Displaying 2 results from an estimated 2 matches for "ratematrix".
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rankmatrix
2006 Jan 02
1
R crash with complex matrix algebra when using EISPACK=TRUE
...e to
investigate further.
## The code :
source("http://www.daimi.au.dk/~olefc/TEST/fct.R")
source("http://www.daimi.au.dk/~olefc/TEST/parm.crash.R")
for(l.v in 1:4){
for(r.v in 1:4){
for(l.x in 1:4){
for(r.x in 1:4){
hvad <-
inhomoWmat.complex(subst.ratematrix(parm.same.str.sym$Gamma[,,l.v,r.v]),subst.ratematrix(parm.same.str.sym$Gamma[,,l.x,r.x]),
EISPACK=TRUE)
print(c(l.v,r.v,l.x,r.x))
}
}
}
}
## gives
[1] 1 1 1 1
[1] 1 1 1 2
[1] 1 1 1 3
[1] 1 1 1 4
[1] 1 1 2 1
Segmentation fault
### whereas the code seems to work fine when E...
2012 Apr 11
0
phangorn and calculation of a rate matrix
Hi, I'm trying to calculate a ratematrix for a RNA aligment (U instead of T)
in order to use it as a ratematrix in Profidst (a phylogenetic program which
takes into account both the primary sequence and the secondary structure of
the RNA, in my case rRNA). The sequence-structure aligment has been made in
4SALE (a java app) and saved as on...