69c5ababa20b540001a9998ca294d0d5 *DESCRIPTION
6107316a002cbd427f8d909cc7661bdc *NAMESPACE
feae24792d078fbd2830b435a2d3ebd1 *NEWS
6808064b81bc29f3e2e7dba42fb53f12 *R/Block.R
bbe27c07263fd65139046893be88277e *R/DemographicModel.R
2b78afe3d9374f1e2585025ca2c16a96 *R/Jaatha.R
8d69e42b7856e97b7c2f8515502967cc *R/confidence_intervals.R
70e4ce67fd25b652614610896ede4b6d *R/estimate_log_likelihood.R
9c9ea5421d758e2cc4202f3422329e19 *R/find_best_par_in_block.R
da69cc2c0103d461401be6040a35bd16 *R/fit_glm.R
2f93fb3c1810b27031da5e1e739bb46a *R/helper_functions.R
1d42dcd0e81aad938af4bc3dd0a0eebe *R/initial_search.R
eed6062c28207d2f82ab232c77618e40 *R/normalize.R
f836f83cb5e2f10484c8a65a260a5f0e *R/parallelization.R
bfda890301f3a5b53bb30cd7c4449641 *R/read_fasta.R
6d50440f661ea41993288f4218f5d7dd *R/refined_search.R
1e0b3936a76b0f74144d404ed433983b *R/run_simulations.R
c425518c1b267e4fa00a2e65b9a6c43e *R/sim_likelihood.R
4d57c324e3801356d8fc2f1a16d75710 *R/sim_program.R
0de6bedd384ff67ff0c118c5092dcfd2 *R/sim_program_ms.R
7c290cce6f7f5e23cbf33dd3ca3d4e79 *R/sim_program_seqgen.R
4d43a6515a4ef3a8c1f628757e1aff12 *R/simulate_within_block.R
8797ac2f6ad80e650438c50986e4a6ff *R/summary_statistics.R
ea46cdc765f1b36aebf0a3844184a5ae *README
a49f942027a34f40f3ca42db77029209 *inst/CITATION
48053b830055b00187d92e88bced69ab *inst/example_fasta_files/sample.fasta
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
3ee55f7753b631d412533446dddd8e96 *inst/integrationTests/it.sim_prog_seqgen.R
cea95aab31c684320cf4b39d8c80277c *inst/integrationTests/it.smoothing_sumstats.R
306d3fba663753b02a16320179de4415 *inst/unitTests/runit.calc_likelihood.R
32e38824beff80fd8c2cac6ec08a34e8 *inst/unitTests/runit.confidence_intervals.R
10e4cff025149723ddb80df45625cdf7 *inst/unitTests/runit.custom_simulator.R
a5b6976724f59bbc8f36adbc6257e1c0 *inst/unitTests/runit.dm-ms.R
5c15bfd3393b0d42144050e5ccdf0f2e *inst/unitTests/runit.dm-seqgen.R
d8d09206cb8b6750fbb078005a7db4cc *inst/unitTests/runit.dm.R
09b6cde01b44a1cd007fd6c819ff9823 *inst/unitTests/runit.estimate_likelihood.R
f55d53e48e77da90ea1c8852ae1105ab *inst/unitTests/runit.fit_glm.R
f6c5018e878ad02e430aabaa9dc9d40d *inst/unitTests/runit.fixed-bugs.R
3d4d141586b8ebd9c8b6fb6fde1675e6 *inst/unitTests/runit.initial_search.R
aa136ccfec9b1ed626bf4edbf43cc6c8 *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
cecebcee9b353dd52c3432bb3bddaf68 *inst/unitTests/runit.sim_likelihood.R
9581c4fc3af17a9f6058df556141a012 *inst/unitTests/runit.sim_program.R
820fa2e21785e29bd89ad57bdf304b3f *inst/unitTests/runit.simulate_dm.R
b3278b6a0db42aa0c3bfcab09ec26223 *inst/unitTests/runit.simulate_within_block.R
a486a5a5d319924b16aad4d88ea8930f *inst/unitTests/test_setup.R
c09713d7cf411df6d2724021d43e3c09 *inst/unitTests/test_setup.Rda
25f4f0b8389d178f3061d20bfa3b4397 *man/Jaatha-class.Rd
