53eeaa84da024d1fbd9860d99438ecc2 *DESCRIPTION
c6a4624c6106109c3d5ee30849357d83 *NAMESPACE
e1400c5bb1108a589a0da5fff0bcb106 *NEWS
6808064b81bc29f3e2e7dba42fb53f12 *R/Block.R
f5bad702c8f46e84b6eb1476a5d6fcc9 *R/DemographicModel.R
564dc3204a50d22865af7bd8aee95339 *R/Jaatha.R
4d57c324e3801356d8fc2f1a16d75710 *R/aaa_SimProgram.R
8d69e42b7856e97b7c2f8515502967cc *R/confidence_intervals.R
893ac12e6ccb7807e47c1f02196aec80 *R/estimate_log_likelihood.R
9c9ea5421d758e2cc4202f3422329e19 *R/find_best_par_in_block.R
678d6c2630930d3ffaa2949c7acbf467 *R/fit_glm.R
2f93fb3c1810b27031da5e1e739bb46a *R/helper_functions.R
e438bb6049fd4ea3d0837079c51aba58 *R/initial_search.R
eed6062c28207d2f82ab232c77618e40 *R/normalize.R
f836f83cb5e2f10484c8a65a260a5f0e *R/parallelization.R
bfda890301f3a5b53bb30cd7c4449641 *R/read_fasta.R
ceab6ec722ba1472da8ae7dee885c2a1 *R/refined_search.R
adad9ce21c81970a92096985f6d30382 *R/run_simulations.R
c425518c1b267e4fa00a2e65b9a6c43e *R/sim_likelihood.R
6f8468308a606d6a3217b1e14c936932 *R/sim_program_ms.R
8b656180a25cc44b7c245e624a45d2e8 *R/sim_program_seqgen.R
4d43a6515a4ef3a8c1f628757e1aff12 *R/simulate_within_block.R
fedd5b3903a6a37fd6d3c38a62650c1b *R/summary_statistics.R
1f6c9f3cf7818285de862b07b1dedc93 *README
a49f942027a34f40f3ca42db77029209 *inst/CITATION
033a6d58b82ff3dcad7eb0444e963a82 *inst/doc/custom_simulator_howto.R
ce0e635dc586d788670da01f317d76ef *inst/doc/custom_simulator_howto.Rnw
926f8df66bfe3034a8441dffde5f20be *inst/doc/custom_simulator_howto.pdf
27dba28c77f0b33b4d5b97a0db12628e *inst/doc/jaatha_howto.R
2abfe5591874300a48e8a368601ffad3 *inst/doc/jaatha_howto.Rnw
481b4e0d325bfea1b8be5cc4dcec9e01 *inst/doc/jaatha_howto.pdf
48053b830055b00187d92e88bced69ab *inst/example_fasta_files/sample.fasta
c5e6fe1176055eed269b2a609f087329 *inst/integrationTests/doRUnit.R
db1b2b10d9621066278914fba405ea70 *inst/integrationTests/it.confidence_intervals.R
1c047f45ddf5b295825ae5f9360f4616 *inst/integrationTests/it.initial_search.R
a6a522da90c301e9ab5553dda432a786 *inst/integrationTests/it.one_par_model.R
0b135754f269312838710b38d4c6a9a1 *inst/integrationTests/it.refined_search.R
c3aa7e0a5cb0760e0fcbd37c91c9699d *inst/integrationTests/it.sim_prog_seqgen.R
86789ee3e4a2a6c359289bc082476c06 *inst/integrationTests/it.smoothing_sumstats.R
f222e14358f5b2a8fd616fb6d09c4fdf *inst/integrationTests/results/detailed.html
0723ce4dcb96af0e23a65243094a4675 *inst/integrationTests/results/detailed.txt
0a7aac8aaeb40d3e1889618e117168d1 *inst/integrationTests/results/summary.txt
979fd0e0fb5264d5bea9409b1d064b72 *inst/integrationTests/samples.save
306d3fba663753b02a16320179de4415 *inst/unitTests/runit.calc_likelihood.R
32e38824beff80fd8c2cac6ec08a34e8 *inst/unitTests/runit.confidence_intervals.R
10e4cff025149723ddb80df45625cdf7 *inst/unitTests/runit.custom_simulator.R
