree (e.g. ladderize which I know sometimes
causes problems), yet my node label bootstrap values are all shuffled
around in some way and I can't figure out why.
My code is simply:
pt - read.nexus('dataset1.bootstrap.swap.NNI.tree')
plot(pt,cex=0.7)
nodelabels(pt$node.label)
Possibly the problem lies with the nexus tree, so here it is for what
it's worth:
tree PAUP_1 = [U]
(1:0,((2:100,(3:100,4:100)80:80,5:100,6:100,(7:100,10:100)60:60,8:100,9:100,(11:100,34:100)60:60,15:100,(16:100,37:100,54:100,56:100,57:100,71:100,72:100)70:70,18:100,(23:100,25:100,30:100,31:100,35:100,116:100,117:100)59:59,26:100,27:100,32:100,33:100,39:100,48:100,58:100,59:100,60:100,64:100,69:100,70:100,78:100,79:100,80:100,82:100,(83:100,84:100,85:100)52:52,94:100,99:100,101:100,102:100,107:100,119:100)70:70,(12:100,(13:100,14:100,53:100,90:100)69:69,28:100,(62:100,63:100)96:96,(66:100,67:100)69:69,68:100,91:100,92:100,93:100,97:100,98:100,100:100)81:81,(17:100,19:100,21:100,24:100,38:100,42:100,43:100,(44:100,45:100)67:67,47:100,49:100,50:100,61:100)82:82,(20:100,40:100,41:100,51:100,52:100,73:100,74:100,108:100,109:100,110:100,118:100)65:65,(22:100,29:100,36:100,46:100,75:100,76:100,105:100,111:100,112:100,113:100,114:100,115:100)97:97,55:100,(65:100,86:100,89:100,96:100)68:68,(77:100,(81:100,95:100,103:100,104:100)68:68,106:100)65:65,(87:100,88:100)98:98)100:100)1
00
;
My apologies for not setting up a standard replication of the error -
but I'm not really sure how to go about it with this example.
Thanks in advance for your help.
Cheers,
Alastair
___
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
___
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Mixup with plotted bootstrap values
Hi All,
I'm sure I've had this problem before and found a way to fix it. I've
spent an hour looking for the solution, but can't seem to find it.
In short, I've run a bootstrap analysis in PAUP* which provided a
consensus tree with bootstrap values. This tree opens fine in FigTree. I
read it in using ape's read.nexus and plot the node using nodelabel and
the $node.label property of the imported tree. I've done nothing else to
the tree (e.g. ladderize which I know sometimes causes problems), yet my
node label bootstrap values are all shuffled around in some way and I
can't figure out why.
My code is simply:
pt - read.nexus('dataset1.bootstrap.swap.NNI.tree')
plot(pt,cex=0.7)
nodelabels(pt$node.label)
Possibly the problem lies with the nexus tree, so here it is for what
it's worth:
tree PAUP_1 = [U]
(1:0,((2:100,(3:100,4:100)80:80,5:100,6:100,(7:100,10:100)60:60,8:100,9:100,(11:100,34:100)60:60,15:100,(16:100,37:100,54:100,56:100,57:100,71:100,72:100)70:70,18:100,(23:100,25:100,30:100,31:100,35:100,116:100,117:100)59:59,26:100,27:100,32:100,33:100,39:100,48:100,58:100,59:100,60:100,64:100,69:100,70:100,78:100,79:100,80:100,82:100,(83:100,84:100,85:100)52:52,94:100,99:100,101:100,102:100,107:100,119:100)70:70,(12:100,(13:100,14:100,53:100,90:100)69:69,28:100,(62:100,63:100)96:96,(66:100,67:100)69:69,68:100,91:100,92:100,93:100,97:100,98:100,100:100)81:81,(17:100,19:100,21:100,24:100,38:100,42:100,43:100,(44:100,45:100)67:67,47:100,49:100,50:100,61:100)82:82,(20:100,40:100,41:100,51:100,52:100,73:100,74:100,108:100,109:100,110:100,118:100)65:65,(22:100,29:100,36:100,46:100,75:100,76:100,105:100,111:100,112:100,113:100,114:100,115:100)97:97,55:100,(65:100,86:100,89:100,96:100)68:68,(77:100,(81:100,95:100,103:100,104:100)68:68,106:100)65:65,(87:100,88:100)98:98)100:100)100;
My apologies for not setting up a standard replication of the error -
but I'm not really sure how to go about it with this example.
