bugNumerical Library for Haploid Genetics - Bugs: bug #30720, Allele frequencies changing...

 
 

bug #30720: Allele frequencies changing without selection or mutation

Submitted by:  None
Submitted on:  Tue 10 Aug 2010 12:02:57 AM UTC  
 
Category:  Library Severity:  3 - Normal
Item Group:  None Status:  In Progress
Privacy:  Public Assigned to:  Joel J. Adamson <trashbird1240>
Open/Closed:  Open

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( Jump to the original submission)

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 -email is 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

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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").

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
Tue 24 Aug 2010 12:32:18 AM UTC, comment #11:

Test fails with three loci and r = 0.3. Why?

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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:

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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:

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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:

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
Tue 10 Aug 2010 03:06:33 PM UTC, comment #2:
  • Possible Programming Errors
  1. Uncaught errors
  2. floating point errors
  3. adding over the wrong indices
Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
Tue 10 Aug 2010 03:04:46 PM UTC, comment #1:

== Possible Programming Errors ==

  1. Uncaught errors
  1. floating point errors
  1. adding over the wrong indices
Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
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.

Anonymous

 

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    Follow 8 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2010-12-02 trashbird1240 Severity5 - Blocker => 3 - Normal
        StatusReady For Test => In Progress
        Open/ClosedClosed => Open
    2010-09-02 trashbird1240 CategoryNone => Library
        Open/ClosedOpen => Closed
    2010-09-01 trashbird1240 StatusNone => Ready For Test
    2010-08-10 trashbird1240 Severity3 - Normal => 5 - Blocker
        Assigned toNone => trashbird1240

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