16a19c11c99489357e2dd2135e7490de *DESCRIPTION
d95558f369417555952ec1cccc49c723 *NAMESPACE
3779f5c1018f383a753733cfea8f67f0 *NEWS
64f93a739559135438dfb28ec93ba84b *R/Block.R
33aa4c745a470e7fcc32fa3a0f47531b *R/DemographicModel.R
77c1ae382f48a9f086f37b01aac9b8d6 *R/Jaatha.R
4d57c324e3801356d8fc2f1a16d75710 *R/aaa_SimProgram.R
69766dde2ce35cf9a4405d15afee0b16 *R/calc_likelihood.R
644fb5eacd526ca84ce72954403e6ad1 *R/glm_fitting.R
9f3789b9d7ed51b42d8e68ead720960c *R/helper_functions.R
c1a739d6c5ee2e3f9291c59bf576bcf8 *R/initial_search.R
a5dcc662091dd1bac14a55ae6814cce9 *R/parallelization.R
bfda890301f3a5b53bb30cd7c4449641 *R/read_fasta.R
a51bc0aa93f219774dfefc0ced21abcc *R/refined_search.R
5a8729ddf1decb607d9fafbcf9bab26d *R/sim_program_ms.R
7f0fcc281a2931ca0e6b455e79b9c168 *R/sim_program_seqgen.R
7b41b19c22e946f84a7084199d447c59 *R/simulate_dm.R
835a6741fd6db5d36c2eeabd0527b7e3 *R/simulate_within_block.R
fedd5b3903a6a37fd6d3c38a62650c1b *R/summary_statistics.R
7a5a15910ce0c15ae875e5838b819442 *README
a49f942027a34f40f3ca42db77029209 *inst/CITATION
48053b830055b00187d92e88bced69ab *inst/example_fasta_files/sample.fasta
9ec0163d08db816f4d69c5c92b61717f *man/Jaatha-class.Rd
d64bdd8b393493f0f674264395ec4ebb *man/Jaatha.getLikelihoods.Rd
f8918d9aee60b6cffae64c6d28dac2e4 *man/Jaatha.getStartingPoints.Rd
e089513c2394985101432d02f1997bfe *man/Jaatha.initialSearch.Rd
3d7d17cf37ef891716ae56c74109d1ef *man/Jaatha.initialize.Rd
18d08a2de2bd549722ec25338183ee45 *man/Jaatha.refinedSearch.Rd
3446bd4c61aea076b1c2bfc6b6bbf903 *man/Jaatha.setSeqgenExecutable.Rd
dde35b93fcc6c7fbf4e295239d1a14ec *man/addFeature.Rd
afdf8bb69053ad116d7027099dd271f8 *man/calculateJsfs.Rd
05870663789804d6d83aeb6e6aadfd6c *man/callMs.Rd
a5166679ef44a03aebf37c668c63cbf6 *man/checkType.Rd
03e581e4af91366bffbffc25c9c58c5b *man/dm.addGrowth.Rd
f35a81167acc9d342138b849ce54197f *man/dm.addMigration.Rd
b6cee0dc7fad2f47fbc923530399cf87 *man/dm.addMutation.Rd
0948afeb092c3455a622440ee1966137 *man/dm.addMutationRateHeterogenity.Rd
ff0cf5cd5eae63490cb48a3739b1248d *man/dm.addOutgroup.Rd
bb12ce88a0cb8b1f4e39271bc44d07d3 *man/dm.addParameter.Rd
15a1ddb7d98306da407beeedff2a7896 *man/dm.addRecombination.Rd
57085eec1c53292d97587f51766a097f *man/dm.addSizeChange.Rd
217b31713c9dc4c196ba5072723114fd *man/dm.addSpeciationEvent.Rd
71e8260cac714ae4ac1c198ebb2e7e5e *man/dm.addSymmetricMigration.Rd
4063c7a9daf92466a3767ac078472434 *man/dm.createDemographicModel.Rd
cb2d4360ea8607355345c91a6c84b989 *man/dm.createThetaTauModel.Rd
80d7a08273d61b7038d87cb536938420 *man/dm.setMutationModel.Rd
2c570e3553d9695a8ee28add99c28bc7 *man/dm.simSumStats.Rd
10eeafd7cfa65af999d748b257819367 *man/getLogFile.Rd
179715690e846e18503487942ef35438 *man/getLogLevel.Rd
95b761c749396635961abd3e3a1192e6 *man/jaatha-package.Rd
7616974b0f052d6c9fb8a34652372fa6 *man/setLogging.Rd
1ccb10eb4f7e1a2d3ea81a1af04e4fa9 *src/Makevars
f2b904ba0d7a3383384761bc9309ee64 *src/msFile2jsfs.cc
b2855e3d5cfcd3a9a11ac586c4e7551a *src/seqgenFile2jsfs.cc