Thanks in advance for your help.
Cheers,
Alastair
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Re: [R-sig-phylo] Mixup with plotted bootstrap values
Hi Alastair,
I copied the Newick string below into R, read it with read.tree, and
this seems to work as normal.
I also tried to do the same with Figtree: the tree and its tip labels
are OK, but the node labels are not (eg, it displays 377 for the root
instead of 100). My guess is that it's a problem when decoding the
strings (maybe specific to Linux).
Best,
Emmanuel
Alastair Potts wrote on 23/02/2011 21:09:
Hi All,
I'm sure I've had this problem before and found a way to fix it. I've
spent an hour looking for the solution, but can't seem to find it.
In short, I've run a bootstrap analysis in PAUP* which provided a
consensus tree with bootstrap values. This tree opens fine in FigTree. I
read it in using ape's read.nexus and plot the node using nodelabel and
the $node.label property of the imported tree. I've done nothing else to
the tree (e.g. ladderize which I know sometimes causes problems), yet my
node label bootstrap values are all shuffled around in some way and I
can't figure out why.
My code is simply:
pt - read.nexus('dataset1.bootstrap.swap.NNI.tree')
plot(pt,cex=0.7)
nodelabels(pt$node.label)
Possibly the problem lies with the nexus tree, so here it is for what
it's worth:
tree PAUP_1 = [U]
(1:0,((2:100,(3:100,4:100)80:80,5:100,6:100,(7:100,10:100)60:60,8:100,9:100,(11:100,34:100)60:60,15:100,(16:100,37:100,54:100,56:100,57:100,71:100,72:100)70:70,18:100,(23:100,25:100,30:100,31:100,35:100,116:100,117:100)59:59,26:100,27:100,32:100,33:100,39:100,48:100,58:100,59:100,60:100,64:100,69:100,70:100,78:100,79:100,80:100,82:100,(83:100,84:100,85:100)52:52,94:100,99:100,101:100,102:100,107:100,119:100)70:70,(12:100,(13:100,14:100,53:100,90:100)69:69,28:100,(62:100,63:100)96:96,(66:100,67:100)69:69,68:100,91:100,92:100,93:100,97:100,98:100,100:100)81:81,(17:100,19:100,21:100,24:100,38:100,42:100,43:100,(44:100,45:100)67:67,47:100,49:100,50:100,61:100)82:82,(20:100,40:100,41:100,51:100,52:100,73:100,74:100,108:100,109:100,110:100,118:100)65:65,(22:100,29:100,36:100,46:100,75:100,76:100,105:100,111:100,112:100,113:100,114:100,115:100)97:97,55:100,(65:100,86:100,89:100,96:100)68:68,(77:100,(81:100,95:100,103:100,104:100)68:68,106:100)65:65,(87:100,88:100)98:98)100:100)100
;
My apologies for not setting up a standard replication of the error -
but I'm not really sure how to go about it with this example.
Thanks in advance for your help.
Cheers,
Alastair
___
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
___
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R-sig-phylo@r-project.org
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Re: [R-sig-phylo] Mixup with plotted bootstrap values
Hi Emmanuel,
I can read in the tree fine using read.nexus too (I've attached the file
this time).
When in FigTree, if you leave the Node Labels display at 'Node Heights',
then you will see 377 at the root of the tree. If you change this
setting to 'label', you will see that the bootstrap values are shown
(i.e. 100 at the root).
If you compare this to:
pt - read.nexus('dataset3.bootstrap.swap.NNI.tree')
plot(pt,cex=0.7)
nodelabels(pt$node.label)
then you will see that the bootstrap values do not mirror the fig tree
placement (which to me looks like the correct placement).
The PAUP analysis and R have been run on a Windows Vista machine.
Thanks for your time,
Cheers,
Alastair
-
Alastair Potts
PhD candidate
Botany Department
University of Cape Town
alastair.po...@uct.ac.za or pott...@gmail.com
University Private Bag, Rondebosch 7700, South Africa
or
PO Box 115, Loxton 6985, South Africa
Cell: 082 491-7275
-
Emmanuel Paradis wrote:
Hi Alastair,
I copied the Newick string below into R, read it with read.tree, and
this seems to work as normal.
I also tried to do the same with Figtree: the tree and its tip labels
are OK, but the node labels are not (eg, it displays 377 for the
root instead of 100). My guess is that it's a problem when decoding
the strings (maybe specific to Linux).
