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ChangeLog
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Following are git commits to Perl-based full Mendel repo
Run "git log" to see changes since July 12, 2015
===========================================================
commit 9cfb552aeb39ad8736e5c0b5ecdc07bbc5608b75
Author: Wesley Brewer <[email protected]>
Date: Sun Jul 12 19:09:21 2015 +0900
Update OSX README file
commit 8a0568a7eb9ae8a3658bc4e5bffbbe6dac67352c
Author: Wesley Brewer <[email protected]>
Date: Fri Jul 10 09:15:07 2015 +0900
Modify OSX install script about non-blank password usage
commit f3df8bfb947f729b426fac49f1c2a49bcf85dc04
Author: Wesley Brewer <[email protected]>
Date: Tue Jul 7 19:27:22 2015 -0400
Update documentation to include waiting time experiments
commit c0a072bd7459303fc56c58dac568d8dab68b99d0
Author: Wesley Brewer <[email protected]>
Date: Tue Jul 7 17:47:19 2015 -0400
Bug fix for bottlenecks that was introduced in 2.4.0
commit 7875ba474ba80d7358067a2a5bce9ef733d41621
Merge: d87c467 7121069
Author: Wesley Brewer <[email protected]>
Date: Mon Jun 29 22:10:29 2015 +0900
Merge branch 'master' of bitbucket.org:whbrewer/mendel
commit d87c467cf14b31fc956e6ab01a943d34ad694059
Author: Wesley Brewer <[email protected]>
Date: Mon Jun 29 22:09:36 2015 +0900
Remove memory allocation section from installation script
commit 2f6e9104ec89149783a304a021da2ed68fb315c0
Author: Wesley Brewer <[email protected]>
Date: Fri Jun 26 06:01:29 2015 +0900
Update ChangeLog
commit 72333b380daca4f1b6d24f4b25502c0e792ffb30
Author: Wesley Brewer <[email protected]>
Date: Fri Jun 26 05:58:27 2015 +0900
Update OSX installation README.txt file
commit fd99c9af26833088c647e2f9cbf9b96288c2fc14
Merge: ae64d9d f4d667a
Author: Wesley Brewer <[email protected]>
Date: Thu Jun 25 16:09:11 2015 +0900
Merge branch 'master' of bitbucket.org:whbrewer/mendel
commit ae64d9d4301c6e63a253448727672302b5c66611
Author: Wesley Brewer <[email protected]>
Date: Thu Jun 25 15:58:26 2015 +0900
Fix some issues with installation script on OSX for 2.5.0
commit 7121069bdb6c6753a0987b03898d03b3726e91c9
Merge: 6fd63df fd99c9a
Author: Wesley Brewer <[email protected]>
Date: Thu Jun 25 00:17:33 2015 -0400
Merge branch 'master' of bitbucket.org:whbrewer/mendel
commit 6fd63dff28a65cf161910d029988828b294074ac
Author: Wesley Brewer <[email protected]>
Date: Thu Jun 25 00:16:56 2015 -0400
A few mods to Makefile for compiling serial version
commit 69a479c199cc50215a0912b31ebc1bbd0315cddd
Author: Wesley Brewer <[email protected]>
Date: Tue Jun 23 15:40:10 2015 +0900
update install uninstall scripts for OSX
commit f4d667abe4b109a29ff130466394b8265362a478
Author: Wesley Brewer <[email protected]>
Date: Tue Jun 23 00:45:10 2015 -0400
Fix some minor issues with parallel waiting time experiments
commit 5774613650d3108b8cffec2b0ada30bb16cc7cc7
Author: Wesley Brewer <[email protected]>
Date: Sat Jun 20 16:10:50 2015 +0900
Add libquadmath.0.dylib to distro
commit 7ee71fb17ef2be5c7f63dae2c071dad36dcb3b22
Author: Wesley Brewer <[email protected]>
Date: Tue Jun 16 21:07:03 2015 +0900
Fix issues with running with "noq" option on OSX
commit 15099ec99c2ea597693b96f91f924253e176027f
Author: Wesley Brewer <[email protected]>
Date: Thu Jun 11 23:44:55 2015 -0400
Mods to user interface to prepare for 2.5.0 release
commit af0afaad5c89c3d982b031dc6418edd49af9b9cd
Author: Wesley Brewer <[email protected]>
Date: Mon Feb 2 16:35:28 2015 +0900
Remove engines/java/nbproject/private directory from repo
commit bda843bbf6e95e3915ffc662876ed4466e6320a4
Author: Wesley Brewer <[email protected]>
Date: Mon Jan 26 12:22:37 2015 -0500
John B's changes for handling recessive polygenic beneficials
commit eb84198bb51bc2be64005f33e54504d3b74ffb58
Author: Wesley Brewer <[email protected]>
Date: Wed Jan 14 13:54:23 2015 -0500
Add polygenic_init to read_parameters output
commit 96207fe45547263e3617cd338253c0d6e432834c
Author: Wesley Brewer <[email protected]>
Date: Tue Jan 13 12:29:41 2015 -0500
Clean up plotting for polygenic beneficials
commit 6302d146e1c4a049635a6757f06c8be640af3fd9
Author: Wesley Brewer <[email protected]>
Date: Mon Jan 12 12:50:57 2015 -0500
Some adjustments output diagnostics for polygenic beneficials
commit dd939b30755c2493a8516860d214712ed47fa9e9
Author: Wesley Brewer <[email protected]>
Date: Thu Jan 8 13:15:29 2015 -0500
Change if/then to select/case for nucl_to_int() function
commit 7fe9515cb2ab9c425036d8602dd54f19157cce16
Author: Wesley Brewer <[email protected]>
Date: Thu Jan 8 12:56:51 2015 -0500
Implement string initialization for polygenic beneficials
commit 8e082ca0dcb3b790d253e5712e41b2292bc9ee4a
Author: Wesley Brewer <[email protected]>
Date: Thu Jan 8 11:57:31 2015 -0500
A bit more cleanup by John B on polygen. bens.
