29fa313a5e720a2860f3cf241c1c11d5 *DESCRIPTION
8a768684be045b82c2967b610e177484 *NAMESPACE
463d63fed3387911a5b18d9acfbddc11 *R/addstimuli.R
984c7fd499ef7d504a986b51fead8f84 *R/adjacencyMatrix_to_logicalRules.R
e30ec302ebcbfe8687aad3962f1061cc *R/bestgam.R
8a8d927f03defd83b17412dda28864f2 *R/center_ddepn.R
234b7ab219c076b44657677d6ca10020 *R/compare.graphs.R
1de81e8039b123298e1be3927ea089f8 *R/coord.R
afb2a4307f3e27c2cd0ba8329d60484d *R/create_signetwork.R
67983b1b5c8e026b35fa7f53b4e22e2b *R/crossover.R
d1149747c44f8f3d77d3312d949b3c54 *R/ddepn.R
6cb50ffdd4b12ca8333898ffb72cfc40 *R/expand.gamma.R
46695bee89dab1a5b9ee3a74d6c4a5fd *R/format_ddepn.R
1117a05252f8940630d287824ee81254 *R/gelman_diag.R
56345bd2c58089f878cb28a62013d9a7 *R/get.phi.final.R
6791024ebc55e35ecf8c63ce0bc3742b *R/getfirstphi.R
86d0d5deb33efd03646efe24ddc25f21 *R/internal.functions.R
de51ca3a9a66df5c0683298af37593de *R/likl.R
684fcf23ec501ebacecb0e915c89a7fc *R/makedata.R
64c55d4084f92564361b948f458523b9 *R/mcmc_accept.R
bf93e71f641e377d04691dad3127c5f5 *R/mcmc_ddepn.R
0216a68b638506253e8f693eae675b3c *R/mcmc_move.R
61ad369d58f313ef5b297058e2c4319c *R/mcmc_performance.R
3df15c22968e84ea0acda5dec0e2da4e *R/modelcomparison.R
686341ddc8b75f59f1d981681ea366c4 *R/netga.R
1e4a08439df27e99bf4c8edbc64ee33e *R/perform.hmmsearch.R
8fc0b3338e584347b2527c7ccb6303b2 *R/plot_edgeconfidences.R
943cf9d71cef040dd40dd24333da2aea *R/plot_mcmctraces.R
305af39ac5a1124cac227d2580bc5b8c *R/plot_profiles.R
0d87639597f3254d43191b4da3d3d267 *R/plotdetailed.R
547e93ec6388e562a5090c13a40d0966 *R/plotdetailed_Rgraphviz.R
d8b684d5dd145b5c99ca31a621f59f07 *R/plotrepresult.R
eea5cfd6e8beca5ffa04143d2b8f177f *R/posterior.R
2406903fd8b17606693011fc7a728830 *R/prior.R
fa1a2c6050f1679ae21408943214007a *R/propagate.effect.R
99541f9d99c3f30b26a77810b29c55ca *R/random.gammaprime.R
74655acde41893d8be1ca24f99668fbd *R/run_checks.R
c1c3853c72ab0e7e533768e40605a3a6 *R/samplephi.R
190993aa1af25ee21729b52753e0c996 *R/signalnetwork.R
db551261b38602b7de4ac44618d441d0 *R/simulatedata.R
ea148b77e0d82f2c1cc4613238c6c1b1 *R/uniquegamma.R
45836a5ea72a4b965dfb2486ac7a4513 *R/zlambda.R
2542470163e497de523ec39587174bfb *data/hcc1954.RData
856570cf175acccdc4591dc0339162e1 *data/hcc1954raw.RData
7fa0ab0e133acb54969c2b70f75acd45 *data/kegggraphs.RData
d2aaa7beb1be7b2f131c0eb9a54e06dc *inst/doc/OLDmcmcoutput.pdf
e1df8b87b3a1c84abfe85c56f6a668ef *inst/doc/ddepn.Rnw
6e6e9da4a5b6479dc303094ebf27bb1e *inst/doc/ddepn.pdf
a48a34114d5f95a9a90458079f0430dd *inst/doc/examplenet.pdf
d8eededaa2f967764284dfd5e6ab319a *inst/doc/mcmcedgeconf.pdf
a0deba3545158ba16e4545c0d7fefdec *inst/doc/mcmcoutput.pdf
0c27d5660ab71c2819b5bf79a356abd8 *inst/doc/mcmcoutput1.pdf
7f3073b81fc312c049d7e77811c28243 *inst/doc/mcmcoutput2.pdf
1a64395e7f79d7e50ac82fccc0a6d887 *inst/doc/mcmcprofiles.pdf
6cf3e4563ca39b03f0c1775560e3812e *inst/doc/mcmctest3_2_stats.pdf