Best,
Emmanuel
Alastair Potts wrote on 23/02/2011 21:09:
Hi All,
I'm sure I've had this problem before and found a way to fix it. I've
spent an hour looking for the solution, but can't seem to find it.
In short, I've run a bootstrap analysis in PAUP* which provided a
consensus tree with bootstrap values. This tree opens fine in
FigTree. I read it in using ape's read.nexus and plot the node using
nodelabel and the $node.label property of the imported tree. I've
done nothing else to the tree (e.g. ladderize which I know sometimes
causes problems), yet my node label bootstrap values are all shuffled
around in some way and I can't figure out why.
My code is simply:
pt - read.nexus('dataset1.bootstrap.swap.NNI.tree')
plot(pt,cex=0.7)
nodelabels(pt$node.label)
Possibly the problem lies with the nexus tree, so here it is for what
it's worth:
tree PAUP_1 = [U]
(1:0,((2:100,(3:100,4:100)80:80,5:100,6:100,(7:100,10:100)60:60,8:100,9:100,(11:100,34:100)60:60,15:100,(16:100,37:100,54:100,56:100,57:100,71:100,72:100)70:70,18:100,(23:100,25:100,30:100,31:100,35:100,116:100,117:100)59:59,26:100,27:100,32:100,33:100,39:100,48:100,58:100,59:100,60:100,64:100,69:100,70:100,78:100,79:100,80:100,82:100,(83:100,84:100,85:100)52:52,94:100,99:100,101:100,102:100,107:100,119:100)70:70,(12:100,(13:100,14:100,53:100,90:100)69:69,28:100,(62:100,63:100)96:96,(66:100,67:100)69:69,68:100,91:100,92:100,93:100,97:100,98:100,100:100)81:81,(17:100,19:100,21:100,24:100,38:100,42:100,43:100,(44:100,45:100)67:67,47:100,49:100,50:100,61:100)82:82,(20:100,40:100,41:100,51:100,52:100,73:100,74:100,108:100,109:100,110:100,118:100)65:65,(22:100,29:100,36:100,46:100,75:100,76:100,105:100,111:100,112:100,113:100,114:100,115:100)97:97,55:100,(65:100,86:100,89:100,96:100)68:68,(77:100,(81:100,95:100,103:100,104:100)68:68,106:100)65:65,(87:100,88:100)98:98)100:100)100
;
My apologies for not setting up a standard replication of the error -
but I'm not really sure how to go about it with this example.
Thanks in advance for your help.
Cheers,
Alastair
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#NEXUS
Begin trees; [Treefile saved Wed Feb 23 19:58:46 2011]
[!
Data file = Aguiler.Feliner.2003.dataset3.nex
Bootstrap method with heuristic search:
Number of bootstrap replicates = 100
Starting seed = 1628266672
Optimality criterion = parsimony
Character-status summary:
Of 615 total characters:
All characters are of user-defined type mymatrix
All characters have equal weight
466 characters are constant
94 variable characters are parsimony-uninformative
Number of parsimony-informative characters = 55
Starting tree(s) obtained via stepwise addition
Addition sequence: random
Number of replicates = 10
Starting seed = 1474473804
Number of trees held at each step during stepwise addition = 1
Branch-swapping algorithm: nearest-neighbor interchange (NNI)
Steepest descent option not in effect
No more than 10 trees of score (length) greater than or equal to 1 will be
saved in each replicate
Initial 'MaxTrees' setting = 1000 (will be auto-increased by 1000)
Branches collapsed (creating polytomies) if maximum branch length is zero
'MulTrees' option in effect
Topological constraints not enforced
Trees are unrooted
100 bootstrap replicates completed
Time used = 01:24:02.7
]
Translate
1
Re: [R-sig-phylo] Mixup with plotted bootstrap values
Hi All,
I think I have located the problem. As usual I had experienced it before
and I found (or someone else found) a workaround - but I couldn't
remember it.
The bootstrap values ($node.label) is mixed up when I save the bootstrap
tree as a nexus file with a translation table in PAUP (this is the
default by the way). If I save the bootstrap tree without a translation
table (i.e. FORMAT=ALTNEX), then the BS values are in their correct places.
If I open both saved bootstrap trees (i.e. with and without translation
tables) in FigTree, I get identical trees with the bootstrap labels in
the correct places. Obviously this has not been the case in R. I think
that there may be a problem when reading in the translation table when
there are values included with each node. I've included examples of both
saved files from PAUP if anyone wishes to play around with the problem.