commit 121ea8ca84107f2f2a39bc6682b352a44741e08e
Author: Wesley Brewer <[email protected]>
Date: Mon Jan 5 19:34:51 2015 -0500
John B's changes to remove most of bugs for polygenic benificials
commit 61e179802d9e73ef404a360b68ef93537d25d589
Author: Wesley Brewer <[email protected]>
Date: Wed Dec 24 00:40:05 2014 -0500
John B's changes for handling mutation rates less than 1.e-4
commit b4b92752b74b1917f84bfb116ab6442ca54349c1
Author: Wesley Brewer <[email protected]>
Date: Thu Dec 18 16:36:45 2014 -0500
Don't print fitness distrib params when equal effect
commit ef402a66709a10dfadbadcba791ab7f011022788
Merge: 5967f7e 2883d8a
Author: Wesley Brewer <[email protected]>
Date: Thu Dec 18 15:56:29 2014 -0500
Merge branch 'master' of bitbucket.org:whbrewer/mendel
commit 5967f7e47ab364e359819a55918eb600918c1cd6
Author: Wesley Brewer <[email protected]>
Date: Thu Dec 18 15:54:47 2014 -0500
Change output label for percentage of individuals not selected
commit 2883d8abde95aeaedb372b1c6899ecd8ae4ebe59
Merge: 75be420 2a5ecdf
Author: Wesley Brewer <[email protected]>
Date: Thu Dec 18 10:17:15 2014 -0800
Merge branch 'master' of bitbucket.org:whbrewer/mendel
commit 75be420e805e18f36cc6b128547b4452aae1e4ed
Author: Wesley Brewer <[email protected]>
Date: Thu Dec 18 10:16:38 2014 -0800
Add config file for running on Amazon EC2 machine
commit 2a5ecdffe7f4702f1e49d487e5fc0781b8d81aec
Author: Wesley Brewer <[email protected]>
Date: Wed Dec 17 19:13:04 2014 -0500
Add in status line that shows first/last generation of poly instance
commit 8c00bc6b9bdd21fe4df09671c4989979b15a13f7
Author: Wesley Brewer <[email protected]>
Date: Wed Dec 17 18:39:57 2014 -0500
John B's change to output DNA of 50th percentile individual
commit 99b112d70c3ac4845c6405459b298d0bf8a11ec3
Author: Wesley Brewer <[email protected]>
Date: Wed Dec 17 00:10:39 2014 -0500
Working version of tabulated poly beneficials output
commit 9ab780b51af407e86e1ae3052915caf39f215801
Merge: ccbb39b c45f6cd
Author: Wesley Brewer <[email protected]>
Date: Wed Dec 17 00:01:21 2014 -0500
Merge branch 'master' of bitbucket.org:whbrewer/mendel
commit ccbb39b158ae1258bb52f09637d671805834fa90
Author: Wesley Brewer <[email protected]>
Date: Tue Dec 16 23:56:44 2014 -0500
John B. has polygenic beneficials working
commit c45f6cdfc8a9e89caf45688f3ecc414ee651fa40
Merge: 5d2211d bd298d6
Author: Wesley Brewer <[email protected]>
Date: Mon Dec 15 22:20:02 2014 -0800
Merge branch 'master' of bitbucket.org:whbrewer/mendel
commit bd298d6d54b0e6ac6e0bc6ac7bbd1a08dbf5857a
Merge: 216a976 fd4149a
Author: Wesley Brewer <[email protected]>
Date: Tue Dec 16 00:59:11 2014 -0500
Merge branch 'master' of bitbucket.org:whbrewer/mendel
Conflicts:
engines/fortran/mendel.f90
commit 216a9766f9f3b2f0b8d019d3ae5ab760411071d7
Author: Wesley Brewer <[email protected]>
Date: Tue Dec 16 00:19:23 2014 -0500
John B's fixes for polygenic beneficials
commit 5d2211df11347e855d897a5c8d6b636264cb2bb0
Author: Wesley Brewer <[email protected]>
Date: Mon Dec 15 21:16:15 2014 -0800
Fix the tabulation of polygenic beneficial alleles (branch wes)
commit cc867dbb956394bacac8f4f6305b6bbabbba39f6
Author: Wesley Brewer <[email protected]>
Date: Mon Dec 15 21:01:41 2014 -0800
Revert "Fix the tabulation of polygenic beneficial alleles"
This reverts commit fd4149ae5591a62a157249358406323ee2626979.
