b47547a4b78c35591dfd298ee3161607 *DESCRIPTION
c298e374756e6c8d21e5407e201c0763 *NAMESPACE
c3463e1aed378e3877cf173661e2ad37 *NEWS.md
b5f03dbe8864792ece07c4b45daf4851 *R/C-generator.R
3372140765c36e64b442d34464b0372b *R/SEIR.R
cb7e9ab7f6a15ae51e5628cd1dff5346 *R/SIR.R
c8ea0f26f820d6883b15821f0415c7f6 *R/SIS.R
2bb635f168ba592f784cdd6e9d961255 *R/SISe.R
d698733b698324a651151f27af653d2c *R/SISe3.R
d4fa7a882a80ef6ef7a4b9d2f36b7b10 *R/SISe3_sp.R
d5a677526896b2bf244cd94cefe8f2d8 *R/SISe_sp.R
cc24a66ea8fb6c3b3c9851c6aa7e280d *R/SimInf-package.R
93e034077248c88d7e25a1fc52fd7595 *R/SimInf.R
ed195601679a9382eb0e4197220f1465 *R/SimInf_events.R
d02cf440a5a7ca270ca80ecd862f06fc *R/SimInf_individual_events.R
8fefbee30a6c4fd04b63a31935e48761 *R/SimInf_model.R
22bfc2cc22563f52fac1238c0c83542f *R/abc.R
1c69772ace81928df074b97269f800ac *R/check_arguments.R
bfcd9f560be75cdc0aa4d2b6296015c3 *R/classes.R
f58da0274c2f0cedca94c2dba2c1d2be *R/degree.R
96e6301663f8bdc24fdb325782693ec9 *R/density_ratio.R
f291e7eea653b9e486a38bb99b29b62c *R/distance.R
1b8dee2ee7906a5da57de0127dce7c83 *R/distributions.R
62a4bcd0bdc69a836ef6491ed07f7281 *R/edge_properties.R
dc551487804d73577a899a2168ec23ad *R/init.R
872fba06ca1d1e3ce053116767920955 *R/lambert.R
d0464b2deb94cf3a5806cfda090db9ad *R/match_compartments.R
2ce1e9396b9bfa68fd8cead7aa55f3c1 *R/mparse.R
b54f21eed3c521d25c4d8396884c5b13 *R/n.R
b6de1d29c9b589ebf79fcfee35d72feb *R/openmp.R
15111729f539ea9bc0b004baf80c89f4 *R/package_skeleton.R
04fc0236934af6b327d1b6ca0779685b *R/pfilter.R
56a2d6cdcdcd84f6da71cbd0918d4ad2 *R/plot.R
ab602aab6336b84ad4ca2cc70b36a526 *R/pmcmc.R
f7d1d2362471af4b747e9b1664e3c332 *R/prevalence.R
23e9e005e868f83086cd8093a34e7bb4 *R/print.R
c46e57078a5d39d9db2feeec25991967 *R/punchcard.R
ffaa9882d92ad66742abd6ddc12f1ba3 *R/run.R
f5c0365fa00be40c8fb31a85881af571 *R/trajectory.R
7ced3ba5c33d37b71875faf5803921c4 *R/u0.R
bdb42665fdc2af7ce55692dfd5fe9074 *R/v0.R
ebf9ee07d5873457a452ff3fa22057d1 *R/valid.R
879441110939b3ebeb6fe3220a053add *README.md
c5260b1bae00ec1fb8d54bd1b69b28ba *build/partial.rdb
ef8942a251593c61b76f90a8c678f298 *build/vignette.rds
09753d871c4c0139a0a81d2f39a3d7f8 *cleanup
7d82513f2feaf8087c17cfdc7e57527e *configure
db624801fcad3757fc1d1806a05108a8 *configure.ac
92d07847d90e0c2a505f41140889d1dc *data/events_SISe3.rda
00a854fbeab1b973edd5ca564af9d03a *data/nodes.rda
e4cc4ca1a5ff459aaa9b3c9d42d6f1dd *data/u0_SISe3.rda
b02e5cd1ef2d8a43b24c8ad1b7716bfd *inst/CITATION
a94f6d4d5d7ed36e5fd4d60f4ec80333 *inst/doc/SimInf.R
23c72cf0ef9eede3e8eedf07c7728d41 *inst/doc/SimInf.Rnw
ad5f355e5f1dee27f3589ba96580512f *inst/doc/SimInf.pdf
34cd08464fd5ad94776343fa32bdc7b6 *inst/doc/mparse.R
b29a9eec376f6d8c81bbc50304c1b974 *inst/doc/mparse.Rmd
c30428a2bd38f90ff360f419874c9f0e *inst/doc/mparse.html
177132d3aca115b65bb39ff7c06f3be6 *inst/doc/post-process-data.R