04dac187d9a06523ce85a4bc8661f2a4 *inst/doc/netgaresult.pdf
dd1a3a40b0f06598e94f5eea932f8f78 *inst/doc/netmcmcresult.pdf
285d468031869ca598b7d5334890749d *inst/doc/references.bib
413da9e3a2f2b7a8d62ef0e091107d84 *inst/doc/scorenetgatest.pdf
a4448a7e7c19869b3163b6fde94972b9 *man/addstimuli.Rd
16062566af9343a6934c60dc04cc32b1 *man/adjacencyMatrix_to_logicalRules.Rd
e2c03ec48caec3f1615eb5788624a155 *man/bestgam.Rd
18f4062d56003b2739db9d73fd90d2e5 *man/center_ddepn.Rd
79627c68e76522f8668583da88d1467f *man/compare.graphs.Rd
5251c112f34a6b5b7d0c39baf31c09bf *man/coord.Rd
15181b1b27eb692302bb0db3ec937dcb *man/create_signetwork.Rd
66dc28e0230c9258b6b7e1f930951a3e *man/crossover.Rd
b1c7cc11b17b53ae1a352cf6104fbfd9 *man/ddepn-package.Rd
ab17c06ade444c35964947e39179880c *man/ddepn.Rd
1603a6c1794945582cd5f15a3240b96c *man/expand.gamma.Rd
ac80e1d13f4e6dc5b6d9caba8870ad43 *man/format_ddepn.Rd
1a20e4ff68ef0d1ad771920492186d3d *man/gelman_diag.Rd
0d3e86dff2eb38735689c87b48d16e2e *man/get.phi.final.Rd
0eee6bbc739bac26085d1d47ac5cce8c *man/getfirstphi.Rd
33bc7a1da26885378bdfba7fd1e985ea *man/hcc1954.Rd
5c3dd2cb79d086eb6a4b9b43b75fa6c2 *man/internal.functions.Rd
30ce71d609008aa7e8a47f14c07c8ec5 *man/kegggraphs.Rd
db9ab9742bd06918114c04b328570d04 *man/likl.Rd
dad430735d53bbba81f7576bf828bc4c *man/makedata.Rd
2b3e3918da53f55070d079796f379dbd *man/mcmc_accept.Rd
1c3ce0976deba44931434c5baad241c7 *man/mcmc_ddepn.Rd
02e4484c47c64d7a6c305aa570db30dd *man/mcmc_move.Rd
0b03b11046faac92e360151cd5c0da48 *man/mcmc_performance.Rd
9bdd79d50e0dbf1c84e1dcba70befb46 *man/modelcomparison.Rd
92acd2fd33984d57922f9ad2321dcadb *man/netga.Rd
a1c2af394b93f1fe8241245c0fe1399b *man/perform.hmmsearch.Rd
d5e89d7c6c7318806bcedc85824a1773 *man/plot_edgeconfidences.Rd
c93efada00648b8e3fe8b61bd8bbadd3 *man/plot_mcmctraces.Rd
67aa19dd097e96bb77e747ecbff5509c *man/plot_profiles.Rd
fd2704b9fbb3f3267fa04499aade8826 *man/plotdetailed.Rd
c7f28bb73db0c9a4a48ba454e59a37c6 *man/plotdetailed_Rgraphviz.Rd
0c26992468b6a5b7e6fa412fc906b0ed *man/plotrepresult.Rd
aa833bc9c540ec32bc5b99a472058d43 *man/posterior.Rd
10c1726ef09f24b6df0ff6b01b4e0269 *man/prior.Rd
e8156e7ab7f1373fe52c849ddff00132 *man/propagate.effect.Rd
e5fc69e1a9f54cec775dde2a14f689e6 *man/random.gammaprime.Rd
c779c2f3037956a677740e14b9e494dd *man/run_checks.Rd
2d47b5e4ebadc2d2fc5dff620df9e256 *man/samplephi.Rd
6c71d1ddf26f3b6108129acf37b317f6 *man/signalnetwork.Rd
ad57c3a8710e579f352789f5a8ecf0ae *man/simulatedata.Rd
a48c83826feb06b0335b8cdf80a8c3a2 *man/uniquegamma.Rd
0065fb3f847c5f3fca117cf0524ec2e2 *man/zlambda.Rd
3b602a606a9fbea4c30f29beedc94c03 *src/perform_hmmsearch.c
c5417e5c7cfa6d9aec31fb48900cfe56 *src/perform_hmmsearch.h
12165a21ecb993ddfb4bbb9a2b874136 *src/perform_hmmsearch_globalest.c
63e6b518b51e7775432383dd1eca0c4a *src/perform_hmmsearch_globalest.h
6f1717fd3fa58185e6e06378638abd12 *src/utility_functions.c
26cd08cfd1440d9372fc3731be7c2d01 *src/utility_functions.h
