bf9845edc4ef9dc36bd277e62cdc1781 *DESCRIPTION
3e7efe91b7f727a4be0b81d2ecc86149 *NAMESPACE
bb78b7ee421b3cec0797ea4b2a508693 *NEWS.md
6ed5dc0c265137b95e7f66b1d838fc9b *R/additional_priors.R
a1780cbf9c691edf291de937521d2e60 *R/as.matrix.epimodel.R
1e04aa5f95dfc0d9c3dc0fabd578205f *R/autocor.R
607eb6fafd92d00767a77938b9743c73 *R/data.R
e6dd86bcdf3b1ba93e2732525d9bd3e7 *R/epidemia-package.R
2eff5340f364df1a4a65383610c9697c *R/epiformula.R
2b17c7df7c728ed63533e71872b32d79 *R/epiinf.R
43074c7d9953c105e7b2fc4ab8fc41fb *R/epim.R
d784ca958bf0d20b878a7511405418f5 *R/epimodel-methods.R
76e571f9f6317497aa3a9d830f2dd49a *R/epimodel-objects.R
1fd6514fe7568faf32c0318eb911a0d4 *R/epimodel.R
ad0b072c3af2dccc920f9a1e6da658c4 *R/epiobs-methods.R
03aabd176e0d56addb06e66dc3bd9eaa *R/epiobs.R
fcda0ea7aa4bcd30f54ac546720bcc6a *R/epirt.R
597caabe295d8d2fb54d68298149882f *R/forecasting.R
4509eb790f291c9ee5d0352b040a5282 *R/geom_stepribbon.R
86a5bb9901e7323c3292249c6b380d42 *R/get_samps.R
4fb3677eca013e756f3d02792b38f32f *R/helpers.R
6cc888f6c9f7e66021cc7dd5aad80a4b *R/misc.R
dea56b7fcd7012fb5bd909b67ea3ffe9 *R/parse_mm.R
035305397055dfc4d150e7896f815e9c *R/plots.R
19a75e3eb9d96875983e9706ced75b29 *R/plots_epi.R
9b32e83a32368f6db72382a524500842 *R/posterior_latents.R
98ce84d691e07e73f3a7e709fef1882b *R/posterior_linpred.R
eb3517427ba1686ddc76ab5da6819410 *R/posterior_predict.R
ad6acd66b2957f97df8b793d3c090dba *R/posterior_sims.R
2d0be99177e9053ae397b18ad974e44f *R/pp_eta.R
efabd6da5ba968997b98bbd3ed8740b8 *R/print.R
3c59cfb866b21694cebf76a8a06afa45 *R/prior_summary.R
3134c3b3f2aa546022cd7e7f8e6ceedf *R/stan_data.R
06a33552e6c997e314eb5d621b4d0190 *R/standata_reg.R
22afc8a07a7b00bc76017ecdb909a620 *R/stanmodels.R
0bc6a4886be8b34ef8c8dcd903328486 *R/summary.R
79333ad91b88368b51b8031ba7022ee7 *R/utilities.R
165a78c66b686ed8e0b834a0f9027fee *README.md
b77920cb3cfe7179c91e82b8ee67f4a3 *build/partial.rdb
1cc60bdd8610449d30184e0bb374bf46 *configure
6bea7bdbd44ffa386677bfdec2d1984b *configure.win
a7472bd5209a74329d98cc1ac345e48a *data/EnglandNewCases.RData
8be280b20b2d3d3c5a58415be12130d1 *data/EuropeCovid.RData
53d2e5d84238044ce2ff840531c5fe7c *data/EuropeCovid2.RData
88a1cc16a8380dfff689a47559a56003 *inst/CITATION
0c75b3e423f14594ebd58867ff39f11b *inst/REFERENCES.bib
eca841458b6f9d25ec33521ddc227563 *inst/include/csr_matrix_times_vector2.hpp
74cd86b9902f331d770385de17175b34 *inst/include/stan_meta_header.hpp
852ae3b00db277a79d623be727ab9dc2 *inst/include/tests.cpp
51b6d477b8db372c066acacff8d26438 *inst/stan/data/NKX.stan
32d93532367fe2f478fbf370d3ffff12 *inst/stan/data/data_ac.stan
