7e1e1d68baac30ca6156fc61e0e2b3de *DESCRIPTION
d9c2d56b08ec4ad730418c5de1c75310 *LICENSE
641f50089666a1d31fc9ea609c380b18 *NAMESPACE
1f2039c432dbc2ff624be1ef671a6157 *NEWS.md
1f1fab84c126ece68fbe3373d3625c8e *R/EpiNow2-package.R
08f5acc92701fe401fb869de3acc6e56 *R/adjust.R
9c841a9a8a2c8fd22093e97c22262206 *R/create.R
550b53f557a96ee7acbd7587f7b2a97d *R/data.R
fe80305f43295c7969858ef94778f5d2 *R/dist.R
142b41c91d3d0d56a2b8f4a2a5521b2c *R/epinow-internal.R
bbd18f2d39d8ee275551e26ba32931b5 *R/epinow.R
297f964690ce2d1ec81772a88daeefa5 *R/estimate_infections.R
a086736f303e2bc9b3c5fa1288db8ea3 *R/estimate_secondary.R
517f6744db55262b64dd06da22ed14ec *R/estimate_truncation.R
571a1db0b9ecad78c60faf7d87a73730 *R/extract.R
20ab0ca247b9e1f08674c28b1de30581 *R/forecast_infections.R
b66fde988e0596c31360dca15a5bc730 *R/get.R
e6977122194184e789aa7083524d957b *R/map.R
49558a44fe530795364a7effbd9fe751 *R/opts.R
cb8945d1e6142a14dea7c3cbaded8c54 *R/plot.R
7984e3be73495d04120e0c8aeb5aa20c *R/regional_epinow.R
c157aa758535eb415d27586d0f87395c *R/report.R
68cc961d300183f68303b490eef0d491 *R/setup.R
0a24a7a7873bcb2a6af6187df6b337c3 *R/simulate.R
a84daddb23e17c4a0e3b6097010bda5b *R/simulate_infections.R
5f70117ad3ebfb2bcb61b9575e2c4d78 *R/stanmodels.R
15f9715467107cc46039127509c2c0ea *R/summarise.R
9b7f9790acdb879a313ec1db66bb7fec *R/utilities.R
4c4fd492d68ca6422a0ad4e5c22f7a40 *README.md
b7d6e27c9b9b35367d6214b8b66a079b *data/example_confirmed.rda
f9eee81cbc011d74e1dc91c2fe2af7f4 *data/generation_times.rda
07651e2270bf54d8602f20f669f9e060 *data/incubation_periods.rda
d61d1d9b1a252332a6551279daa1505d *inst/CITATION
356acb24f46b1659c60dd0d7b6a0121d *inst/WORDLIST
855c064dbf8deaff96c8dc8a87169109 *inst/include/stan_meta_header.hpp
c57c3beb065e944c9f7e44366b8f9845 *inst/stan/data/backcalc.stan
5cf25587219c29a5629adb6a24c543e9 *inst/stan/data/delays.stan
49487253814a0a11973624e8facd5ecf *inst/stan/data/gaussian_process.stan
6a210267e6eff73eff0c05c03b3bb000 *inst/stan/data/generation_time.stan
9d99693ee43289120a13408bb85d3417 *inst/stan/data/observation_model.stan
7f8fa75f356ca076dc7faf16a49e0f64 *inst/stan/data/observations.stan
4e65f2a6a3234f6102956a34450e1607 *inst/stan/data/rt.stan
c674321922f0e60218da72fbcb9cf0b0 *inst/stan/data/secondary.stan
6a7391177d6a60d048bce7a360743d8f *inst/stan/data/simulation_delays.stan
21b7e3bfc94ba58f2bb700855df3772e *inst/stan/data/simulation_observation_model.stan
1a1b70437dde92c8bc59245d86882e26 *inst/stan/data/simulation_rt.stan
c788a7d6dad25780d9c9ac0b9e860c3c *inst/stan/estimate_infections.stan
8b6d39e0d3fe4f32af335fb1abd4e842 *inst/stan/estimate_secondary.stan
fb45f70d449c095bda2674e0f9eac473 *inst/stan/estimate_truncation.stan
