25dea8b4b3f527e83c3149c4bf41c7b1 *DESCRIPTION
fadd458923374830b8385df5c5210688 *NAMESPACE
63a1d7a22742469ecc78cec3759ab8f3 *NEWS
b1e2209b1f7c57727d2abec002766a78 *R/Block.R
ea2d833850e347c8bd4f0414bfe009b4 *R/DemographicModel.R
68406d3cab8e456bb31c8be0f860d32e *R/Jaatha.R
7b86aa24e26952ccf3c6f6e4a1ad5f09 *R/RcppExports.R
8d69e42b7856e97b7c2f8515502967cc *R/confidence_intervals.R
70e4ce67fd25b652614610896ede4b6d *R/estimate_log_likelihood.R
9c9ea5421d758e2cc4202f3422329e19 *R/find_best_par_in_block.R
070b0ba0c751eebed1de64784da2c50c *R/fit_glm.R
58a94eae00e4201dc192badf85cf30ae *R/helper_functions.R
b735b5c93532c4932102f01d2ccce1ff *R/initial_search.R
eed6062c28207d2f82ab232c77618e40 *R/normalize.R
18e512f638165c90ee85d24b841b587c *R/package_info.R
f836f83cb5e2f10484c8a65a260a5f0e *R/parallelization.R
bfda890301f3a5b53bb30cd7c4449641 *R/read_fasta.R
00ff2c264d6352e708cfd3a8d5d3e8fb *R/refined_search.R
1e0b3936a76b0f74144d404ed433983b *R/run_simulations.R
c425518c1b267e4fa00a2e65b9a6c43e *R/sim_likelihood.R
8c1e05e7308e516e9eeccbb51da0d9a6 *R/sim_program.R
8cf51e8e6b39ef1749404bacdd5b3fe2 *R/sim_program_ms.R
7892053ba10ef2c2dd75c3d3084ec198 *R/sim_program_msms.R
f349b76d73280f02f523ded28a91b865 *R/sim_program_seqgen.R
4d43a6515a4ef3a8c1f628757e1aff12 *R/simulate_within_block.R
8c8a4581e8f70fa8c8cb4c3768ac144c *R/sum_stat_fpc.R
8797ac2f6ad80e650438c50986e4a6ff *R/summary_statistics.R
7d9681532fb4e5c56e27fcf90b6bc9fe *README
a49f942027a34f40f3ca42db77029209 *inst/CITATION
48053b830055b00187d92e88bced69ab *inst/example_fasta_files/sample.fasta
db1b2b10d9621066278914fba405ea70 *inst/integrationTests/it.confidence_intervals.R
a9a0850fa3a24700ca7720488d8c2444 *inst/integrationTests/it.initial_search.R
ce170b45ae6a97bdfa55426143941d6e *inst/integrationTests/it.one_par_model.R
526b57345716f3cce200080287778891 *inst/integrationTests/it.refined_search.R
7476c28fcfc3dfa5f0bb44a7225ac34e *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
40231d6856baf9f63fa40f1a82b19272 *inst/unitTests/runit.cpp-parse-output.R
c629fba9d66c950fa9a802a44db35990 *inst/unitTests/runit.cpp-parse-seqgen.R
b6d7ccc0c9166b7591d2bff969f5fb47 *inst/unitTests/runit.cpp-sumstat-fpc.R
fae6fb193edd3d1cc6f2f1b69fcf1416 *inst/unitTests/runit.cpp-sumstat-jsfs.R
10e4cff025149723ddb80df45625cdf7 *inst/unitTests/runit.custom-simulator.R
517461db568baf5a752034e405a7595a *inst/unitTests/runit.dm.R
09b6cde01b44a1cd007fd6c819ff9823 *inst/unitTests/runit.estimate-likelihood.R
fcc99a54e1b470922d7bef7f06bcaefe *inst/unitTests/runit.fit-glm.R
3a0605c025daa760c0b16f5907a073e2 *inst/unitTests/runit.fixed-bugs.R
3d4d141586b8ebd9c8b6fb6fde1675e6 *inst/unitTests/runit.initial-search.R
fab48f98c8619f229587ff2cb0697368 *inst/unitTests/runit.jaatha.R
eca728935a27ef00a24c0231dc4ed10d *inst/unitTests/runit.normalize.R
20ced8e81d4dd5edb6babc92e34be0de *inst/unitTests/runit.read-fasta.R
545894350c7ace64215e88a65bc67d3d *inst/unitTests/runit.refined-search.R
cecebcee9b353dd52c3432bb3bddaf68 *inst/unitTests/runit.sim-likelihood.R
4a92fe84d6896c9ae9515e1d8a5906f9 *inst/unitTests/runit.sim-prog-ms.R
5c15bfd3393b0d42144050e5ccdf0f2e *inst/unitTests/runit.sim-prog-seqgen.R
22883c79912d16e0c5b0b990d7db6629 *inst/unitTests/runit.sim-program.R
ce10dd61c0db0c86aaedcee88192531b *inst/unitTests/runit.sim_program_msms.r
820fa2e21785e29bd89ad57bdf304b3f *inst/unitTests/runit.simulate-dm.R
b3278b6a0db42aa0c3bfcab09ec26223 *inst/unitTests/runit.simulate-within-block.R
ed2f97c281bf9981da70ddc469b59e7e *inst/unitTests/runit.sum-stat-fpc.R
a60a6acae258ac17350e4793f007ba59 *inst/unitTests/test-setup.R
ce2ca763a8fe293cb9dbbefde752777f *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
d0de21ec53540fd5e40746f00bc6a04a *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
1e5e94803859854ec4afc89479fde201 *man/dm.addMigration.Rd
27efd8e89e248429e022f320a9565c72 *man/dm.addMutation.Rd
04e3eb1d381cc6bed20876311496d8a1 *man/dm.addMutationRateHeterogenity.Rd
98ea49c284618cdb023798fad6a4112b *man/dm.addOutgroup.Rd
66937a070a9d183ddc6c84a72616d41e *man/dm.addParameter.Rd
a1dd8d02d5f3e5d5c9b8d692ccce895a *man/dm.addRecombination.Rd
60ac2be4e8bc1e1e71697527345f8461 *man/dm.addSampleSize.Rd
d842f554350af076cfe417ca83f18222 *man/dm.addSizeChange.Rd
0c9b62ddde37a955d47e999dbb453a4e *man/dm.addSpeciationEvent.Rd
86a4346a83743fe5bfafea62119ff0d0 *man/dm.addSymmetricMigration.Rd
e6ae952c3a92ca28ee081d6c9f32537c *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
f2961bc5445df4bbe7828d74a479f027 *man/jaatha-package.Rd
de1326baaea3d1f166fd50b98c0d8de4 *man/normalize.Rd
da48334b6a58dd13cc224d1b7478c888 *man/runSimulations.Rd
78a57d5ef66ccb6b99388746bc609c4b *man/setLogging.Rd
f8562580f1fa28740f636c45d4245fe7 *man/simulateWithinBlock.Rd
3f7f49eddf4a81e8456118effc053fee *src/RcppExports.cpp
0c6bad2d77d9d7cae9ccf4efee929bc9 *src/parse_output.cpp
851a306bf6efbed06f77754074570979 *src/sum_stat_fpc.cpp
40f08cfc6b3364210660aee8f3745306 *src/sum_stat_jsfs.cpp
af3000a072bba5a9bf467bdd5081c103 *tests/doRUnit.R
