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

 
 

bug #30720: Allele frequencies changing without selection or mutation

Submitter:  None
Submitted:  Tue 10 Aug 2010 12:02:57 AM UTC
 
Category:  Library Severity:  3 - Normal
Item Group:  None Status:  In Progress
Privacy:  Public Assigned to:  trashbird1240
Open/Closed:  Open
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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 Administrator
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 Administrator
Thu 02 Sep 2010 12:33:22 PM UTC, comment #15: 

With 9 loci (= 512 genotypes) the test failed, printing

Change in allele frequency detected:
Starting frequency: p[0] = 0.50000000
New frequency: p[0] = 0.50000000

We can conclude that this is a floating-point error.

Joel J. Adamson <trashbird1240>
Project Administrator
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 Administrator
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 Administrator
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 Administrator
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 Administrator
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 Administrator
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 Administrator
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 Administrator
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 Administrator
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:

0.00 0.00 0.00 0.25
0.00 0.00 0.25 0.50
0.00 0.25 0.00 0.50
0.25 0.50 0.50 1.00

but instead it is

Offspring 3:
0:0.00000000 0.00000000 0.00000000 0.25000000
1:0.00000000 0.00000000 0.00000000 0.50000000
2:0.00000000 0.25000000 0.00000000 0.50000000
3:0.25000000 0.50000000 0.50000000 1.00000000

Joel J. Adamson <trashbird1240>
Project Administrator
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:

0.00 0.00 0.00 0.25
0.00 0.00 0.25 0.50
0.00 0.25 0.00 0.50
0.25 0.50 0.50 1.00
-verbatim+

but instead it is

+verbatim+
Offspring 3:
0:0.00000000 0.00000000 0.00000000 0.25000000
1:0.00000000 0.00000000 0.00000000 0.50000000
2:0.00000000 0.25000000 0.00000000 0.50000000
3:0.25000000 0.50000000 0.50000000 1.00000000
-verbatim-

Joel J. Adamson <trashbird1240>
Project Administrator
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:

0.00 0.00 0.00 0.25
0.00 0.00 0.25 0.50
0.00 0.25 0.00 0.50
0.25 0.50 0.50 1.00
-verbatim+

but instead it is

+verbatim+
Offspring 3:
0:0.00000000 0.00000000 0.00000000 0.25000000
1:0.00000000 0.00000000 0.00000000 0.50000000
2:0.00000000 0.25000000 0.00000000 0.50000000
3:0.25000000 0.50000000 0.50000000 1.00000000
-verbatim-

Joel J. Adamson <trashbird1240>
Project Administrator
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:

(gdb) p 0.81000000000000005 + 0.090000000000000011 + 0.088987500000000011 + 0.0089875000000000024
$41 = 0.99797499999999983
(gdb) p 0.81000000000000 + 0.090000000000000 + 0.088987500000000 + 0.0089875000000000
$42 = 0.99797499999999983
(gdb) p 1.0 - $42
$43 = 0.0020250000000001656

Joel J. Adamson <trashbird1240>
Project Administrator
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 Administrator
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 Administrator
Tue 10 Aug 2010 12:02:57 AM UTC, original submission:  

See the following output of nrm:

joel@ezra: ~/Downloads/haploid-svn > ./nrm
0.01974340 0.44058534 0.02151351 0.51815775 0.00075166
0.00481892 0.42372376 0.00512739 0.56632993 0.00055650
0.00097273 0.37189410 0.00102674 0.62610643 0.00022720
0.00017616 0.28200642 0.00019377 0.71762365 0.00007177
0.00002753 0.15952647 0.00003409 0.84041191 0.00001770
0.00000337 0.05297994 0.00000520 0.94701149 0.00000292
0.00000032 0.00920273 0.00000067 0.99079628 0.00000031
0.00000003 0.00111590 0.00000008 0.99888399 0.00000003
0.00000000 0.00012535 0.00000001 0.99987464 0.00000000
0.00000000 0.00001394 0.00000000 0.99998605 0.00000000
0.00000000 0.00000155 0.00000000 0.99999845 0.00000000
0.00000000 0.00000017 0.00000000 0.99999983 0.00000000
0.00000000 0.00000002 0.00000000 0.99999998 0.00000000
0.00000000 0.00000000 0.00000000 1.00000000 0.00000000
0.00000000 0.00000000 0.00000000 1.00000000 0.00000000
0.00000000 0.00000000 0.00000000 1.00000000 0.00000000

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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