afea2814755afcd40d68022787ac344b *DESCRIPTION
94f3baa9f3c6214668a97c4e663cdedb *NAMESPACE
f3d8910321c8831a2fd3ab0cd34a8e23 *NEWS
731ed39fe8cd6cbacfd323a779776d17 *R/RcppExports.R
b1e2209b1f7c57727d2abec002766a78 *R/block.R
6db28df0c95b2dd766beeeb5de150f34 *R/confidence_intervals.R
e1955997e1b22bf1b5160dbb0af3a257 *R/demographic_model.R
70e4ce67fd25b652614610896ede4b6d *R/estimate_log_likelihood.R
9c9ea5421d758e2cc4202f3422329e19 *R/find_best_par_in_block.R
e85481e2535fc70eb420bfcce2c92b7b *R/fit_glm.R
d2d9f3cd7abb67cadc434bc5fb4baa2e *R/helper_functions.R
ac6e8f10036967f428a3a5e4f32b6d9a *R/initial_search.R
f2271db04e2fd5925a488da3a5f7cf2f *R/jaatha.R
eed6062c28207d2f82ab232c77618e40 *R/normalize.R
18e512f638165c90ee85d24b841b587c *R/package_info.R
55965df5a85f773fb10d4b397144e0e3 *R/parallelization.R
21f1b1de8e2f89785f616c20f5429509 *R/read_fasta.R
9740e834e49876e04c87a3231cdecfc4 *R/refined_search.R
56bba4e91d0d050f1862aa6be454bd84 *R/run_simulations.R
c425518c1b267e4fa00a2e65b9a6c43e *R/sim_likelihood.R
8c1e05e7308e516e9eeccbb51da0d9a6 *R/sim_program.R
714947b27012ef833e8ab7aa6a35ba6e *R/sim_program_ms.R
81f678e01735625d7c458da515c1acb0 *R/sim_program_msms.R
b3746d37d9a8f9f132b395a50bac45e3 *R/sim_program_seqgen.R
4d43a6515a4ef3a8c1f628757e1aff12 *R/simulate_within_block.R
9e6f3505b088567ed560389ba0dca3e6 *R/sum_stat_fpc.R
79b67f95aea531d8a4d553154ba7ac2f *R/sum_stat_generate.R
f53bfa246c35550ce6eb152bebdfc7d5 *R/sum_stat_jsfs.R
4732d97669a31e5134da73d6c825e07c *R/sum_stat_pmc.R
bf367f51fff5ad2afee1308d01e79645 *README.md
a49f942027a34f40f3ca42db77029209 *inst/CITATION
48053b830055b00187d92e88bced69ab *inst/example_fasta_files/sample.fasta
324197fd5ed3d98ec10a73d8e1fe43de *man/Jaatha-class.Rd
c6932d6aa81e00ba80be5846282496e6 *man/Jaatha.confidenceIntervals.Rd
461f443d03c80e93ff90c8f9be88c8b8 *man/Jaatha.getCIsFromLogs.Rd
6502d402c3215b0df9f3efd0e4f97fb2 *man/Jaatha.getLikelihoods.Rd
3ae60151cb9763ccc55f7d6259ce8c4e *man/Jaatha.getStartingPoints.Rd
c5d09a71f7846aac7aa0d73364e3df50 *man/Jaatha.initialSearch.Rd
22ff3c8bee83081bd2d4914d020c8287 *man/Jaatha.initialize.Rd
6e7c947a0637bed56e4a9a227ad8b220 *man/Jaatha.refinedSearch.Rd
3a8cfe01aa00b3436e3a9bfb9fa73b7e *man/Jaatha.setSeqgenExecutable.Rd
3b5cd52cf2893422472a87b5977dbc3b *man/addFeature.Rd
5fe773fa7f952a1f16ba7646509dbc68 *man/calcJsfs.Rd
3fb4d0c97e37e8054e61237d74ac21d7 *man/calculateJsfs.Rd
6d4e3c7bda8b87dfcc5ed7ad7dff7b7d *man/checkType.Rd
dc6b3d83996d1692d1db537355aed3a3 *man/convertSimResultsToDataFrame.Rd
077060e2bc39c7061161d4e8c9aa4086 *man/denormalize.Rd
c664c1e8dbe8d002c1055fefb17c13f3 *man/dm.addGrowth.Rd
cc2f95eae1956640965d106ba1e1e60d *man/dm.addMigration.Rd
fb265671a23ca9f34dc8cb2e38039e5a *man/dm.addMutation.Rd
40f5a12cef746c3a073379860c17b93a *man/dm.addMutationRateHeterogenity.Rd
0350c699ab9a4894f8e005563c5a618a *man/dm.addOutgroup.Rd
06739ac8dbb9d1d548742a28835e8eb9 *man/dm.addParameter.Rd
a946d1247c8d9a391bda5dce714bff79 *man/dm.addRecombination.Rd
e1ec856f8cf84e32e36c2eecdcafe9b1 *man/dm.addSampleSize.Rd
fea07b88eecd5d3ccf84a082a979abfc *man/dm.addSizeChange.Rd
f8fbfda7eda3485af97bc107b926f233 *man/dm.addSpeciationEvent.Rd
b084f28a4cb71e8322950f019d456efe *man/dm.addSummaryStatistic.Rd
6660950c0ca61b4af564e1859f71b34a *man/dm.addSymmetricMigration.Rd
c67a82d947b5645d548a67c42b6c074f *man/dm.createDemographicModel.Rd
f6ae95958d7e6efb2c51eace2253b40a *man/dm.createThetaTauModel.Rd
516dd7f05c42a739ac05f60632bd8ed8 *man/dm.getGroups.Rd