commit fd4149ae5591a62a157249358406323ee2626979
Author: Wesley Brewer <[email protected]>
Date: Mon Dec 15 12:24:24 2014 -0800
Fix the tabulation of polygenic beneficial alleles
commit 716e160ff3ea7c55e6548f63af0abd20ad7e8443
Author: Wesley Brewer <[email protected]>
Date: Thu Dec 11 10:06:38 2014 -0500
Finish the rewrite of polygenic beneficials, but still not correct
commit fb266372504756f369e9b6be8dfb236c8a9ffce4
Author: Wesley Brewer <[email protected]>
Date: Wed Dec 10 09:19:20 2014 -0500
Add John B's proposed changes for suppressing crossover
commit 06e24aa4e4ecc5a8f8d8a934b570ddea00f4b697
Author: Wesley Brewer <[email protected]>
Date: Wed Dec 10 08:59:47 2014 -0500
Fix problems with neutrals accumulating with polygenic_beneficials on
commit 389bfdf40e4db3b35d71e64a867236ce27f2021c
Author: Wesley Brewer <[email protected]>
Date: Tue Dec 9 15:35:31 2014 -0500
First working version of new polygenic beneficials treatment
commit 81e1c1d0cdf8cc506d23e6850960a6348636774f
Author: Wesley Brewer <[email protected]>
Date: Tue Dec 9 13:01:25 2014 -0500
Strip out old treatment of poly. bens. to prepare way for new
commit 6ff43d7d3499edc08b2eb96ac72b81723a81b59f
Author: Wesley Brewer <[email protected]>
Date: Sat Dec 6 13:28:57 2014 -0500
Fix minor bug related to suppressed recombination option
commit 86d22c9814b63ca5deeabc6f095c2c07514989ae
Author: Wesley Brewer <[email protected]>
Date: Fri Dec 5 18:28:35 2014 -0500
Add suppressed recombination option
commit ccad6276be9f5e764b05696f1fd75141e0ace1d7
Author: Wesley Brewer <[email protected]>
Date: Fri Dec 5 13:57:01 2014 -0500
Minor tweaks in plot_flot.pl and start.js
commit 43bc91400fd2930e7715e31e8823001c2b55616d
Author: Wesley Brewer <[email protected]>
Date: Sat Oct 25 07:41:52 2014 -0400
Annotate Poisson methods with year
commit 834c400f26ed55f9c72c258aad3f9bd48eb338a5
Author: Wesley Brewer <[email protected]>
Date: Sat Oct 25 20:26:48 2014 +0900
Add interface option to use RANLIB's Poisson RNG
commit 04a18da5f34e4e032cf41720b5d659c48e124c8f
Author: Wesley Brewer <[email protected]>
Date: Sat Oct 18 18:16:53 2014 +0900
Rename mendel.in to mendel.cin
commit b962f2a56f0d397ed16ea86cfa1ed11e473a1bad
Author: Wesley Brewer <[email protected]>
Date: Sat Oct 18 18:01:11 2014 +0900
Convert mutn_rate to exponential format
commit 4427edc6c4480b1a3eeaeb31c84ea79e4fb72734
Author: Wesley Brewer <[email protected]>
Date: Sat Oct 18 17:54:31 2014 +0900
Convert mutn_rate to exponential format
commit b20425968e591637fa3ce4962daa2ecb73dd93a5
Author: Wesley Brewer <[email protected]>
Date: Mon Sep 1 22:21:05 2014 +0900
Change default plot_allele_gens to 1 when using polygenic beneficials
commit 898500264fab49e3455103d1000811d48b1f91ff
Author: Wesley Brewer <[email protected]>
Date: Thu Aug 21 15:27:03 2014 +0900
Some minor fixes and cleanup related exit gen for polygenic beneficials
commit c47dc341269baa9a41f8d6cad364b1d35257459c
Author: Wesley Brewer <[email protected]>
Date: Thu Aug 21 00:04:09 2014 +0900
Add docs folder.. also more info in main README.md
commit 6fde77301f172043e721893f4f3d99531a7a2e46
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 19 22:16:12 2014 +0900
Add top-level Makefile
commit 906d6f6698ca87ab847e2acd25383536e43addad
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 19 22:01:08 2014 +0900
Remove .o and .mod files
commit b7f0e7e12bc4b311a1d86cebe2b4db34ea78f7f9
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 19 21:53:01 2014 +0900
Compute polygenic exit gen...Directory structure
commit 7cff9e6ba8d0b20093543aa680f32d37a10bc87b
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 5 17:03:15 2014 +0900
Add cmendel.exe symbolic link
commit 4b2cb096fda7e20fbdd8a04002ce7dd7637dbfc7
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 5 16:57:03 2014 +0900
Add login directory to repo
commit d028c8eb47ea4fa0f4076efc4c7791784349cb5b
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 5 16:55:29 2014 +0900
Remove login dir
commit fede67c6a193fe4462af9c5ad23706ffe66c6252
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 5 16:14:32 2014 +0900
Readded htdocs correctly
commit 7c0ae9315d1fb792772b442f5167a45f0ef0fc55
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 5 16:14:00 2014 +0900
Remove htdocs
commit b220c953e2666cf90b565d3bf39a2fcfb0ef0541
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 5 16:01:40 2014 +0900
Add scrolling outputs. Add htdocs in distro.