c6e9f4b8baf58e811af6193703d14f75 *inst/stan/exp.stan
02219ccb9cb93d50bafe43cef86bbd27 *inst/stan/functions/convolve.stan
bdb5a1caa6998fb0b0ffb4abe05c4146 *inst/stan/functions/gaussian_process.stan
b8b968927f5f4604ca7773f8e7e4cb4e *inst/stan/functions/generated_quantities.stan
7ad9fe4479a31f98937397421f357e5b *inst/stan/functions/infections.stan
60d6540b2d7a605aec6c21239a70d9b6 *inst/stan/functions/observation_model.stan
6a7e6c573b7a99a786c51ee125e0ecd9 *inst/stan/functions/pmfs.stan
ea1796a447a51b2e6e9f6436a95ee5c9 *inst/stan/functions/rt.stan
8c1e4f0974ea2697d171e40ecd28421c *inst/stan/functions/secondary.stan
0db00a9333df0ac5a313f2bae6721a6a *inst/stan/gamma.stan
4a4e476cadf37a7da530161716941473 *inst/stan/include/license.stan
15a527b35c3387906eb6a9ef74783a72 *inst/stan/lnorm.stan
f90a75b277cdc714b43ee4179fcc368f *inst/stan/simulate_infections.stan
f94ebe4ec2fabc1cfba5583cf255680e *inst/stan/simulate_secondary.stan
7d0134ec0d55635f8cf44da6fdc1539c *inst/stan/tune_inv_gamma.stan
592a041185f7231f76ae888a6f6c1731 *inst/templates/_add-region-reports.Rmd
d2f9ef1659bc21ba074cdeffcd0147bb *inst/templates/_all-region-summary.Rmd
e1e58fcef25570b5dd937f1ed2a07ca8 *inst/templates/_region-report.Rmd
1a12b3ce78a8d8ca171a88176412cb79 *inst/templates/_regional-summary.Rmd
aebbf181eb15cab5a555a10e0a0fc51d *man/EpiNow2-package.Rd
a9dfeb30d1aeb18be935e333a75615c6 *man/R_to_growth.Rd
6f801fd7d8c3949c0de88d8de47a0a86 *man/adjust_infection_to_report.Rd
fb310f289110fc582cf31e611f6a0e67 *man/allocate_delays.Rd
496b6674003c4ac4511b6eb5f50aca64 *man/allocate_empty.Rd
3c41e33f615c8ee3a9ca6d3e5b4e5c21 *man/backcalc_opts.Rd
d6837493ec8fd0dba5baf4be584b7578 *man/bootstrapped_dist_fit.Rd
a1ef6b77f7130a26ad01c7a28d1b3f90 *man/calc_CrI.Rd
f5bbea1cd82a954b4423919ba0688c78 *man/calc_CrIs.Rd
c37708b0f426431f6027ac8a16cf80c8 *man/calc_summary_measures.Rd
d719aac6e29ab3ebb21d0481294655ce *man/calc_summary_stats.Rd
b40c7ee8860f9a1f9874f3d481b787c0 *man/clean_nowcasts.Rd
b575112f4d479ffabd33c75a85b56384 *man/clean_regions.Rd
29bd280667f8914437dc53d7d27a1f2a *man/construct_output.Rd
82e8647b7aa691bedc41e77d3ef46a7e *man/convert_to_logmean.Rd
4254fe496cfb0806741e4e84ff11b236 *man/convert_to_logsd.Rd
dade9901648dcfd6185556d75cbb6351 *man/copy_results_to_latest.Rd
ec0c3380153745161217c38ccb01056e *man/country_map.Rd
fb10401a9c6181e1203fbcc982eb4484 *man/create_backcalc_data.Rd
b166102015906c2bfed25db01c615b8b *man/create_clean_reported_cases.Rd
874b053cf41058637c80588f66227adf *man/create_future_rt.Rd
7711b14d68396c36964de62464d96998 *man/create_gp_data.Rd
a658680374474d07cd416fd28dc4a392 *man/create_initial_conditions.Rd
9cd3a4f0c9f5ac8943db98cc6993757e *man/create_obs_model.Rd
