e9237974f283d0add5c9bbe70e3b2bd3 *DESCRIPTION
3b2343cba65455872b4837f597b6e74d *NAMESPACE
1718ff36221999495df843f83f4becd0 *NEWS
6808064b81bc29f3e2e7dba42fb53f12 *R/Block.R
bbe27c07263fd65139046893be88277e *R/DemographicModel.R
c52b80856d03421060de7093f24de6ef *R/Jaatha.R
8d69e42b7856e97b7c2f8515502967cc *R/confidence_intervals.R
893ac12e6ccb7807e47c1f02196aec80 *R/estimate_log_likelihood.R
9c9ea5421d758e2cc4202f3422329e19 *R/find_best_par_in_block.R
9570d4549ad8fb9776df65450c19cd13 *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
6d50440f661ea41993288f4218f5d7dd *R/refined_search.R
adad9ce21c81970a92096985f6d30382 *R/run_simulations.R
c425518c1b267e4fa00a2e65b9a6c43e *R/sim_likelihood.R
4d57c324e3801356d8fc2f1a16d75710 *R/sim_program.R
13762e654d95f98b308fb6470ebf6d1e *R/sim_program_ms.R
01126b658e4dc1be054f8af7a99eaf86 *R/sim_program_seqgen.R
4d43a6515a4ef3a8c1f628757e1aff12 *R/simulate_within_block.R
fedd5b3903a6a37fd6d3c38a62650c1b *R/summary_statistics.R
1f6c9f3cf7818285de862b07b1dedc93 *README
51f0e2cbead1716e0145670866088926 *build/vignette.rds
a49f942027a34f40f3ca42db77029209 *inst/CITATION
ce0e635dc586d788670da01f317d76ef *inst/doc/custom_simulator_howto.Rnw
fa232983d545523cdf6000b47e60c074 *inst/doc/custom_simulator_howto.pdf
2abfe5591874300a48e8a368601ffad3 *inst/doc/jaatha_howto.Rnw
2643033221426524e2e47652e84468a3 *inst/doc/jaatha_howto.pdf
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
86789ee3e4a2a6c359289bc082476c06 *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
64945c81b355d3a1e8aebe4298ad96ac *inst/unitTests/runit.dm-ms.R
f360e5d6060b45beb8dee206a28a5999 *inst/unitTests/runit.dm-seqgen.R
d8d09206cb8b6750fbb078005a7db4cc *inst/unitTests/runit.dm.R
b67205451c5730148526dbbca620b74c *inst/unitTests/runit.fit_glm.R
f6c5018e878ad02e430aabaa9dc9d40d *inst/unitTests/runit.fixed-bugs.R
d67d751df3a992e7151abae27da0d02a *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
86c1ba8f094d8472632dd8d3a7df1bd1 *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
ff2d3e932b11448fbf47ec0c9ea3453d *inst/unitTests/test_setup.R
763298237ee67a4c65bfff37a19b7aa4 *inst/unitTests/test_setup.Rda
2de0c974081fbd11ebc544ec1127b62f *man/Jaatha-class.Rd
0f2b743fdc08d4fb084ef3341598b11c *man/Jaatha.confidenceIntervals.Rd
c0fc4b515289f73a466d5599771c0068 *man/Jaatha.getLikelihoods.Rd
dcb2b05f50e53e0695bfadfcbbfc6287 *man/Jaatha.getStartingPoints.Rd
52c14b32f44c3920b8eca5f92216260a *man/Jaatha.initialSearch.Rd
33e8c3d0a17ad3c4ed200e9a3b4cfe9f *man/Jaatha.initialize.Rd