commit e7011e84cc2a322618d4ce658bcb682b07d1953e
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 5 14:05:07 2014 +0900
Write polygenics diagnostics info to .poly file
commit e11725911bd92dec03c4a9ab24a266c45131cd20
Author: Wesley Brewer <[email protected]>
Date: Tue Aug 5 00:11:26 2014 +0900
Ensure polygenic mutns never mutate to same nucleotide
commit ca074878995ed59d4d95422e8d107321b56bb4ff
Author: Wesley Brewer <[email protected]>
Date: Fri Jul 25 23:50:33 2014 +0900
Output info about when polygenic beneficials are fixed
commit d48a450e28257cac07d77c6c60a8e427ab50d9ae
Author: Wesley Brewer <[email protected]>
Date: Thu Jul 24 21:32:32 2014 +0900
Output table of polygenic morphism instances
commit 18127e7ae950234b0c58ec92dbedd5907b2b7991
Author: Wesley Brewer <[email protected]>
Date: Thu Jul 24 00:45:02 2014 +0900
Add output verbosity parameter
commit c0026a218aacfefc07c492b62f013a2797a1bd1a
Author: Wesley Brewer <[email protected]>
Date: Wed Jul 23 16:38:43 2014 +0900
Output the generation of last instance of polygenic benefical
commit ac84a9b9bc1fc617b47173c6811bb3fb34958a3a
Author: Wesley Brewer <[email protected]>
Date: Mon Jul 21 21:34:58 2014 +0900
Add $use_templates in config file to turn templates on/off
commit ddf86fe232ec2bb3adbe46dab0b0a3a1376ed046
Author: Wesley Brewer <[email protected]>
Date: Sun Jul 20 22:16:22 2014 +0900
Rename engine to enginef
commit 68793cc7039e501baa06b03a15e8e41cbba460bd
Author: Wesley Brewer <[email protected]>
Date: Sun Jul 20 22:13:54 2014 +0900
Allow num_generations to go > 999,999
commit 3c2607a8caa29cf0d594ebc5fd83de54b6f65c51
Author: Wesley Brewer <[email protected]>
Date: Sat Jul 12 17:59:42 2014 +0900
Add Java source code into distribution
commit 6f4cca6a20d6b3175478bf16d3c247babbcd60d1
Author: Wesley Brewer <[email protected]>
Date: Sat Jul 12 17:19:10 2014 +0900
Cleanup output of polygenic beneficials
commit 7ecb5a4a19d8f474c94da7bb5660486c23332ca8
Author: Wesley Brewer <[email protected]>
Date: Sat Jul 12 15:52:13 2014 +0900
Rename cmendel>>enginec; jmendel>>enginej
commit 3407fa38e873d2330deb0d1be867deb73e2d79ec
Merge: 08931a2 5330047
Author: Wesley Brewer <[email protected]>
Date: Sat Jul 12 15:19:04 2014 +0900
Merge branch 'master' of bitbucket.org:whbrewer/mendel-back
mering changes made on hs84 with changes made on my local machine
commit 08931a22376e927c985a55ca8f9fbdc016f7a016
Author: Wesley Brewer <[email protected]>
Date: Sat Jul 12 15:18:12 2014 +0900
Compute group selection intensity
commit 5330047e93abe2cfdc47cfba15dc9ff7eec21175
Author: Wesley Brewer <[email protected]>
Date: Sat Jul 5 11:16:11 2014 -0400
Cleanup one line
commit f8b3427faca6f36812bedab088ea9a57f0b553cb
Author: Wesley Brewer <[email protected]>
Date: Sat Jul 5 09:16:07 2014 -0400
Add ability to run jmendel with PBS queue
commit 8a553f4f29830d501411aba777a2540f90beddfc
Author: Wesley Brewer <[email protected]>
Date: Sat Jul 5 19:32:31 2014 +0900
Add jmendel to repo
commit 5de4935a8de56b1101ac1a94a829d575b7f8837a
Author: Wesley Brewer <[email protected]>
Date: Tue Jul 1 17:25:19 2014 +0900
Add ability to use Java and C engines with interface
commit 836c23ab63ebc9922071aaa1eb6f7996d91f6d49
Author: Wesley Brewer <[email protected]>
Date: Wed Jun 11 12:41:44 2014 +0800
Implement polygenic_effect to specify fitness
commit 5c72755e43ea35c0196e42af81972020d723c78e
Author: Wesley Brewer <[email protected]>
Date: Thu Mar 6 10:06:26 2014 -0500
Enable polymorphism plot for equal effect fitness
commit fbe64fce00c7c43a0e3434819ce4cc3d4eec521a
Author: Wesley Brewer <[email protected]>