d5c6f76cd11364f190a5f00a0e141d0f *man/create_rt_data.Rd
d84a3e7587e9fa64373a265af6cfcc68 *man/create_shifted_cases.Rd
4aacb067f0e78d935b38dc7a6ecc0ac5 *man/create_stan_args.Rd
fb46e81b5e400f12720dd9fc5ab1eca2 *man/create_stan_data.Rd
7617c53b1e61edc7b89a2fa1f0221afc *man/delay_opts.Rd
d81956d2f6d9fdce77d13e7eba1d2dfb *man/dist_fit.Rd
5824905baf1ae197214bf580358f9c92 *man/dist_skel.Rd
4e8b9be24dc86cf824ad10b0c2a5038a *man/epinow.Rd
9ecd276486bb1353ec1242640404ad53 *man/estimate_delay.Rd
028c215edeecc281ccf8fb1a810e5c5b *man/estimate_infections.Rd
604e14b0599ce06427345014545ad063 *man/estimate_secondary.Rd
2e85143061b52c2970928d326997e17e *man/estimate_truncation.Rd
860caf8a170f8f0fd46b70b0d35dc20b *man/estimates_by_report_date.Rd
2c8d65c4dfed2e1423cc8564082e780a *man/example_confirmed.Rd
4e9afaa8992c1155f1214ec4473c4ef7 *man/expose_stan_fns.Rd
032a57e75cb0d6d589f7a492bc8e0304 *man/extract_CrIs.Rd
428a630ae954d9a73e8efdb89a7eb3e6 *man/extract_inits.Rd
a84b9b8d74afaa83f7c552511f7fc453 *man/extract_parameter.Rd
be31e563e22ea1f4e8ebedb7f9f449d7 *man/extract_parameter_samples.Rd
50f60da04b90dd10070e476b0a38d4fe *man/extract_stan_param.Rd
f9a936ffe8bbc75fb65adf9d2a05802d *man/extract_static_parameter.Rd
cb1e46f469cfbbbde29c8b5113e1d789 *man/figures/lifecycle-archived.svg
c0d2e5a54f1fa4ff02bf9533079dd1f7 *man/figures/lifecycle-defunct.svg
a1b8c987c676c16af790f563f96cbb1f *man/figures/lifecycle-deprecated.svg
c3978703d8f40f2679795335715e98f4 *man/figures/lifecycle-experimental.svg
952b59dc07b171b97d5d982924244f61 *man/figures/lifecycle-maturing.svg
27b879bf3677ea76e3991d56ab324081 *man/figures/lifecycle-questioning.svg
6902bbfaf963fbc4ed98b86bda80caa2 *man/figures/lifecycle-soft-deprecated.svg
53b3f893324260b737b3c46ed2a0e643 *man/figures/lifecycle-stable.svg
1c1fe7a759b86dc6dbcbe7797ab8246c *man/figures/lifecycle-superseded.svg
f17f924144396c402905421e2d9ba95e *man/figures/unnamed-chunk-13-1.png
2102aae0c0f6457dbb1489f014b73bd7 *man/figures/unnamed-chunk-17-1.png
1b352e16713da0a2a0d082985e96c9d0 *man/filter_opts.Rd
bf3d8475983ec3e094357b75ff8abfd4 *man/fit_model_with_nuts.Rd
4027a2a7f509b0fdf5a8e0e79a3e93f2 *man/fit_model_with_vb.Rd
2fcd661089f55eb6eb3520d22049cdb5 *man/forecast_infections.Rd
ff4c7db5185b1f0bb09861804d5e5d30 *man/forecast_secondary.Rd
829e48faea15b62a3063deac4f837b5f *man/format_fit.Rd
5eb24e1eeabde3d6754ae1d716b2953f *man/gamma_dist_def.Rd
c2e5a03b70db7351f77af65e2396c681 *man/generation_times.Rd
3a95597384e0dc0f3e241d318f77ed71 *man/get_dist.Rd
2fd934792da494bd6997aab3f14ea425 *man/get_generation_time.Rd
95d2f1261cf08591a0f0ae2584845c94 *man/get_incubation_period.Rd
590a8123b5eee1fa9b3b947fca8a1f98 *man/get_raw_result.Rd
425f99268ecc5172865b3d14321c33c5 *man/get_regional_results.Rd
