Mon 06 Dec 2010 04:38:34 PM UTC, comment #17:
-- mode: compilation; default-directory: "~/Public/src/haploid/" --
Compilation started at Thu Dec 2 13:28:16
make -k check
make sim_stop pop_ck sparse_test diseq rec_test
make[1]: Entering directory `/home/joel/Public/src/haploid'
make[1]: `pop_ck' is up to date.
make[1]: `sparse_test' is up to date.
make[1]: `diseq' is up to date.
make[1]: `rec_test' is up to date.
make[1]: Leaving directory `/home/joel/Public/src/haploid'
make check-TESTS
make[1]: Entering directory `/home/joel/Public/src/haploid'
PASS: sim_stop
PASS: pop_ck
PASS: sparse_test
Change in allele frequency detected:
Starting frequency: p[0] = 0.50000000000000000000000000000000000000000000000000000
New frequency: p[0] = 0.50000000000001088018564132653409615159034729003906250
[...]
/bin/sh: line 5: 11068 Aborted (core dumped) ${dir}$tst
FAIL: rec_test
Value by hand: 0.170442
Value by ld_from_geno: 0.170442
PASS: diseq
=========================================
1 of 5 tests failed
Please report to -unavailable-
=========================================
make[1]: *** [check-TESTS] Error 1
make[1]: Leaving directory `/home/joel/Public/src/haploid'
make: *** [check-am] Error 2
make: Target `check' not remade because of errors.
Compilation exited abnormally with code 2 at Fri Dec 3 04:31:32
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Thu 02 Dec 2010 06:35:59 PM UTC, comment #16:
With 9 loci there is a difference at the ninth decimal place. At this point it looks like a floating point error and we will have to conduct further tests to determine if it is significant.
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Thu 02 Sep 2010 12:33:22 PM UTC, comment #15:
With 9 loci (= 512 genotypes) the test failed, printing
We can conclude that this is a floating-point error.
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Wed 01 Sep 2010 07:51:05 PM UTC, comment #14:
The test as it is goes pretty close the limits of published recombination algorithms (with r = 0.5), so we may be waiting a while for the test to finish.
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Wed 01 Sep 2010 07:46:20 PM UTC, comment #13:
Changes in revision 1112 fix this. Revision 1113 includes a thorough test. We can close this as soon as the test finishes on my machine.
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Mon 30 Aug 2010 12:15:45 AM UTC, comment #12:
We need to track the parental genome we are starting with. Use the branching array design to keep track of genuine branch points (true "maybes").
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Tue 24 Aug 2010 12:32:18 AM UTC, comment #11:
Test fails with three loci and r = 0.3. Why?
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Mon 23 Aug 2010 09:35:39 PM UTC, comment #10:
Four-locus simulation chokes; my suspicion is that we are ending up with more than two expressions to sum, thereby not subtracting enough. We need to find a way to add the expressions on the fly so we get as many as we need.
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Mon 23 Aug 2010 06:55:04 PM UTC, comment #9:
Now producing correct tables for two and three loci; we should not close this bug until we have tested larger numbers of loci.
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Tue 10 Aug 2010 08:27:45 PM UTC, comment #8:
Revising the mating table calculations for the random mating examples produces allele frequencies that do not change. See mating.c in revision 1086.
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Tue 10 Aug 2010 07:59:04 PM UTC, comment #7:
Revision 1084 fixes the problem of not assigning to crosses that can produce certain offspring.
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Tue 10 Aug 2010 06:18:06 PM UTC, comment #6:
Rec_gen_table is producing incorrect recombination tables!
For example, the table for offspring 3 in a tlta with r = 0.5:
but instead it is
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Tue 10 Aug 2010 06:17:05 PM UTC, comment #5:
Rec_gen_table is producing incorrect recombination tables!
For example, the table for offspring 3 in a tlta with r = 0.5:
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Tue 10 Aug 2010 06:15:22 PM UTC, comment #4:
Rec_gen_table is producing incorrect recombination tables!
For example, the table for offspring 3 in a tlta with r = 0.5:
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Tue 10 Aug 2010 05:11:11 PM UTC, comment #3:
Removing the denominator from rec_mating is logical (the denominator should be taken care of in the mating table calculation). However, small errors lead to a large deviation from frequencies that sum to 1.0:
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Tue 10 Aug 2010 03:06:33 PM UTC, comment #2:
- Possible Programming Errors
- Uncaught errors
- floating point errors
- adding over the wrong indices
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Tue 10 Aug 2010 03:04:46 PM UTC, comment #1:
== Possible Programming Errors ==
- Uncaught errors
- floating point errors
- adding over the wrong indices
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Tue 10 Aug 2010 12:02:57 AM UTC, original submission:
See the following output of nrm:
According to Emacs calc, the frequency of the focal allele at locus 1 changes from 0.95874309 to 0.99005369.
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