Date: Thu Mar 6 22:33:25 2014 +0800
Fix equal effect fitness polymorphism analysis bug
commit e47d66bbd378dcbfda06a9bf239127c53fe7a7ee
Author: Wesley Brewer <[email protected]>
Date: Fri Feb 28 14:35:18 2014 +0900
Simplify output for polygenic beneficials
commit 406a921bb0f2451da46b3e10682835924fa94591
Author: Wesley Brewer <[email protected]>
Date: Mon Feb 17 12:02:43 2014 -0500
Polygenic: stop 100 gens after fixation
commit 88ae9ad50eb7ae7dd18e2be94219c45df035055e
Author: Wesley Brewer <[email protected]>
Date: Sun Feb 16 00:26:53 2014 -0500
Fix equal effect fitness_distrib_type with polygenics
commit 9a5f5fd42a1dd2ed371f899eb64625a4f5dd0544
Author: Wesley Brewer <[email protected]>
Date: Thu Feb 13 12:42:16 2014 -0500
Third version of polygenic beneficials (inc parallel)
commit f86f1d762d8ce1ecc0cd8fe5d8d56d4f8bbcc1fe
Author: Wesley Brewer <[email protected]>
Date: Wed Feb 5 14:08:20 2014 -0500
Second version polygenic beneficials
commit 547ec79414cb8eddfa2d2bef189cf3a20fb00312
Author: Wesley Brewer <[email protected]>
Date: Tue Feb 4 19:02:15 2014 -0500
First version of polygenic beneficials implementation
commit 8bc949fad882522f7312dc9551f63a6f55e65557
Author: Wesley Brewer <[email protected]>
Date: Fri Jan 31 11:48:55 2014 -0500
Get some polygenic test functions working
commit 2b3a50f438398b93be2ea6fd9456dab839cb74fd
Author: Wesley Brewer <[email protected]>
Date: Wed Jan 15 12:37:35 2014 -0600
Some changes... dont remember what
commit 9a00ca7734c611613819b1dd4616bc629d4605a1
Merge: f3486db e4a7f20
Author: Wesley Brewer <[email protected]>
Date: Thu Aug 15 00:57:43 2013 -0400
Merge branch 'master' of bitbucket.org:whbrewer/mendel
commit f3486db06a75d7f3581c2f6cd876d6228eee2b3f
Author: Wes <[email protected]>
Date: Thu Aug 15 00:57:05 2013 -0400
A few cosmetic changes related to navbar
commit e4a7f20171f65760cc0b49e8e93525d061a1b55b
Author: whbrewer <[email protected]>
Date: Wed Jul 31 10:46:31 2013 +0900
Cleanup a couple files
commit c8b7366a3dfe6c4aa3e50a0e751d32a65a8db064
Author: whbrewer <[email protected]>
Date: Mon Jul 29 17:18:53 2013 +0900
Close mendel.in file after reading
commit eee4ef2bdc9ccd8763ce0a149147c3d098f0195d
Author: whbrewer <[email protected]>
Date: Fri Jul 26 16:40:16 2013 +0900
Fix bug int(work_fitness) was causing crash
commit 7e147d7fc0d2efd45dba4425c34a416ce40ffebc
Author: whbrewer <[email protected]>
Date: Fri Jul 26 15:36:05 2013 +0900
add navbar and $fepath var
commit 118a57cab33fc711eda7841d9f0ca9971f8b0eca
Author: whbrewer <[email protected]>
Date: Fri Jul 26 02:08:19 2013 +0900
Add oo-code for genome representation in engine
commit 64bce9135e8ec75ebd63b92d3e4b1ee61eb10ad4
Author: whbrewer <[email protected]>
Date: Thu Jul 25 17:53:13 2013 +0900
module selection ... unit testing framework
commit 3717b4773f11896ac63dc2e816c8832c1947ac10
Author: whbrewer <[email protected]>
Date: Thu Jul 25 14:49:26 2013 +0900
add start.js ... start work on btc.py
commit ade3d7cb54a60ac4d9fefcbc4ef4fa4fff966eca
Author: whbrewer <[email protected]>
Date: Tue Jul 23 23:32:16 2013 +0900
Renamed .cgi files .pl -- take two.
commit 5179f8ec22a79dc9ff8fa2a2c55639503b70d1ef
Author: whbrewer <[email protected]>
Date: Tue Jul 23 15:43:00 2013 +0900
Rename all .cgi files to .pl
commit eb1a6be1a51d6ee8693c9a0b5d5afffd4ad0cb99
Author: whbrewer <[email protected]>
Date: Tue Jul 23 15:15:56 2013 +0900
Renamed fmendel to engine.
commit 7e54c3c7530d3f5ca7b68de02732ea2ecf5ce214
Author: whbrewer <[email protected]>
Date: Tue Jul 23 15:14:51 2013 +0900
Rename fmendel to engine. Doing more cleanup and rearranging.
