Dear list members!
First of all thanks Mr Paradis for the vector thing. I never used that
before.
I am still having problems with the reconstruction.
I used drop.tip to get rid of taxa that don`t have a value in my
continuous character:
tree.drop <- vector(length=2500, mode="list")
for (i in 1:2500)
{ tree.drop[[i]] <-
drop.tip(tree[[i]], c(7,109,123,139,206,238)) }
Then I used ace again:
AncTest <- vector(length=2500, mode="list")
>
> for (i in 1:2500)
+ { AncTest[[i]] <-
+ ace(character, tree.drop[[i]], type = "continuous", method = "ML",
CI = TRUE) }
I get back an error meassage:
Fehler in solve.default(out$hessian) :
Lapackroutine dgesv: System ist genau singulär
Zusätzlich: Es gab 50 oder mehr Warnungen (Anzeige der ersten 50 mit
warnings())
Error in solve.default(out$hessian) :
Lapackroutine dgesv:system is exactly singular
Additional: .......50 or more warnings
warnings()
1: In nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), ... :
NA/Inf durch größte positive Zahl ersetzt
1: In nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)), ... :
NA/Inf replaced by highest positive number
Does somebody know what is wrong with my data?
Many thanks in advance
Birgit
Am 19.02.2009 um 19:16 schrieb Emmanuel Paradis:
Birgit Lemcke <birgit.lem...@systbot.uzh.ch> a écrit :
Hello Helplist!
This is a question of somebody who has not a lot of experience
using R
(me).So please excuse me if it is an obvious problem for somebody who
is good in R.
I try to use ace with a treefile containing 2500 Bayesian trees and a
continuous character to reconstruct.
Class "multiPhylo"
List of 2500
$ :List of 4
..$ edge : int [1:596, 1:2] 300 301 301 302 303 303 302 300
304
305 ...
..$ edge.length: num [1:596] 0 1 0.147 0.147 1.53 ...
..$ Nnode : int 298
..$ root.edge : num 1
..- attr(*, "class")= chr "phylo"......
'data.frame': 299 obs. of 1 variable:
$ Dissimis221108MedOutgr: num 0.224 0.357 0.195 0.327 0.218 ...
I tried this:
#create list object with dummy numbers
AncTest<-list(rep(list(edge=cbind(x,x),
edge.length=c(rep(999,596)),Nnode=999,root.edge=999),2500))
I wonder why you want to create this list... why not do this instead:
AncTest <- vector(2500, "list")
#ancestral state reconstruction for each of the 2500 trees
for (i in 1:2500)
+ { AncTest[[i]] <-
+ ace(data.frame$variable, Tree[[i]], type = "continuous", method =
"ML", CI = TRUE, ) }
Fehler in nlm(function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)),
hessian = TRUE) :
fehlender Wert in Parameter
Error in nlm function(p) dev.BM(p), p = c(1, rep(mean(x), nb.node)),
hessian = TRUE) :
missing value in parameter
With such a big data set, I'd recommend you first try with the
simpler (and faster) method="pic".
When you can get above error, you can type:
i
in R to see if this happened right on the first tree.
EP
I would be very happy if somebody could help me.
Many thanks in advance
Birgit
=============================
Birgit Lemcke
Institut of Systematic Botany
University of Zurich
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8416
mail: birgit.lem...@systbot.uzh.ch
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=============================
Birgit Lemcke
Institut of Systematic Botany
University of Zurich
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8416
mail: birgit.lem...@systbot.uzh.ch
=============================
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