4084850d1e22afbeb58a75e5c15425e8 *man/Jaatha.confidenceIntervals.Rd
414848bffd823aa5e46acb9ec51ebb1d *man/Jaatha.getLikelihoods.Rd
92149f957fd411003b17a2c44285124f *man/Jaatha.getStartingPoints.Rd
177c7dfd42c92a402afe911f66645cbf *man/Jaatha.initialSearch.Rd
d2a53cddb54e97ec25b49275232bd7d7 *man/Jaatha.initialize.Rd
5068c2d949adec80c444237488f46a66 *man/Jaatha.refinedSearch.Rd
d4fc454c1f330202807278bfb0dcdbbb *man/Jaatha.setSeqgenExecutable.Rd
f0e60c1ecb62966e215251696701f465 *man/addFeature.Rd
17d3c04fcefb63ddef8f795b6b7b30d2 *man/calculateJsfs.Rd
1ae78b7a39228f9f1344cb27ef9b6b33 *man/callMs.Rd
945d37294f1da8a30fbad8f143e2ae38 *man/checkType.Rd
1872a2d46c537e78103ff2c9e5bd2baf *man/convertSimResultsToDataFrame.Rd
70aa6341125c8e76707cbaa74cf9e099 *man/denormalize.Rd
e12d21b38d840e065ecefa49f1ddd62f *man/dm.addGrowth.Rd
a1cf0e8139876973c5768a71798faafe *man/dm.addMigration.Rd
c8c2136942c0b4e296dc57ca5a1480ec *man/dm.addMutation.Rd
04e3eb1d381cc6bed20876311496d8a1 *man/dm.addMutationRateHeterogenity.Rd
4d3be662de30b3072a5f85ed6cea6c22 *man/dm.addOutgroup.Rd
66937a070a9d183ddc6c84a72616d41e *man/dm.addParameter.Rd
2e6125818aeea65a6352fe052ca6848a *man/dm.addRecombination.Rd
60ac2be4e8bc1e1e71697527345f8461 *man/dm.addSampleSize.Rd
0b16ed78728c83ea60ecc261b9f93a93 *man/dm.addSizeChange.Rd
647a05a795cd247a915d3fec52789691 *man/dm.addSpeciationEvent.Rd
86a4346a83743fe5bfafea62119ff0d0 *man/dm.addSymmetricMigration.Rd
ec1796f7113eb7149691f66eb46de5d6 *man/dm.createDemographicModel.Rd
6cfeab99a1184bfbea953872d1252ec5 *man/dm.createThetaTauModel.Rd
1c003002619aaf7f26db24aeee67b2b3 *man/dm.getGroups.Rd
b4a2e4b5769392c5fb5307577662bddf *man/dm.getLociLength.Rd
9e9ed54a074fae3363f3889fa89dc283 *man/dm.getLociNumber.Rd
05cfed655ce067958b87203aeb3af640 *man/dm.setLociLength.Rd
0ca4fa6de6fb40f56359dab7ad49c486 *man/dm.setLociNumber.Rd
dcf8ea76074b709d7dc12a61a515b299 *man/dm.setMutationModel.Rd
86a2904ab0f89898353a779bbe1dc5a9 *man/dm.simSumStats.Rd
4f4eaf50630d7ac1326136148a9bb110 *man/estimateLogLikelihood.Rd
4f57375b3712bae184c9ced67569c799 *man/findBestParInBlock.Rd
5a854be2bf743f8298df9fce989da281 *man/fitGlm.Rd
a9e73638514cbe8271707769662798ec *man/fitGlmPoiTransformed.Rd
15707dfc55fcd2f1f4a3f35bb1e2d930 *man/fitPoiSmoothed.Rd
24465cfe0615517f339eb436f0fdb2d9 *man/getLogFile.Rd
dbc88e819270bb9a07ab631a0ff5f00e *man/getLogLevel.Rd
f2961bc5445df4bbe7828d74a479f027 *man/jaatha-package.Rd
de1326baaea3d1f166fd50b98c0d8de4 *man/normalize.Rd
da48334b6a58dd13cc224d1b7478c888 *man/runSimulations.Rd
efb1cf6247fbe15e3a7bba7c9a4c0d6e *man/setLogging.Rd
f8562580f1fa28740f636c45d4245fe7 *man/simulateWithinBlock.Rd
a726b4ffa43904ab87e7f938cdcca274 *src/msFile2jsfs.cc
21dfa564d4303e2bcfcabc8ce836779a *src/seqgenFile2jsfs.cc
241e85821c1e6b5e646c70942c9f5859 *tests/doRUnit.R