commit 00e12d33027607e71b397daa752e65821f072a43
Author: whbrewer <[email protected]>
Date: Mon Jul 22 23:22:24 2013 +0900
Modfy README.md and move over some unit test files from the Johann repository.
commit 3ae3007c026133d4070a4b88c84b77fe0d3f7136
Author: whbrewer <[email protected]>
Date: Mon Jul 22 17:28:04 2013 +0900
Remove .o files
commit 3c0510b87b67f858c4d5f9c1bb8f72620c85f92c
Author: whbrewer <[email protected]>
Date: Mon Jul 22 17:25:57 2013 +0900
Modify files so that can use mendel-x.y.z format.
commit 9af39a431b2b2ffa9999c9867ec1448c71f56169
Author: whbrewer <[email protected]>
Date: Mon Jul 22 16:41:02 2013 +0900
First git commit...
commit 54c9cb800880dab61d68d3972d67e8d441f0294f
Author: whbrewer <[email protected]>
Date: Mon Jul 22 16:15:32 2013 +0900
First commit. Adding a README.
NOTE: This is the change log for just the Fortran engine
before the revision control system was changed to git instead of CVS.
--------------------------------------------------------------------------------
RCS file: /usr/local/cvs/fmendel/Attic/mendel.f,v
Working file: mendel.f
head: 1.309
branch:
locks: strict
access list:
symbolic names:
keyword substitution: kv
total revisions: 309; selected revisions: 309
description:
Main file of Mendel -- a genetic simulation program to study mutation accumulation over time
----------------------------
revision 1.309
date: 2013-02-16 01:34:31 +0900; author: wes; state: dead; lines: +0 -0; commitid: 1d2511e63894567;
Moved to mendel.f90
----------------------------
revision 1.308
date: 2013-02-09 02:42:29 +0900; author: wes; state: Exp; lines: +235 -235; commitid: da1511538de4567;
Convert all "c" comment statements to "!" to prepare for converting to
f90 free formed files.
----------------------------
revision 1.307
date: 2013-02-09 02:16:58 +0900; author: wes; state: Exp; lines: +0 -1519; commitid: 7800511532e24567;
Separate out file I/O routines to fileio.f and initialization routines to init.f
----------------------------
revision 1.306
date: 2013-02-09 01:39:32 +0900; author: wes; state: Exp; lines: +546 -3928; commitid: 5e9a51152a0f4567;
Separate out offpsring, selection, and diagnostics subroutines into
separate files.
----------------------------
revision 1.305
date: 2013-02-08 03:52:11 +0900; author: wes; state: Exp; lines: +33 -30; commitid: 4a885113f7294567;
Fix a bug in diagnostics_polymorphisms_plot that allowed allele frequence
to be greater than 100/num_tribes. Also some code refactoring: replace all
100's with the NBINS parameter.
----------------------------
revision 1.304
date: 2013-02-08 00:58:13 +0900; author: wes; state: Exp; lines: +63 -19; commitid: 3ba5113ce524567;
This is the initial implementation of tribal fission. In this version
only the population size has been modified with no migration of individuals.
----------------------------
revision 1.303
date: 2013-02-06 01:29:47 +0900; author: wes; state: Exp; lines: +5 -11; commitid: 1eac511133364567;
Undo previous version changes. Using nint ended up generating step
size changes. The previous way of handling discrete changes in
offspring works much better.
----------------------------
revision 1.302
date: 2013-02-05 00:52:05 +0900; author: wes; state: Exp; lines: +11 -5; commitid: 678510fd8ec4567;
Solve problem of shrinking tribes (especially when the pop sizes are small)
when doing tribal competition by using nint function instead of int function.
----------------------------
revision 1.301
date: 2013-02-04 22:34:03 +0900; author: wes; state: Exp; lines: +42 -32; commitid: 40c5510fb8444567;
Make various improvements to tribal competition, including outputting
more diagnostic information such as fertility_factor, and
global_genetic_fitness. Also, make several variables used in
tribal competition as real*8 rather than just real.
----------------------------
revision 1.300
date: 2013-01-05 06:48:55 +0900; author: wes; state: Exp; lines: +31 -30; commitid: 23850e74db54567;
Fix a bug that showed up when trying to run 10 tribes in parallel. The
portion of the code which was meant for tribal competition was being
executed for every parallel run, but did not crash until we tried at
least 8 tribes. Fix involved simply putting wrapping the portion code
of code with an if (tribal_competition) statement.
----------------------------
revision 1.299
date: 2012-12-23 12:22:02 +0900; author: wes; state: Exp; lines: +1 -2; commitid: 21da50d678cf4567;
Remove debug statement.
----------------------------
revision 1.298
date: 2012-12-23 10:42:28 +0900; author: wes; state: Exp; lines: +169 -24; commitid: 7c6950d660504567;
Add coding for command-line options for running mendel from the command
line (mendel -h displays help options). Put default parameters inside the
mendel.f code itself giving proper error message when mendel.in file does
not exist. This allows one to run "mendel -d" to run mendel with default
parameters. Also, add coding for displaying proper error message when
mendel.in file does not exist.