b347db2ec2e477f560d2a102b534a619 *man/Jaatha.refinedSearch.Rd
efdc80e35345987cd593692873c42365 *man/Jaatha.setSeqgenExecutable.Rd
91681fbd66ec57a43bcc7876160a86ad *man/addFeature.Rd
2a42d992928cfa7923ffb315cc32adf4 *man/calculateJsfs.Rd
a6b3d40b50113130795485d5ebc8670a *man/callMs.Rd
5cefd7dee5fc4f13137f8c4ad57ad318 *man/checkType.Rd
8d0d2ce80f254047366d20feae999885 *man/convertSimResultsToDataFrame.Rd
62046fee3ef30941ec6d571a6aa4d0c0 *man/denormalize.Rd
a944d963a805865ec9c81cf67f2233a4 *man/dm.addGrowth.Rd
deb5ce82dc8e58562f45a2cc2592aa73 *man/dm.addMigration.Rd
52491cda5f486bb479cbfd6b6b940cd3 *man/dm.addMutation.Rd
2ce0de69c7f31c1528d7cc91b1e44bf3 *man/dm.addMutationRateHeterogenity.Rd
bf41f4ccd488f0f0cef0ca74616077f3 *man/dm.addOutgroup.Rd
27a781e08c1290e69a25496d76ce7bf7 *man/dm.addParameter.Rd
b53b160eb034fad40f6b8850155db920 *man/dm.addRecombination.Rd
6bfb13de786f85f7172603bef67d196b *man/dm.addSampleSize.Rd
c051a8d25747d8723d24b6b4e352ebe1 *man/dm.addSizeChange.Rd
8310e5c80607a0e4003af9c252ec535b *man/dm.addSpeciationEvent.Rd
83a60f03fab5a1da1c4291e1628b9670 *man/dm.addSymmetricMigration.Rd
ced0ade3641660f35e06d33048389315 *man/dm.createDemographicModel.Rd
3fe6c7a2c4dbe1b5d173fa5236a4bdde *man/dm.createThetaTauModel.Rd
78a90b7ee721ac3e6e63aed93953e02b *man/dm.getGroups.Rd
50bdf61202da3db8a25a9c3055dd73c9 *man/dm.getLociLength.Rd
73c23cb161fe60a0f72e5953ab94bb06 *man/dm.getLociNumber.Rd
2bc44ffa91b4ef730f35283aff5233f8 *man/dm.setLociLength.Rd
3cfcc50778ae84eaee5d6b99320844ce *man/dm.setLociNumber.Rd
e1ee4e7d01b9a624aa78073938d542a8 *man/dm.setMutationModel.Rd
a13e57bd846f8cd16b628799e2a47228 *man/dm.simSumStats.Rd
d5bc5bb3f4d3c44616db26d99b028094 *man/findBestParInBlock.Rd
ee62382d4068e155265ee459b835687d *man/fitGlm.Rd
be7a954921c017f6f15f156868e2c8d9 *man/fitGlmPoiTransformed.Rd
f491292acdd7d4a3d37a28f5a523cc0f *man/fitPoiSmoothed.Rd
571f0c05f8a8cea5eb7df08bcd556573 *man/getLogFile.Rd
185a28d8e20463a73b43dabccb101047 *man/getLogLevel.Rd
a450186b46adc916cc5e266548b1c207 *man/jaatha-package.Rd
afc233ae27529c909ae32b9f972157ba *man/normalize.Rd
b57e21345fbcbc870f9fbee58b2e92f4 *man/runSimulations.Rd
28cdb0b63acf0233db2f1480bc7af6ef *man/setLogging.Rd
5f400e71d435fd4137acededf73d7442 *man/simulateWithinBlock.Rd
a726b4ffa43904ab87e7f938cdcca274 *src/msFile2jsfs.cc
21dfa564d4303e2bcfcabc8ce836779a *src/seqgenFile2jsfs.cc
241e85821c1e6b5e646c70942c9f5859 *tests/doRUnit.R
ce0e635dc586d788670da01f317d76ef *vignettes/custom_simulator_howto.Rnw
2abfe5591874300a48e8a368601ffad3 *vignettes/jaatha_howto.Rnw