1e1d4c637c6c61de3422cfef18a27378 *man/dm.getLociLength.Rd
026f05906bc46e853738e906524673a2 *man/dm.getLociNumber.Rd
add071436ff392c74ae4c17e177fd820 *man/dm.setLociLength.Rd
025c1dcb0e3405f6ce8b73bdd2db7498 *man/dm.setLociNumber.Rd
7bf0061e24e9e89d9b7097c40ebabe76 *man/dm.setMutationModel.Rd
814d5572fb69fed73a0938a7dad3ccdd *man/dm.simSumStats.Rd
3ab0235d439da095a0eb8dc071a36582 *man/estimateLogLikelihood.Rd
f21b5d29075adab22d2f6058bffd9528 *man/findBestParInBlock.Rd
262dc27cf86532bf8a3f1fb798d296c0 *man/fitGlm.Rd
eac8deef1ec2bad673ae139366fd2048 *man/fitGlmPoiTransformed.Rd
4a875b3fe309978c3981ff6155a8cf5e *man/fitPoiSmoothed.Rd
1447cae7583fb2c48de89781bdcf2ba5 *man/jaatha-package.Rd
138623ace405f1353f778b645e3ea760 *man/normalize.Rd
832774f9c25540031ef922280ddfaf15 *man/runSimulations.Rd
d09b16b43b57a8d94c26392d4dbe174d *man/setCores.Rd
a6ce51afc8b5121e168ad6637e3d7d80 *man/simulateWithinBlock.Rd
1cde5546248772cef6c0722ec3e2b983 *src/RcppExports.cpp
99b2afa7952f7ce81c472953375b1582 *src/parse_ms_output.cpp
a0692a269b309017121834f454f13eaa *src/parse_seqgen_output.cpp
66544ec19123ff745bccbfafff102976 *src/parse_trees.cpp
fb28ffb012395346467777fee59893b2 *src/seg_sites.h
20cccfe2665c5ce34c17a86f0596088d *src/sum_stat_fpc.cpp
35edfed8fbcd834b0961cbb10034999c *src/sum_stat_jsfs.cpp
a386b0d735855e4fd576403b16d33546 *src/sum_stat_pmc.cpp
08e488553cc919b9f30b0fe72722e4a1 *tests/integration/run-tests.R
c75b497799cf9839d7eb242478c1eeff *tests/integration/test-00-test-setup.R
b8b32ec2896b49f30fb3ec7f3706d0a9 *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
087f002339696e8472120f6c0e883fe7 *tests/testthat.R
fe6e931d9c0cf8226dad8701f5011297 *tests/testthat/setup-custom-simulation-interface.R
35bbef4520eca2e611cf7625313a16d8 *tests/testthat/setup-demographic-models.R
96295b91b6de8cc96050783cd0f358fa *tests/testthat/test-aaa-setup.R
a284e3cee3aa565dec0b2ce4ab08c7d3 *tests/testthat/test-calc-likelihood.R
9bc7a9cfb447a68b219a62b1167f340c *tests/testthat/test-confidence-intervals.R
18b378229c5fe7d8388df350b7485b54 *tests/testthat/test-demographic-model-class.R
abdb403fb11d84e84a9cd4cd9a704fa3 *tests/testthat/test-estimate-likelihood.R
841b398d2c5b10adea38af803714b292 *tests/testthat/test-fit-glm.R
aa8319dfcf3161becce716b6b1321b48 *tests/testthat/test-initial-search.R
f08ebbede53fb5e86d2802f967c40e0b *tests/testthat/test-jaatha-class.R
d5a1f5bc44e857c63a7085a6e10e462c *tests/testthat/test-normalize.R
6ee6764017b5a30b37ca85f5cd199728 *tests/testthat/test-parse-ms-output.R
f314fd24d2a2efc3f3db84205d61ebc9 *tests/testthat/test-parse-seqgen-output.R
bdfc17c3b29463cdfd9e21430179c17c *tests/testthat/test-parse-trees.R
87f4bd678658b4038de4c85d6a66065d *tests/testthat/test-read-fasta.R
32fda4be370eb0e7ef3c80376ab119a2 *tests/testthat/test-refined-search.R
eb8a68689471b2cba0ca8623193861b1 *tests/testthat/test-sim-likelihood.R
ba5da0aae096e76ea3c1c64e3def487e *tests/testthat/test-sim-program.R
d70faa53cdf2908a3401b7291c633eb7 *tests/testthat/test-simprog-ms.R
1f52f4d27953371f119abb4dab387e0b *tests/testthat/test-simprog-msms.R
f65998461e441185b3a076343e2a44cb *tests/testthat/test-simprog-seqgen.R
138a6b803efb3b864e3c65c095dc8ad7 *tests/testthat/test-simulate-within-block.R
724604fe8bf19580952db8577288f866 *tests/testthat/test-sumstat-fpc.R
64bdca113e7479eb93c28e08ac7c7b66 *tests/testthat/test-sumstat-jsfs.R
3f80210d698cd3229c19301203751688 *tests/testthat/test-sumstat-pmc.R
265e6d2a5e7b2cae40ef7e79df39bc57 *tests/testthat/test-zzz-temp-files.R