So, for those of you using PAUP, the quick work-around to avoid this
problem in future is to use SAVETREES ... FORMAT=ALTNEX ...
Cheers,
Alastair
-
Alastair Potts
PhD candidate
Botany Department
University of Cape Town
alastair.po...@uct.ac.za or pott...@gmail.com
University Private Bag, Rondebosch 7700, South Africa
or
PO Box 115, Loxton 6985, South Africa
Cell: 082 491-7275
-
Emmanuel Paradis wrote:
Hi Alastair,
I copied the Newick string below into R, read it with read.tree, and
this seems to work as normal.
I also tried to do the same with Figtree: the tree and its tip labels
are OK, but the node labels are not (eg, it displays 377 for the
root instead of 100). My guess is that it's a problem when decoding
the strings (maybe specific to Linux).
Best,
Emmanuel
Alastair Potts wrote on 23/02/2011 21:09:
Hi All,
I'm sure I've had this problem before and found a way to fix it. I've
spent an hour looking for the solution, but can't seem to find it.
In short, I've run a bootstrap analysis in PAUP* which provided a
consensus tree with bootstrap values. This tree opens fine in
FigTree. I read it in using ape's read.nexus and plot the node using
nodelabel and the $node.label property of the imported tree. I've
done nothing else to the tree (e.g. ladderize which I know sometimes
causes problems), yet my node label bootstrap values are all shuffled
around in some way and I can't figure out why.
My code is simply:
pt - read.nexus('dataset1.bootstrap.swap.NNI.tree')
plot(pt,cex=0.7)
nodelabels(pt$node.label)
Possibly the problem lies with the nexus tree, so here it is for what
it's worth:
tree PAUP_1 = [U]
(1:0,((2:100,(3:100,4:100)80:80,5:100,6:100,(7:100,10:100)60:60,8:100,9:100,(11:100,34:100)60:60,15:100,(16:100,37:100,54:100,56:100,57:100,71:100,72:100)70:70,18:100,(23:100,25:100,30:100,31:100,35:100,116:100,117:100)59:59,26:100,27:100,32:100,33:100,39:100,48:100,58:100,59:100,60:100,64:100,69:100,70:100,78:100,79:100,80:100,82:100,(83:100,84:100,85:100)52:52,94:100,99:100,101:100,102:100,107:100,119:100)70:70,(12:100,(13:100,14:100,53:100,90:100)69:69,28:100,(62:100,63:100)96:96,(66:100,67:100)69:69,68:100,91:100,92:100,93:100,97:100,98:100,100:100)81:81,(17:100,19:100,21:100,24:100,38:100,42:100,43:100,(44:100,45:100)67:67,47:100,49:100,50:100,61:100)82:82,(20:100,40:100,41:100,51:100,52:100,73:100,74:100,108:100,109:100,110:100,118:100)65:65,(22:100,29:100,36:100,46:100,75:100,76:100,105:100,111:100,112:100,113:100,114:100,115:100)97:97,55:100,(65:100,86:100,89:100,96:100)68:68,(77:100,(81:100,95:100,103:100,104:100)68:68,106:100)65:65,(87:100,88:100)98:98)100:100)100
;
My apologies for not setting up a standard replication of the error -
but I'm not really sure how to go about it with this example.
Thanks in advance for your help.
Cheers,
Alastair
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#NEXUS
Begin trees; [Treefile saved Thu Feb 24 09:43:41 2011]
[!
Data file =
E:\ITS.PROJECT\Aguiler.Feliner.2003\Aguiler.Feliner.2003.dataset4.nex
Bootstrap method with heuristic search:
Number of bootstrap replicates = 100
Starting seed = 1353324558
Optimality criterion = parsimony
Character-status summary:
Of 615 total characters:
All characters are of type 'unord'
All characters have equal weight
467 characters are constant
97 variable characters are parsimony-uninformative
Number of parsimony-informative characters = 51
Starting tree(s) obtained via stepwise addition
Addition sequence: random
Number of replicates = 10
Starting seed = 2055594967
Number of trees held at each step during stepwise addition = 1
Branch-swapping algorithm: nearest-neighbor interchange (NNI)
Steepest descent option not in effect
No more than 10 trees of score (length) greater than or equal to 1 will be