7c9d325c83f36d758e0a8c614b16d7ee *inst/stan/data/data_glm.stan
c2e37b613187ac11e5f770a895dce405 *inst/stan/data/data_indices.stan
fd524fe08924e49e9d777d1f0e74a7e1 *inst/stan/data/data_inf.stan
f18b6fc1568f872c96c3ad96da4e97e4 *inst/stan/data/data_model.stan
f2cf5e42b96a4533e5bef4c781248e3b *inst/stan/data/data_obs.stan
57416be6638761dbe518ac6ce4ce0d93 *inst/stan/data/data_obs_mm.stan
606b2448c963499b58d9bc8d589b2266 *inst/stan/data/glmer_stuff.stan
d331a067c626e53d25fd0a0f191102a3 *inst/stan/data/glmer_stuff2.stan
d8b25b848846e22bbc84ee4a3fd6b029 *inst/stan/data/hyperparameters.stan
71a137ddd88aa279abccce57b8437533 *inst/stan/epidemia_base.stan
37cd783afb8678fc7431d64f235ba9f8 *inst/stan/epidemia_pp_base.stan
a99327e3eb3c00370b3eeb6e5a3467e0 *inst/stan/functions/common_functions.stan
fba3c2c23297bf2e6eb5a1382dc7b94e *inst/stan/functions/continuous_likelihoods.stan
db01db280ffe42292f4b0a4680a7e847 *inst/stan/functions/linkinv.stan
1b088c09759d53684e06c0c8af123b70 *inst/stan/functions/reverse.stan
7359c5e1e345c75ea831cc5b52acdd42 *inst/stan/functions/trunc_normal.stan
8411e3d8c8d14c975bed53cee8c35214 *inst/stan/generated_quantities/gen_infections_pp.stan
88aa71b02cf7d0b330d2d3a6efc4540e *inst/stan/include/license.stan
213b8333844e7edb9f3b1c913524250f *inst/stan/model/priors_ac.stan
1360eae226c549e1ae3bfbc3d6c8d272 *inst/stan/model/priors_glm.stan
e41dda87722db5a8d1a120da155ebba7 *inst/stan/model/priors_inf.stan
492dacb5b95487f0642d129dbc8f8d61 *inst/stan/model/priors_obs.stan
b9e3361c74e2d3059da42ee0f68f866b *inst/stan/parameters/parameters_ac.stan
6102d7730923fb876020f4cdb0a59ec9 *inst/stan/parameters/parameters_glm.stan
235a003680be351e5037a5398a12ef41 *inst/stan/parameters/parameters_inf.stan
fc62e9e5fd1d13ad24b87ac0b1ed16dd *inst/stan/parameters/parameters_obs.stan
03d87322ae2223187eea7862535cc56f *inst/stan/tdata/tdata_glm.stan
4011a87e38f63dd63a39f4646a7ea306 *inst/stan/tdata/tdata_reverse.stan
9c2d2b926dbdd3fbc496891bfe3d2316 *inst/stan/tparameters/eta_add_Zb.stan
7fd1f18feb10e7746a7363e0adeff7fe *inst/stan/tparameters/eta_add_ac.stan
5f94bb583fa9a1508dfd6fda700f891b *inst/stan/tparameters/eta_no_intercept.stan
93e49db0666da9697937dc9d44b07b8f *inst/stan/tparameters/gen_eobs.stan
bfff3de74e4e4e89b07d252e0f628ec1 *inst/stan/tparameters/gen_infections.stan
8b2c176d209b751764e7d8e0d1bfdefc *inst/stan/tparameters/infections_rt.stan
2ca52625f5a8ce898854ee7d1f6c8033 *inst/stan/tparameters/make_eta.stan
a2b8a1c15343dff85eae802017f98950 *inst/stan/tparameters/make_oeta.stan
1654be1cbd00bcb13a4c790ca057c25b *inst/stan/tparameters/tparameters_ac.stan