ee48897376861124546f29c531df7866 *inst/doc/post-process-data.Rmd
bfa9a16c08bbe856038b74845e4a9931 *inst/doc/post-process-data.html
0bc1ff6ee991a8516b603e1cb6440c05 *inst/doc/scheduled-events.R
f21c9af061273ad52f66e878c3085be6 *inst/doc/scheduled-events.Rmd
a676329f032e72ee4dd5070cb4baa176 *inst/doc/scheduled-events.html
32d13f747609363c3e985de84d08acd3 *inst/include/SimInf.h
0d2e73a57cf2e88ae5b8d893d9109d01 *man/C_code.Rd
32e47f9bc2795dcca192aeb5bd45f7dc *man/SEIR-class.Rd
055c3f7c51478f9b5c0260155df2fd34 *man/SEIR.Rd
407310b87268581322f347fd6bd40da8 *man/SIR-class.Rd
b6278154ee4435cbdd779555f2392984 *man/SIR.Rd
d0f89a8a9a53d58dfe94b49761da302a *man/SIS-class.Rd
49571a92499d0d5d3692e34205d65c84 *man/SIS.Rd
1a18eec742d05e31497897629887f0c8 *man/SISe-class.Rd
b0f6f2c6c8c301ebf2b0bda92d210851 *man/SISe.Rd
ba481ebe9848c3aeae46880cae63a61c *man/SISe3-class.Rd
8bbd8b13bd7a912355ddf366a1ad81a0 *man/SISe3.Rd
c43ce526ae2e966548e071ccf804f5c1 *man/SISe3_sp-class.Rd
be344a4e58c8021bb5f92dcedb8c86a8 *man/SISe3_sp.Rd
24f3471c3610605a996afe49c2dfec03 *man/SISe_sp-class.Rd
d153298b297ee500503b610f8407816d *man/SISe_sp.Rd
e767181323522d1cd332a7b4ec7cd5b9 *man/SimInf.Rd
5ae92a80ed56c05734a92618afeabba5 *man/SimInf_abc-class.Rd
64f2288e3fc4a7fe461ae292425f2587 *man/SimInf_events-class.Rd
5c839f46d7a8ae1d6a073960979fdb47 *man/SimInf_events.Rd
a62e2c82c8c98a022fc361da996c6f22 *man/SimInf_individual_events-class.Rd
8206849839dbed689dc3879d31c19030 *man/SimInf_model-class.Rd
07567d52a04643b34cb7080153991e13 *man/SimInf_model.Rd
579cfdf0c1b3bb1cfd698d8ea3e602a3 *man/SimInf_pfilter-class.Rd
a460ed3cc7f36b752b46a3c2e5a4bd14 *man/SimInf_pmcmc-class.Rd
62e8e5fffa81d34d32605a9fcd155115 *man/abc.Rd
8a30716ff6d6252f24565e3007a9aa0a *man/add_spatial_coupling_to_ldata.Rd
107f465abd4ff6c680c8c2eec39b8f8e *man/as.data.frame.SimInf_abc.Rd
3be2b5f1c8928b7dc4d0125995426e56 *man/as.data.frame.SimInf_events.Rd
f03d4b9f93e612285bbfd48133c55bbf *man/as.data.frame.SimInf_individual_events.Rd
29d66f944376a46e476110628f715116 *man/as.data.frame.SimInf_pmcmc.Rd
ed1a294685d254aed0702418e814e6a4 *man/boxplot-SimInf_model-method.Rd
9825eeed4ee33522d823e1367b8e93a9 *man/continue_abc.Rd
a4a35586dcec1eb3c04f3263b94d1b53 *man/continue_pmcmc.Rd
65cb409e7c98b86651d4d0685f05764d *man/distance_matrix.Rd
eec82146522ecfbead20d95b02eff578 *man/edge_properties_to_matrix.Rd
7976cf6340bdf657366c45ad36559059 *man/events.Rd
0fe05eabc4c21019534d461c97f8a2ad *man/events_SEIR.Rd
95693f085e032b06a0545bd6e28893b3 *man/events_SIR.Rd
80e41e892a0f56eae0724d2faf5d4f99 *man/events_SIS.Rd
b7d13e1d27b244f2dc033527a240a637 *man/events_SISe3.Rd
922e7ddf08736ec332a4f702835573fd *man/examples/SEIR.R
01b2a78ff982294c22d16d70f19c1c17 *man/examples/SIR.R
13737da4a65d76e2e283d0c3c12a982b *man/examples/SIS.R
922a561e5fa6891abb657e3b400c669a *man/examples/SISe.R
