Hello,
I need to handle in R 10M trees produced with the program evolver of
PAML. With a smaller number of trees one could create a multi-phylo
object with ape as
tree.m <- read.tree("filename.tre")
but this is impractical in this case because it takes all the RAM
memory. I've tried something like
> library(ape)
> con = file("evolver.out", open="r") # where evolver.out contains 10M
trees
> lin = readLines(con)
> for (i in 1:length(lin)) {
+ tree <- read.tree(lin[i])
+ # my additional syntax mrca analysis etc. here
+ }
But it doesn't work:
Error in file(file, "r") : cannot open the connection
In addition: Warning messages:
1: closing unused connection 3 (evolver.out)
2: In file(file, "r") :
cannot open file '((((S6: 0.33544, (S1: 0.02314, S10: 0.02314):
0.31230): 0.53388, S5: 0.86932): 0.04830, (S4: 0.51901, (S7: 0.05901,
S2: 0.05901): 0.46000): 0.39861): 0.08238, (S3: 0.30236, (S8: 0.13236,
S9: 0.13236): 0.17000): 0.69764);': No such file or directory
I would very much appreciate your help. Note that computing efficiency
is key here.
Thank you very much for your attention.
Juan A. Balbuena
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