----------------------------
revision 1.297
date: 2012-11-16 14:46:49 +0900; author: wes; state: Exp; lines: +6 -3; commitid: e8750a5d3314567;
Fix a bug in the new handling of neutral mutations.
----------------------------
revision 1.296
date: 2012-07-20 23:18:41 +0900; author: wes; state: Exp; lines: +354 -226; commitid: 309e500967e74567;
Create a new array nmutn to handle neutral mutations. This required changes
to many lines of code. The neutral mutations were being stored in the dmutn
array. The user can control the size of each of the mutation arrays
(dmutn, nmutn, fmutn) from the user interface, so as to only appropriate
the amount of space that is needed.
----------------------------
revision 1.295
date: 2012-02-19 01:04:39 +0900; author: wes; state: Exp; lines: +5 -5; commitid: 38bb4f3fcbdf4567;
Replace absolute path for /usr/local/include/mpif.h with just mpif.h
and set the include path in the Makefile. This was done so I could
test using Open MPI as an alternative solution to MPICH.
----------------------------
revision 1.294
date: 2012-02-13 21:57:41 +0900; author: wes; state: Exp; lines: +25 -1; commitid: 9414f3908384567;
Envelope all MPI commands with START_MPI and END_MPI. These will act like
preprocessor directives, although instead of using the Fortran preprocesser
(fpp), we will use sed. So, to produce a serial version of the code,
one only needs to run "make serial" which will strip the MPI portions of
code, and then run "make".
----------------------------
revision 1.293
date: 2012-02-01 22:31:44 +0900; author: wes; state: Exp; lines: +24 -17; commitid: 8904f293e8b4567;
Fix some format specifiers which are causing the new Intel compiler to
give warnings. Also, prepare code for adding a new option for
fitness_distrib_type == 2.
----------------------------
revision 1.292
date: 2012-01-31 04:06:08 +0900; author: wes; state: Exp; lines: +142 -159; commitid: 373b4f26ea024567;
Clean up read_parameters output; make consistent with namelist.input format.
Make slight improvements to diagnostics_selection.
Rename new_mutn_per_offspring to mutn_rate to handle more general cases and
be consistent with user interface.
----------------------------
revision 1.291
date: 2012-01-11 02:32:21 +0900; author: wes; state: Exp; lines: +8 -3; commitid: 12b04f0c75944567;
1. Also, add code to compute initial_alleles_mean_effect from input parameters.
This was originally done in the interface but led to some confusion.
2. Change declaration of mfirst in diagnostics_polymorphisms_plot to real*8
from integer to remove bug when compiling with gfortran.
----------------------------
revision 1.290
date: 2011-10-13 21:29:50 +0900; author: wes; state: Exp; lines: +87 -1; commitid: 25e54e96d9b74567;
Added routine to output the distribution of contrasting alleles at the
end of the run.
----------------------------
revision 1.289
date: 2011-10-13 21:28:32 +0900; author: wes; state: Exp; lines: +0 -86; commitid: 25c04e96d8fc4567;
Change all integer*1 logicals to true Fortran logicals. These were changed
to integer*1 in the past to allow using 0 and 1 for the mendel.in file,
so that it would be compatible with the C version of Mendel. Since
using the namelist.input format, this is no longer an issue, and
true logicals must be used in order to compile mendel.f using GNU's
fortran compiler, gfortran.
----------------------------
revision 1.288
date: 2011-10-07 07:21:34 +0900; author: johnrb; state: Exp; lines: +125 -43; commitid: 66594e8e298b4567;
Added routine to output the distribution of contrasting alleles at the
end of the run.
----------------------------
revision 1.287
date: 2011-08-11 06:54:24 +0900; author: johnrb; state: Exp; lines: +19 -12; commitid: 5e864e42fd854567;
Modified SE treatment so that SE contribution could never increase fitness.
----------------------------
revision 1.286
date: 2011-07-30 03:09:44 +0900; author: wes; state: Exp; lines: +66 -51; commitid: 492f4e32f7524567;
Include John Baumgardner's latest changes to Synergistic Epistatis treatment.
----------------------------
revision 1.285
date: 2011-07-30 02:55:34 +0900; author: wes; state: Exp; lines: +103 -97; commitid: 48314e32f3f74567;
Remove plot numbers from diagnostic subroutine names, because we keep
changing the numbers in the interface as we add new plots.
Increase the 25000 limit of polymorphisms to 1E6, and use a parameter
MNP so that it is more easily changed in the future.
Add a variable, plot_allele_gens, which the user change change to
indicate the how often (i.e. time interval in generations) to call
the function diagnostics_polymorphisms_plot.
----------------------------
revision 1.284
date: 2011-06-23 00:49:01 +0900; author: wes; state: Exp; lines: +11 -7; commitid: 42854e020ec54567;
Implement extinction_threshold as a user input parameter.
----------------------------
revision 1.283
date: 2011-05-31 12:48:58 +0900; author: wes; state: Exp; lines: +3 -3; commitid: 7f204de464f84567;
Fix minor bug when clonal_reproduction is turned on, do not set
dominant_hetero_expression to 1.0 unless clonal_haploid is also set.