877afd6b9c90386516af3f620bc07151 *inst/stan/tparameters/tparameters_glm.stan
99f9044f068671ae4b687adfc1a16b5b *inst/stan/tparameters/tparameters_obs.stan
e2ba9f77d1cf1b640da119fa875bc2c1 *man/EnglandNewCases.Rd
a715c73f0f1a4ad4362a567335212735 *man/EuropeCovid.Rd
257277b73bcaed85978e9b672f380271 *man/EuropeCovid2.Rd
d4addc4e122e93ce45a494f978273c0b *man/all_obs_types.Rd
c266f43a12191d50d6724141849b17b1 *man/as.matrix.epimodel.Rd
46e11a1deda0ff7bf831753c91a22207 *man/epidemia-package.Rd
dc2870c4df139be2333bbf1c3fa87837 *man/epiinf.Rd
4288e4e21ed35c8251b74526b16b7923 *man/epim.Rd
2e1231e5e5ec70cf66794cde504d4a92 *man/epimodel-objects.Rd
c44014836d3ef1e20fb2c91029c1e230 *man/epiobs.Rd
00a40328cceca6f9ee4fa72498666d8c *man/epirt.Rd
1575879e592248c2bf9f5a1fa71cb26a *man/evaluate_forecast.Rd
cd9653261b6208937403d1937efd78b2 *man/figures/favicon.ico
bdc5c3f59b29503285ba9a75b1406e85 *man/figures/logo.png
870d16fe8db2eea6dde7fa10324b00ab *man/figures/logo_big.png
64435b953c54d8eabb5841bf73f682ad *man/figures/logo_padded.png
55084be460a0f2cb7fd5229ae46e383b *man/formula.epimodel.Rd
ee9a1bc129a25a15b402acc0713f1d4d *man/get_samps.Rd
9656ed7aba35cc55c19e744e74f78799 *man/get_x.Rd
509b249ac9e561cd8cd6d2c9056921dc *man/hexp.Rd
a10cdd3aac38a060d1dc68d04b9e5c83 *man/model.frame.epimodel.Rd
dea2af95271669fe2fd71c3762c84c1c *man/ngrps.mixed.Rd
770c2e515dc9196f795085ee4fd4fe98 *man/pairs.epimodel.Rd
d889db115d07e7b5930dfd6031686cee *man/plot.epimodel.Rd
529f1ea8cc357ee7c6e30647feeb345a *man/plot_coverage.Rd
aa6c4fa0c8f956dd55a95bb77a05077b *man/plot_infections.Rd
e547864e7d0d2b5abda11cd6d80ce29b *man/plot_infectious.Rd
c6b8c6ea6ed7fab1fe1173f26024bd41 *man/plot_linpred.Rd
8230e3e53f5c63b694837333eeb74d37 *man/plot_metrics.Rd
5eb892f51ffc23d0e8e0e911e3c73dba *man/plot_obs.Rd
aa46e44fa69d2bf3c4a374d3ea931077 *man/plot_rt.Rd
0af800e2f82f4ef05344f700cc7816f0 *man/posterior_coverage.Rd
12d4928a41c349d525239f11bfc0d67b *man/posterior_infections.Rd
09bd431a0ef4882a5ed2e66b403a2618 *man/posterior_infectious.Rd
bda8f6951341dce01448b91d4e57932d *man/posterior_latent.Rd
b5527e1925b05b661408cb16bf839d03 *man/posterior_linpred.Rd
60f3538687c67bbdeba611ba6a21c75a *man/posterior_metrics.Rd
d10e7c9512c31626c368c918d302d2d3 *man/posterior_predict.epimodel.Rd
083883f7f447076629bafcda8b026f67 *man/posterior_rt.Rd
eebb7f7f51a1e4470da16c9a9535e4c7 *man/posterior_sample_size.Rd
3eefa6d41cf13f5c7f46ca4f376a4cdc *man/print.epimodel.Rd
6e16b7e91950f4f721054e46917b72ac *man/print.prior_summary.epimodel.Rd
2f08e6fc866cada60f6227989511b37d *man/print.prior_summary_reg.epimodel.Rd
454d77e8b12ba90ae8ccdc3b34d4d581 *man/prior_summary.epimodel.Rd