a8c17b745890f8aacbe82432bf41316b *inst/unitTests/runit.dm-ms.R
f56dc7b75f25c49a3614ab01c559506f *inst/unitTests/runit.dm-seqgen.R
c79d30f6c17e103ab98bfda378b43105 *inst/unitTests/runit.dm.R
a27fa82780cf1b1b25d50ff3028dff1b *inst/unitTests/runit.fit_glm.R
f6c5018e878ad02e430aabaa9dc9d40d *inst/unitTests/runit.fixed-bugs.R
d67d751df3a992e7151abae27da0d02a *inst/unitTests/runit.initial_search.R
5c7680495172646c38e7fcdc38799886 *inst/unitTests/runit.jaatha.R
eca728935a27ef00a24c0231dc4ed10d *inst/unitTests/runit.normalize.R
20ced8e81d4dd5edb6babc92e34be0de *inst/unitTests/runit.read_fasta.R
9a48c6a75719bc90cb1ec99dd9faef6a *inst/unitTests/runit.refined_search.R
86c1ba8f094d8472632dd8d3a7df1bd1 *inst/unitTests/runit.sim_likelihood.R
9581c4fc3af17a9f6058df556141a012 *inst/unitTests/runit.sim_program.R
820fa2e21785e29bd89ad57bdf304b3f *inst/unitTests/runit.simulate_dm.R
99de6339b27700f238663e12b78c0e6d *inst/unitTests/runit.simulate_within_block.R
0d3bfa9c9d0258b2f077decae23ac947 *inst/unitTests/test_setup.R
afb0cd426e0dafa937595e10b385323d *inst/unitTests/test_setup.Rda
826fd18bb00211d6ee2f61c41d4974a8 *man/Jaatha-class.Rd
1e862e20cc3f554ee873dab2ea72c51e *man/Jaatha.confidenceIntervals.Rd
4e0d592f185b6b8863c3643515b89b8f *man/Jaatha.getLikelihoods.Rd
29db57b4f23ece93f4bd1cf5181ed282 *man/Jaatha.getStartingPoints.Rd
4bf258271a939258612b78ba86ee1217 *man/Jaatha.initialSearch.Rd
f5faa503a83a00e44741587bf49ad4ef *man/Jaatha.initialize.Rd
796719409bc6646e2346106e42bdf2f4 *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
ed2fd7fad9d820c652497efd68e225ae *man/convertSimResultsToDataFrame.Rd
d7f2849c26b55286047e700e1b30cf37 *man/denormalize.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
9affe5c91fb187f97e68d42b258e65c9 *man/dm.simSumStats.Rd
ad750e4110157c7178259c700bd22c55 *man/findBestParInBlock.Rd
6cd26585e807507d58fc4f3d3e19b3c9 *man/fitGlm.Rd
cacc1c50e8909526213e0728766c5850 *man/fitGlmPoiTransformed.Rd
ee81dae1f6148992c92a5d78d360fa3b *man/fitPoiSmoothed.Rd
10eeafd7cfa65af999d748b257819367 *man/getLogFile.Rd
179715690e846e18503487942ef35438 *man/getLogLevel.Rd
95b761c749396635961abd3e3a1192e6 *man/jaatha-package.Rd
b9fd68859db85d978e146a59ba2a346c *man/normalize.Rd
7bfd3b328135a50038342f6c5893738a *man/runSimulations.Rd
7616974b0f052d6c9fb8a34652372fa6 *man/setLogging.Rd
77f27a714d9867d8e0dfb5b344d73004 *man/simulateWithinBlock.Rd
f504bc4b764d7b3d6f3451a0f297b051 *src/Makevars
c498f50a5482a8e4ae8835f711a0843c *src/Makevars.win
a726b4ffa43904ab87e7f938cdcca274 *src/msFile2jsfs.cc
21dfa564d4303e2bcfcabc8ce836779a *src/seqgenFile2jsfs.cc
241e85821c1e6b5e646c70942c9f5859 *tests/doRUnit.R
ce0e635dc586d788670da01f317d76ef *vignettes/custom_simulator_howto.Rnw
2abfe5591874300a48e8a368601ffad3 *vignettes/jaatha_howto.Rnw