----------------------------
revision 1.282
date: 2011-03-01 13:28:29 +0900; author: wes; state: Exp; lines: +14 -100; commitid: 3c0b4d6c75a84567;
Rename uniform_fitness_effect to uniform_fitness_effect_del.
Replace max_fav_fitness_gain*uniform_fitness_effect with
uniform_fitness_effect_fav.
Remove read_input_parameters_old() subroutine. WHB v1.9.4
----------------------------
revision 1.281
date: 2011-03-01 12:26:20 +0900; author: wes; state: Exp; lines: +17 -58; commitid: 28fd4d6c66544567;
Read in uniform_fitness_effect_fav. Also, get rid of section in
read_restart_dump and write_output_dump where parameters get stored
in the output dump, which requires much maintenance every time a new
input variable is added or removed. I'm trying to simplify the amount
of maintenance that is required for Mendel. WHB
----------------------------
revision 1.280
date: 2011-02-25 08:57:14 +0900; author: wes; state: Exp; lines: +112 -60; commitid: 366e4d66efb94567;
Convert to using namelist input files.
Remove organism_type parameter as it is not used.
----------------------------
revision 1.279
date: 2011-02-23 11:43:37 +0900; author: wes; state: Exp; lines: +243 -127; commitid: 681f4d6473644567;
Add the ability to be able to analyze allele statistics on a global level
for parallel cases. Fix a parallel bug which was causing strange results
on the new Cornell server. There needed to be an added check for
tribal competition, as well as one variable needed to be initialized.
Also, change the variable num_procs to num_tribes, since with overloading
num_procs is not an accurate descriptor. WHB
----------------------------
revision 1.278
date: 2011-02-18 21:28:08 +0900; author: wes; state: Exp; lines: +2 -2; commitid: 3b614d5e659e4567;
Fix parallel bug that showed up on v1.9.2 of the new server. Wes
----------------------------
revision 1.277
date: 2011-02-17 04:00:19 +0900; author: johnrb; state: Exp; lines: +12 -20;
Fixed back mutation bug.
----------------------------
revision 1.276
date: 2011-02-17 00:41:09 +0900; author: johnrb; state: Exp; lines: +89 -101;
Fixed problem in polymorphism analysis for multiple tribes.
----------------------------
revision 1.275
date: 2011-02-16 06:22:51 +0900; author: johnrb; state: Exp; lines: +4 -6;
Fixed small bug relating to neutral treatment.
----------------------------
revision 1.274
date: 2011-02-15 01:56:24 +0900; author: gregor; state: Exp; lines: +7 -7;
Make some corrections to the way social bonus is being handles. Treat
it as a scaling coefficient rather than an exponential factor. Wes
----------------------------
revision 1.273
date: 2011-02-14 08:27:00 +0900; author: johnrb; state: Exp; lines: +352 -193;
Fixed problems with neutral mutation treatment and a problem with the SE
treatment that caused trouble for parallel runs.
----------------------------
revision 1.272
date: 2011-02-08 10:19:27 +0900; author: johnrb; state: Exp; lines: +39 -2;
Fixed a problem with the clonal reproduction and self fertilization
treatments.
----------------------------
revision 1.271
date: 2011-02-08 07:37:58 +0900; author: johnrb; state: Exp; lines: +2 -2;
This version fixes one more mistake in the treatment of neutrals.
----------------------------
revision 1.270
date: 2011-02-08 07:33:00 +0900; author: johnrb; state: Exp; lines: +6 -4;
This version fixes a few more problems with the treatment of neutrals.
----------------------------
revision 1.269
date: 2011-02-08 07:23:57 +0900; author: johnrb; state: Exp; lines: +26 -13;
This version makes some corrections in the treatment of neutral mutations.
----------------------------
revision 1.268
date: 2011-02-06 11:44:46 +0900; author: gregor; state: Exp; lines: +133 -81;
v1.9.1 John Baumgardner added ability to track neutral mutations.
----------------------------
revision 1.267
date: 2011-02-06 11:37:33 +0900; author: gregor; state: Exp; lines: +45 -39;
v1.9.0 Add, remove, and modify a number of variables:
* remove opf_user_input
* change offspring_per_female to reproductive_rate
* rename haploid_genome_size to genome_size
* add parameters:
- track_neutrals
- fraction_neutral
- organism_type
----------------------------
revision 1.266
date: 2011-02-05 08:21:15 +0900; author: wes; state: Exp; lines: +147 -156;
John Baumgardner made some very significant revisions to the treatment
of synergistic epistasis.
----------------------------
revision 1.265
date: 2011-01-14 07:53:22 +0900; author: wes; state: Exp; lines: +14 -33;
Fix some problems in computing tribal fitness. Also, remove
tc_scaling_exponent and random_death_exponent inputs.
----------------------------
revision 1.264
date: 2011-01-12 06:36:14 +0900; author: wes; state: Exp; lines: +193 -131;
This version includes all of John Baumgardner's fixes to get tribal
competition working correctly. It also includes some of my changes
for tribal competition.
----------------------------
revision 1.263