Comments (11)
Death was cast to an int in processing cmd line args; changed to float. I don't think this was the problem responsible for neg branch lengths, but I cannot recreate the problem now. However, do get seg fault on some parameter combinations (e.g. ./pxbd -e 10 -b 0.5 -t 1). Perhaps allow -e OR -t, not both.
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agreed about OR. hm that could be it. lets close and open again when the problem comes back.
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Still getting a bunch of negative branch lengths
from phyx.
Do you have an example that will generate this (b, d, e/t, and seed)?
from phyx.
how do you mean? birth death extant time and seed? can only do birth death
time seed or birth death extant seed
should be pxbd -b 1 -d 0.1 -t 5 -s 1 or pxbd -b 1 -d 0.1 -e 5 -s 1
On Tue, Jun 23, 2015 at 10:55 AM, Joseph W. Brown [email protected]
wrote:
Do you have an example that will generate this (b, d, e/t, and seed)?
—
Reply to this email directly or view it on GitHub
#2 (comment).
from phyx.
Yeah, the "e/t" was supposed to mean e or t.
I just meant a combination that generates negative branch lengths so it could be identified and fixed.
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Oh, I see. I don't have an example that does that.
On Tue, Jun 23, 2015 at 11:27 AM, Joseph W. Brown [email protected]
wrote:
Yeah, the "e/t" was supposed to mean e or t.
I just meant a combination that generates negative branch lengths so it
could be identified and fixed.—
Reply to this email directly or view it on GitHub
#2 (comment).
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Ok, I can set up a loop to try and find an example.
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I tried a bunch of iterations of:
./pxbd -b 0.5 -d 0.45 -e 10000 -o oot.tre && grep ":-" oot.tre
(including different parameter values) and cannot recreate the problem.
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pxbd
now has a nreps
option:
./pxbd -h
Birth-death simulator.
Usage: pxbd [OPTION]...
-e, --extant=INT number of extant species, alt to time
-t, --time=INT depth of the tree, alt to extant
-b, --birth=DOUBLE birth rate, default=1
-d, --death=DOUBLE death rate, default=0
-n, --nreps number of replicates, default=1
-o, --outf=FILE output file, stout otherwise
-s, --showd show dead taxa
-x, --seed=INT random number seed, clock otherwise
--help display this help and exit
--version display version and exit
This should help in the search for negative edge lengths. However, I've simulated a ton and have not hit anything yet.
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I think this is behaving correctly. Closing.
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