beaf5f733678b84079e95605a997d9b6 *man/examples/SISe3.R
37470f7468332bc29a0e46273dd61396 *man/examples/abc.R
776c66633afc9e8054457a143c53b61e *man/examples/pfilter.R
c0c751b182cc882bd8a19ec245cbcebf *man/figures/README-mparse-SIR-1.png
c43c0d85d6ae8f0c56d1a5206f641550 *man/gdata-set.Rd
97eae7c51afb3d172e9cba0e41e9c5b5 *man/gdata.Rd
adec134e306fb8a3ea0c4509c2b14c7c *man/get_individuals.Rd
f0455c50177d34799abc2c5625acd818 *man/indegree.Rd
7467659f19bb3b468e1140a35a8bffa3 *man/individual_events.Rd
2b49a0fd4c702891b9c0e973d4406e50 *man/lambertW0.Rd
9cd06504d1f61bcbe4f55079a85b94d4 *man/ldata.Rd
b3b3682d1bcc80a9ab2edf6d70240afa *man/length-SimInf_pmcmc-method.Rd
b4ea8b3afbfcbc98dc593afef5d96a7d *man/logLik-SimInf_pfilter-method.Rd
e3dc89216ed4df7b8be0c138966251d0 *man/macros/citations.Rd
037adbaba69a9fce58c4c5f013ea24a4 *man/mparse.Rd
de80b4f059b8957fa19a8565202650a7 *man/n_compartments.Rd
6c4d83751704d8d243212e07da7d4457 *man/n_generations.Rd
3bd300ed412f75a052010457b721c578 *man/n_nodes.Rd
561c8728d55dda25662b0b90c5c687c8 *man/n_replicates.Rd
d4b59f3864caf8cbc59d00293dd35c7f *man/node_events.Rd
a2031571817d8be2ebc5f1a8861ccf1c *man/nodes.Rd
c4b9c5c65f644286295d848507f2a998 *man/outdegree.Rd
6ae2d20e1f14568308fe8f11e4280e43 *man/package_skeleton.Rd
ceef55831190017d04a3857a759787dd *man/pairs-SimInf_model-method.Rd
241300c4b3cfeda746f9bf2dde55bbff *man/pfilter.Rd
2be795ad05c057bcb770d211c1159dfd *man/plot-SimInf_abc-method.Rd
be9e6bb7cab4274d8d72061a80d6c21b *man/plot-SimInf_events-method.Rd
7656731d1c74eab75d54490cdbcbbf99 *man/plot-SimInf_individual_events-method.Rd
4b85c2be5729bf2bc1304ba00d23b076 *man/plot-SimInf_pfilter-method.Rd
cd5018d2e981186f18807125c2274d10 *man/plot-SimInf_pmcmc-method.Rd
3ba522fc86b2a3facd411ee4365ea1f9 *man/plot.Rd
06eb4c0d8ddadc79b4ff585f3a389960 *man/pmcmc.Rd
aa2e86e6147f48e182b4eae9f19a2eec *man/prevalence-SimInf_model-method.Rd
5838a959cbe32f66f497786022ba0c69 *man/prevalence-SimInf_pfilter-method.Rd
0d0919f179e5bd3ce6af0860474d8b92 *man/prevalence-SimInf_pmcmc-method.Rd
0904821327011ea786e3fd0ebcddd131 *man/prevalence.Rd
3652e7c90530806a92887002f243caf1 *man/punchcard-set.Rd
9ebe26962b73f2f7aedab75dc145866c *man/run.Rd
a97149738a8ba5fa4ed191dee7a3c61b *man/select_matrix-set.Rd
4ecbf079eddacc809d9f5dcf3cd11b2f *man/select_matrix.Rd
445ce49d7d2d580b64353b6bc1f9e908 *man/set_num_threads.Rd
cbb012f3e8c4acb6475e07f1682a8cec *man/shift_matrix-set.Rd
be2763f5e7b56d3a0a5257f8b4007ca1 *man/shift_matrix.Rd
3978e8ed7ef4d92dfe2603e47db17e59 *man/show-SimInf_abc-method.Rd
a5e57d692e513a902fe493c961ceb82a *man/show-SimInf_events-method.Rd
92a18b249a2671540f2b405a16250c81 *man/show-SimInf_individual_events-method.Rd
c9c7fb63fb452bf2f898463c605afd87 *man/show-SimInf_model-method.Rd
79024685165c05f6afd0787489e7ee55 *man/show-SimInf_pfilter-method.Rd
