1befcdaa44bee6014bc8e45ef512d227 *DESCRIPTION
9bba65075b24c78c21f541da499f7ba6 *NAMESPACE
a6a90b72bb4fd558863db2ee384867e3 *NEWS
df285660b8d5bde7f764e688d2c98650 *R/Block.R
e8886556225cd2fe95bd6896f4337b5c *R/DataProcessor.R
415d5bf8103efaeaf7ce2ae1b8401bdb *R/DemographicModel.R
60338b47c3819a5ce29cd585299873be *R/Jaatha.R
82756ec105599718efa33ec9773cd60e *R/ModelFitting.R
8b2ed94cf4b55dc0e772c6023101ee78 *R/Simulator.R
4d57c324e3801356d8fc2f1a16d75710 *R/aaa_SimProgram.R
20bf4900b3f7e058a18c3678bf4b9f78 *R/helper_functions.R
176be88e03051e6f4692eaf0a45fcb4b *R/parallelization.R
ccce32d93da3d8390f63a582e7f566f3 *R/read_fasta.R
eb0a8d9366b8e59a94915da55809eee5 *R/sim_program_ms.R
93ab7f63625bb674de312c4f1b989057 *R/sim_program_seqgen.R
67bb13c78943d2981f8098d0fa4a3952 *R/summary_statistics.R
afa223f9efcc66f5f60bbce5417cd8ae *inst/doc/jaatha.Rnw
6e44b4c2652dac5537e4239647d8cebb *inst/doc/jaatha.pdf
c2365df97778adf7ca7a7cea60e1616f *inst/example_fasta_files/sample.fasta
987279c76e6b5441ebb04595444d290a *man/Jaatha-class.Rd
20017e07e3896f28eb4745c000bc2470 *man/Jaatha.defaultSumStats.Rd
d64bdd8b393493f0f674264395ec4ebb *man/Jaatha.getLikelihoods.Rd
c4d515f7e8339fc960301fe2286c404b *man/Jaatha.getStartingPoints.Rd
e089513c2394985101432d02f1997bfe *man/Jaatha.initialSearch.Rd
1376900fefd04254fc38c11d5e314cb9 *man/Jaatha.initialize.Rd
eafa90448f39a0ce8d158995476d7705 *man/Jaatha.refinedSearch.Rd
3446bd4c61aea076b1c2bfc6b6bbf903 *man/Jaatha.setSeqgenExecutable.Rd
dde35b93fcc6c7fbf4e295239d1a14ec *man/addFeature.Rd
afdf8bb69053ad116d7027099dd271f8 *man/calculateJsfs.Rd
05870663789804d6d83aeb6e6aadfd6c *man/callMs.Rd
a5166679ef44a03aebf37c668c63cbf6 *man/checkType.Rd
03e581e4af91366bffbffc25c9c58c5b *man/dm.addGrowth.Rd
f35a81167acc9d342138b849ce54197f *man/dm.addMigration.Rd
b6cee0dc7fad2f47fbc923530399cf87 *man/dm.addMutation.Rd
0948afeb092c3455a622440ee1966137 *man/dm.addMutationRateHeterogenity.Rd
ff0cf5cd5eae63490cb48a3739b1248d *man/dm.addOutgroup.Rd
bb12ce88a0cb8b1f4e39271bc44d07d3 *man/dm.addParameter.Rd
15a1ddb7d98306da407beeedff2a7896 *man/dm.addRecombination.Rd
57085eec1c53292d97587f51766a097f *man/dm.addSizeChange.Rd
217b31713c9dc4c196ba5072723114fd *man/dm.addSpeciationEvent.Rd
71e8260cac714ae4ac1c198ebb2e7e5e *man/dm.addSymmetricMigration.Rd
4063c7a9daf92466a3767ac078472434 *man/dm.createDemographicModel.Rd
cb2d4360ea8607355345c91a6c84b989 *man/dm.createThetaTauModel.Rd
80d7a08273d61b7038d87cb536938420 *man/dm.setMutationModel.Rd
573dfdc7624c2b6a5b87a5ac11425261 *man/dm.simSumStats.Rd
10eeafd7cfa65af999d748b257819367 *man/getLogFile.Rd
179715690e846e18503487942ef35438 *man/getLogLevel.Rd
95b761c749396635961abd3e3a1192e6 *man/jaatha-package.Rd
7616974b0f052d6c9fb8a34652372fa6 *man/setLogging.Rd
1ccb10eb4f7e1a2d3ea81a1af04e4fa9 *src/Makevars
f9a4c1c5772f6cc8afbd45f3c3363570 *src/ms2jsfs.cc
253680af10341ed7ad036b6d2e876c57 *src/msFile2jsfs.cc
4865b04bf7b0a5090e8a440904e7c888 *src/seqgenFile2jsfs.cc
d2e509d071430ed7341480b3f73919c2 *vignettes/cache/initialSearch.Rnw
551446118e48e16020c96bf7a59f3a1e *vignettes/cache/initialSearch.tex
0b637bb517ba75bb2733b3e7616847cc *vignettes/cache/refineSearch.Rnw
d48ff900ae074cd96cd8187154c051d5 *vignettes/cache/refineSearch.tex
e352e938d4a96a7a797bea4292a4f5de *vignettes/cache/saved_objects/jaatha-complete.Rsave
7a42f6a599f01cc803b9806589ecb188 *vignettes/cache/saved_objects/jaatha.Rsave
de07bf3292b67e995c3b7c9ca013c45d *vignettes/cache/saved_objects/start-points.Rsave
430315b3e358a3761f547a83b45222f1 *vignettes/img/dm.png
f8c0544381a20476b33f0eafea8be5f4 *vignettes/img/dm.svg
afa223f9efcc66f5f60bbce5417cd8ae *vignettes/jaatha.Rnw
0063ff8a7dcdd66cf1c7970133b6cdc0 *vignettes/jaatha.bib