5deb419fcb174bb4fc773a8851224e83 *man/reexports.Rd
0e7c75fd29cc7f288511527a33d46319 *man/rw.Rd
b9739d67efa7233e26a86da468c7a3da *man/scaled_logit.Rd
956a70c59f03261ebddc13a4e1911674 *man/shifted_gamma.Rd
ba5ce9fac356f601e99dd56c1d98ddb1 *man/summary.epimodel.Rd
13be049e6de0d195435e8e7a751e3b30 *man/terms.epimodel.Rd
80577765abfc33cf817f82a810ebbe9b *man/terms_rw.Rd
ec1f7adc46f14d6b1c5481244554415e *src/Makevars
cebeb8bdd5adb558f381741990eb1085 *src/Makevars.win
54fd049870ea635df3c1004310e10450 *src/RcppExports.cpp
6a7370450dce8c80b3e375245da0ea7f *src/stanExports_epidemia_base.cc
4d7b2195bf20b18668fa8527a90c9aeb *src/stanExports_epidemia_base.h
728f21b3db79757ecc6f43ef91298d64 *src/stanExports_epidemia_pp_base.cc
74881350856ba9ba0b5efe2a33dedb2d *src/stanExports_epidemia_pp_base.h
f4ffbf95827590d9a58eda713179f355 *tests/data/NYWA.RData
273b23af8f8e7d11d28a9c6f378c9069 *tests/data/NYWA2.RData
e71847f1703002b4d87a676923e65ab9 *tests/data/fm-uk.rds
2c3c73b993e30e1bc135cee93e95d716 *tests/data/forecast-test-data.rds
83f1392a0fb9a8c1a69bc92f0aa44e20 *tests/data/plot_test_fit.RData
830b3c6c1edaab0d4d5034b157ac4680 *tests/data/plot_test_fit.rds
441ea35fc3adc9c697e304225e1f4d0a *tests/testthat.R
a226aaaccbb92129ee4141aa50e552cd *tests/testthat/test-FE-priors.R
a0210d03205c20e7a698d0a675ebfccb *tests/testthat/test-FE-stan_data.R
8a7635ac4b97a01d09c78cd6995a737a *tests/testthat/test-Model-stan_data.R
4fc1590038d8f3e9d138ea7a109649d9 *tests/testthat/test-RE-stan_data.R
f1328f4da6e375756002a6e1a414e1e8 *tests/testthat/test-autocor.R
f4112cdbce384050cc5c5acb5b5ea6a5 *tests/testthat/test-data.R
f0b618ea611b71a8d8f3adbe45fd43ca *tests/testthat/test-epiinf.R
636ac4b7a0d906559822681c6446eee4 *tests/testthat/test-epim-args.R
6a27bd191983dc550442983b1e99c5a1 *tests/testthat/test-epim.R
bd9c504f8d6e42fdc0a005fcdca56cff *tests/testthat/test-epiobs.R
211dfecb3f80e89c7077d53844fe63d9 *tests/testthat/test-epiobs_.R
a8bf8f8076ec55642f65ad2d4620278d *tests/testthat/test-epirt.R
b82cd1d2674beb1253cf4e668171b3f0 *tests/testthat/test-forecasts.R
fb7e6997cf56ece950882f80f9df5519 *tests/testthat/test-intercepts.R
5c98aa7d1a313761e4186c7270f73ea2 *tests/testthat/test-make-names.R
e328c569d6158a8f7bb53b6b06d9a8c5 *tests/testthat/test-newdata.R
1534ac013cd506086060a14cc9182c84 *tests/testthat/test-obs-autocor.R
524596ee63da9b0f24299e429f3421aa *tests/testthat/test-parse-data.R
c7ccdff639eefa4db9b11755bef80945 *tests/testthat/test-plotting.R
65a656698e254a1f3b18af37a76775ea *tests/testthat/test-standata_data.R
01f6a74e5c937eb72c5e704d1f9be619 *tests/testthat/test-standata_inf.R