2523a4eed881a3a5f5b0ff2eee4e49bb *man/show-SimInf_pmcmc-method.Rd
0428426ef7c310af7ff8f41dc1c6a011 *man/summary-SimInf_abc-method.Rd
651dee5e1ad43c6bb92aa7959e00555e *man/summary-SimInf_events-method.Rd
a7671f09738a2ed0f46d947953e18ecf *man/summary-SimInf_individual_events-method.Rd
8c520c1396f52fe8608a44fa073e63d6 *man/summary-SimInf_model-method.Rd
85c0b308a114d388d4eb32d135493c1a *man/summary-SimInf_pfilter-method.Rd
93372f4da4909d27ddea58526f52b082 *man/summary-SimInf_pmcmc-method.Rd
7c44ec8578a0f1cb97de682941878ec5 *man/trajectory-SimInf_model-method.Rd
c3cead3769cfb8a1f7f84f3e863df8fd *man/trajectory-SimInf_pfilter-method.Rd
38a87b771673b9e350c93c3893701424 *man/trajectory.Rd
3773ec62d3e790327c3a794efda87aee *man/u0-set.Rd
11edc4dd228c0460d71a1f89f1b55e4c *man/u0.Rd
090b4c3eda7b79cdc6ac67f825cd834e *man/u0_SEIR.Rd
aa6863fe17c9f4c3f3f99bb8d9c41410 *man/u0_SIR.Rd
d5cf6dd260408281f57276b4ed2509f7 *man/u0_SIS.Rd
94a5209242c7e1b716a28be7d92ad89c *man/u0_SISe3.Rd
f0ea4df341049b14619084645b515bc1 *man/u0_from_individual_events.Rd
037ca72da31ac1277e76ca1984b9eb7a *man/v0-set.Rd
927315a5fcadb8ec7b16ec89fd13e32f *src/Makevars.in
b4cc2aa9fcc0188f08f6151ebcaf29a9 *src/Makevars.win
15e9813224d748f5eb09b5fcde7f632c *src/SimInf-win.def
9200860ac29b195ab7a86d60217b4dec *src/SimInf.c
37b2b10430c1ddeab01a11ec08fad572 *src/SimInf_internal.h
2292cd0d0c71ee4b10ce2cf4df1b8471 *src/init.c
2189da16900c35f9860bc33169b12af7 *src/misc/SimInf_LambertW.c
b56ce64f4d15d054f21de111477d0ed5 *src/misc/SimInf_abc.c
1a3e01bed029e7509c70fd1c4d5a4af3 *src/misc/SimInf_arg.c
bf3fd4057d202eb9867f760dc65db74e *src/misc/SimInf_distance_matrix.c
9b4bc9812e4464f05c09ad3a28fd16e7 *src/misc/SimInf_forward_euler_linear_decay.c
9f9f61e0a3ad87cdbd21d7280e28abe6 *src/misc/SimInf_individual_events.c
0541fc671c2c53a7df293db833476f28 *src/misc/SimInf_ldata.c
bbd9c9d8389397e1a33ce659a7b8f4d5 *src/misc/SimInf_local_spread.c
e5e1209eafd04010556084fc2208c0b6 *src/misc/SimInf_openmp.c
f68d4dce7f8409fc67173679fdff4b7c *src/misc/SimInf_particle_filter.c
f1090ca042cf0a93efc7efce04b0fe36 *src/misc/SimInf_trajectory.c
f8c1094955c8530b79c73e0b271a7c11 *src/misc/binheap.c
d677197c8ce447e0c833f200fd7c1e53 *src/misc/kvec.h
544d391c04db026450c35ebb336b3bb5 *src/models/SEIR.c
a5e7669f7c7872e74d91e9394e2e31bd *src/models/SIR.c
1b0aa36c91e4c88cdbd4c22d4c03e24f *src/models/SIS.c
f932f7704be774dc1980fd03063b2109 *src/models/SISe.c
e313af6d923f1d624cc4b2374ea4b888 *src/models/SISe3.c
11397e4cfca577c40e3d09995ed274e8 *src/models/SISe3_sp.c
26452a23c2b64306e894adcf071803eb *src/models/SISe_sp.c
2f1c3d4324fe025fa5b6ffa60e9516e2 *src/solvers/SimInf_solver.c
3314815aac11a588569a2688749221f5 *src/solvers/SimInf_solver_aem.c
b0603462710955c12838adcd18d50c89 *src/solvers/SimInf_solver_mssm.c
560211cf70184865d8a52d82ddedb0d1 *src/solvers/SimInf_solver_mssm_crn.c
