9bb6840f1a6176208683c84d0e240fd2 *DESCRIPTION
e1ef2f91aa608d8b16e138fd003675f0 *NAMESPACE
af9adc6c2d5a551fb6f900102a3fa3ea *NEWS
98aad14f9db8035f08bdd4c5b8a63153 *R/RcppExports.R
b1e2209b1f7c57727d2abec002766a78 *R/block.R
3bf23d4733879222d5186e929e1be74f *R/confidence_intervals.R
1b107801d80482f730864ab0299f7179 *R/demographic_model.R
70e4ce67fd25b652614610896ede4b6d *R/estimate_log_likelihood.R
9c9ea5421d758e2cc4202f3422329e19 *R/find_best_par_in_block.R
e85481e2535fc70eb420bfcce2c92b7b *R/fit_glm.R
df3165085941ea1082f285bd69b829de *R/helper_functions.R
ac6e8f10036967f428a3a5e4f32b6d9a *R/initial_search.R
8c26ae44dfb0cf862b34c6c96a67b445 *R/jaatha.R
eed6062c28207d2f82ab232c77618e40 *R/normalize.R
18e512f638165c90ee85d24b841b587c *R/package_info.R
55965df5a85f773fb10d4b397144e0e3 *R/parallelization.R
bfda890301f3a5b53bb30cd7c4449641 *R/read_fasta.R
9740e834e49876e04c87a3231cdecfc4 *R/refined_search.R
1e0b3936a76b0f74144d404ed433983b *R/run_simulations.R
c425518c1b267e4fa00a2e65b9a6c43e *R/sim_likelihood.R
8c1e05e7308e516e9eeccbb51da0d9a6 *R/sim_program.R
0787b22d08dbe7e663df346c82ecd536 *R/sim_program_ms.R
0bfe584723aaa0dffeceec913d0c7009 *R/sim_program_msms.R
641424a1c8d082815f229de8be21b233 *R/sim_program_seqgen.R
4d43a6515a4ef3a8c1f628757e1aff12 *R/simulate_within_block.R
8c8a4581e8f70fa8c8cb4c3768ac144c *R/sum_stat_fpc.R
8797ac2f6ad80e650438c50986e4a6ff *R/summary_statistics.R
39cf1d85a44906ce52750a04ca538a8d *README
a49f942027a34f40f3ca42db77029209 *inst/CITATION
48053b830055b00187d92e88bced69ab *inst/example_fasta_files/sample.fasta
25f4f0b8389d178f3061d20bfa3b4397 *man/Jaatha-class.Rd
addaf3ef6dc803900b236fd6505e5755 *man/Jaatha.confidenceIntervals.Rd
c6fbec173317dbb2c3b1663e20fc249c *man/Jaatha.getCIsFromLogs.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
6b6bd15783cbfc021262e7ba23aec2d6 *man/dm.addSummaryStatistic.Rd
86a4346a83743fe5bfafea62119ff0d0 *man/dm.addSymmetricMigration.Rd
e6ae952c3a92ca28ee081d6c9f32537c *man/dm.createDemographicModel.Rd
6cfeab99a1184bfbea953872d1252ec5 *man/dm.createThetaTauModel.Rd
1c003002619aaf7f26db24aeee67b2b3 *man/dm.getGroups.Rd
774009a0b98f441cd1a00333ab485454 *man/dm.getLociLength.Rd
50b61a55e3e7eb4f06aafdb7ed9abb8d *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
b93ea50d7e0a9ab64b66067bfaf1f2fe *man/setCores.Rd
f8562580f1fa28740f636c45d4245fe7 *man/simulateWithinBlock.Rd
2243875b68ae655ea971b80544af94aa *src/RcppExports.cpp
34757eadf1663004ffb8b6a21737ff61 *src/parse_output.cpp
b3e6eff679549017a0366006ebe00258 *src/parse_trees.cpp
851a306bf6efbed06f77754074570979 *src/sum_stat_fpc.cpp
40f08cfc6b3364210660aee8f3745306 *src/sum_stat_jsfs.cpp
9a6f4a85a8df43d9df820505e91c0741 *src/sum_stat_polym_classes.cpp
08e488553cc919b9f30b0fe72722e4a1 *tests/integration/run-tests.R
7dd19ab65f52eef79444b089357a4216 *tests/integration/test-00-test-setup.R
050a9c267350e5bf8ef48b4d4cb74166 *tests/integration/test-01-initial-search.R
87bba29ccbcd0f11d7b6eacedbd6ea9b *tests/integration/test-02-smoothing-sumstats.R
74ee7103e3d294f03b71edb5fd22423c *tests/integration/test-03-confidence-intervals.R
ae0bd250d5f82ad54d01919a70231ce6 *tests/integration/test-04-one-par-model.R
fe6e931d9c0cf8226dad8701f5011297 *tests/testsetup/custom_simulation_interface.R
dbcbb1ce0060ad7a4643f2391b9ee2e6 *tests/testsetup/demographic_models.R
087f002339696e8472120f6c0e883fe7 *tests/testthat.R
86a4db513b09a67ea61e3333641ca954 *tests/testthat/test-aaa-setup.R
a284e3cee3aa565dec0b2ce4ab08c7d3 *tests/testthat/test-u-calc-likelihood.R
9bc7a9cfb447a68b219a62b1167f340c *tests/testthat/test-u-confidence-intervals.R
7ed571e2a5ecf495d8d970a1c94d1e1c *tests/testthat/test-u-cpp-parse-output.R
768703c4d9e54ca5db0ce571d0995d33 *tests/testthat/test-u-cpp-parse-seqgen.R
12252692e206cb21a87791603685f33c *tests/testthat/test-u-cpp-parse-trees.R
d1454906720a6e75c74ad7c361178e32 *tests/testthat/test-u-cpp-sumstat-fpc.R
3ec51760a2fe3915daa40f1df3017d9f *tests/testthat/test-u-cpp-sumstat-jsfs.R
c917d68549d31c2e2a335a3d9eca2818 *tests/testthat/test-u-cpp-sumstat-polym_classes.R
74684fb9bc948fb40d16af819a75055f *tests/testthat/test-u-demographic-model-class.R
abdb403fb11d84e84a9cd4cd9a704fa3 *tests/testthat/test-u-estimate-likelihood.R
841b398d2c5b10adea38af803714b292 *tests/testthat/test-u-fit-glm.R
405dd83752ccd448ae24307c1d8ee421 *tests/testthat/test-u-fixed-bugs.R
aa8319dfcf3161becce716b6b1321b48 *tests/testthat/test-u-initial-search.R
3e938b8cfa0a81f1deea7a2bd417ea24 *tests/testthat/test-u-jaatha-class.R
d5a1f5bc44e857c63a7085a6e10e462c *tests/testthat/test-u-normalize.R
74a88cc8b1f2f02b45aba344a860b413 *tests/testthat/test-u-read-fasta.R
32fda4be370eb0e7ef3c80376ab119a2 *tests/testthat/test-u-refined-search.R
eb8a68689471b2cba0ca8623193861b1 *tests/testthat/test-u-sim-likelihood.R
8b3c35084e90c131796d20a4e697cecf *tests/testthat/test-u-sim-prog-ms.R
029ebb37c783049ac6c0a2caab47aa61 *tests/testthat/test-u-sim-prog-msms.r
4b33d1a57c8f6b9afcadd4c469ded6c3 *tests/testthat/test-u-sim-prog-seqgen.R
ba5da0aae096e76ea3c1c64e3def487e *tests/testthat/test-u-sim-program.R
138a6b803efb3b864e3c65c095dc8ad7 *tests/testthat/test-u-simulate-within-block.R
4e1edc4e3bd78ba2709e1b2fc99a6fe9 *tests/testthat/test-u-sum-stat-fpc.R