1e8b3e2f9dd71b2edf2b67bf229cc03f *src/solvers/SimInf_solver_ssm.c
dc23621f39670d17e04911dc3d061c0d *tests/SEIR.R
b9f390715a346dfcdf8c43b82688f889 *tests/SIR.R
a311826e3a316faa902931b58a60d051 *tests/SIS.R
08bef81b08fdda741d2b9286b876ae25 *tests/SISe.R
c9ab122913eebee099a85afd8b46a791 *tests/SISe3.R
fe2779f5cdcbe88d55fc85856927a532 *tests/SISe3_sp.R
fbfb1f3bea7ee3a4a0dd04530d36259f *tests/SISe_sp.R
f73d9da8b3ededa38dfd98e02617da02 *tests/SimInf.R
b5436a2f68cc725809c8c1baaa0543d6 *tests/SimInf_events.R
9d2de9d26fe276943d763304baefe536 *tests/SimInf_model.R
99832c9de92c606046594d360f211b43 *tests/abc-gdata.R
d571853adedba89b32b76ebd8c14e895 *tests/abc-ldata.R
5dfa0ed939ac98ca51188cac8f5c15e1 *tests/abc.R
3c20770f167e29a130d06eabfe82ae85 *tests/density_ratio.R
707dd121203b1577ecc20836522b8043 *tests/distributions.R
21d48ea3a9c6b87b77b9b668370d4ef6 *tests/edge_properties.R
6164b5c3f2a8c77ed7dcb9bb4fc8297c *tests/individual_events.R
e2965618eee8abee7b719d5118dafbeb *tests/lambert.R
3c71dd64fdf0cb8b935d04c34a21d9fc *tests/ldata_sp.R
2fa880a2025ac7c5d1683f22c6bafd5e *tests/match_compartments.R
291f78f4797875bf31362368a2817d2c *tests/measures.R
63315cb61c0b156a4f0e6890a9821ce6 *tests/mparse.R
8d26e2aa6e14d4ba3d33beaab4fafd0d *tests/package_skeleton.R
b65a6012ec227880903eb6dff6a61de6 *tests/pfilter.R
767be8ef4e67a210d09ceb25ee143160 *tests/phi.R
eb2bbcaca53d8e8685d0e40e6e0461a8 *tests/pmcmc.R
c9fe18fccf4d9d5eefb5e64ea5a4fe58 *tests/prevalence.R
801fc1620434e266cd7332cd90e63fcc *tests/punchcard.R
bc5450eb092f32394e47731ead6aea7d *tests/sample_select.R
b2f71ae64f00f28cf0cfdb5b6de66146 *tests/solver_aem.R
34b993d435a4122d6f3d56ff294d9970 *tests/trajectory.R
4056fc86395fe989722f4685ad3737bf *tests/u0.R
754991e91dea17d73c02024bfc15b78c *tests/util/check.R
fc98ff6986d11b399671c759c3069a29 *tests/v0.R
23c72cf0ef9eede3e8eedf07c7728d41 *vignettes/SimInf.Rnw
af6a848936dcdfe5519e422f59fc3e8c *vignettes/SimInf.bib
5c04c8b8a805c78e452c7b7e9c23479e *vignettes/img/SISe_sp-prevalence.pdf
79dda74236a5213b9c0f36df73846ae8 *vignettes/img/enter.pdf
8e4592483c76825ee1f56177845973f5 *vignettes/img/exit.pdf
fb2a52d0e7f02a565aac0934eee1cb69 *vignettes/img/external-shift.pdf
ca278f60569a51c96a4a1fd11f2950fd *vignettes/img/external.pdf
186c3113fc6036f653ccdb2eb15d6ab4 *vignettes/img/internal.pdf
51032abc3157d6e606a9445a6a0df938 *vignettes/img/mparse-epicurve.pdf
cf55ff8869ea41f4364197f167a09ce7 *vignettes/img/overview.pdf
225aac95467bc4a8366bb1b19baab2f1 *vignettes/img/predator-prey.png
5a2c02478802a3e26064b3198b2d539f *vignettes/img/temporal-network.pdf
687cefa8bc0c59abc72e938648b6c485 *vignettes/img/temporal-network.svg
b29a9eec376f6d8c81bbc50304c1b974 *vignettes/mparse.Rmd
ee48897376861124546f29c531df7866 *vignettes/post-process-data.Rmd
f21c9af061273ad52f66e878c3085be6 *vignettes/scheduled-events.Rmd