22601bd9d876c74a9fa22621c44e721e *man/get_regions.Rd
065da6c57484ac42f03a1dc9cc9ed9a4 *man/get_regions_with_most_reports.Rd
a51e2e2dadc2b377484de7031a795250 *man/global_map.Rd
3eb01155ea60aa5fe6677cec969ffd7b *man/gp_opts.Rd
0b61edb3bfdeafa173e0695f595f07a0 *man/growth_to_R.Rd
f0a6775fe44ec482274bba37a624dd2c *man/incubation_periods.Rd
2cfa2bd6e376b3f592928c4ff5d5bfe6 *man/init_cumulative_fit.Rd
9a1a99aef4d3ac6916ee8a801340c4e4 *man/lognorm_dist_def.Rd
ea82ce32dbd061a3daf21ab268f31aa4 *man/make_conf.Rd
3f63f48a535527eabdc92e3d0737cfbd *man/map_prob_change.Rd
38088e3bffba873ab823d7ad9f6a302c *man/match_output_arguments.Rd
89d3302eb82ba48a4b384f4a190e1a5b *man/obs_opts.Rd
6056c958fb3187f1c59d16cd25b5763f *man/opts_list.Rd
0d71771cda1cf8970965f861783f7d73 *man/plot.epinow.Rd
48445a5d628c787318ba0f0d843045a7 *man/plot.estimate_infections.Rd
c9e701571b470fbed936ec938f01b38e *man/plot.estimate_secondary.Rd
c277a0e9229b8b0cdaf798dcce734b65 *man/plot.estimate_truncation.Rd
5a1f381869791e58ca69eb77e810492c *man/plot_CrIs.Rd
a52cca090309a067cbe2cd07b8d0a53d *man/plot_estimates.Rd
b5fb35b6662b8d03296b3f21bbbd019d *man/plot_summary.Rd
5e903e517dd00e090a4efe0a230e0575 *man/process_region.Rd
24e33c05d735f49a672f0af0f088114c *man/process_regions.Rd
2dbb10f190e938f23656a1ce59377581 *man/regional_epinow.Rd
8079a229fad2a57fb05227411230ecf8 *man/regional_runtimes.Rd
981327a99cd0b3d7d9c8379ad03ac79a *man/regional_summary.Rd
d470f06c64e1fec41c494e58f1793de2 *man/report_cases.Rd
746171d811344e2225a1a8b6a9d2f578 *man/report_plots.Rd
8d4690eea933018f055562e5fe364c86 *man/report_summary.Rd
a2fc74ec3b6fc34b067ac64597755efd *man/rstan_opts.Rd
98d8fccf4372f22a0b5346a56510cf68 *man/rstan_sampling_opts.Rd
e37edbf2d3d3cc37a4063bf404364087 *man/rstan_vb_opts.Rd
b83250ba6ec903c8f950206958027d7d *man/rt_opts.Rd
cc6251181d3131fd141960926eeae1c7 *man/run_region.Rd
4fd40ae5a79a7235a1efe33a4b68d226 *man/sample_approx_dist.Rd
26e4b2e6ae991addbcd731301127232b *man/save_estimate_infections.Rd
3d5df1ba02ed3875e38fb6ce81bfb6c9 *man/save_forecast_infections.Rd
4f9ca358f9dd1b590b14b69eb5ab8d4b *man/save_input.Rd
ef0e5cd5eb96043bbfd0979b737780fd *man/secondary_opts.Rd
8b8202716fe44e7ed14368c51d12393c *man/setup_default_logging.Rd
9b2b80b994dfcb00193dda8c02bb5bc2 *man/setup_dt.Rd
77de2f9da8ef7e929e0b3bc31374abfd *man/setup_future.Rd
434d6b0f9159ef0ded49bdfc55fd51d8 *man/setup_logging.Rd
3b30dc7daf7fd6da232862220020f938 *man/setup_target_folder.Rd
970467997d57f04ab5bc405902047ec2 *man/simulate_cases.Rd
134a805bf714135ef375b93ff2a4e000 *man/simulate_infections.Rd
9274d7efbf952b0ffcb778e3f4264442 *man/stan_opts.Rd
292a3a33edcc19d5028221d28ec470ee *man/summarise_key_measures.Rd
819a6f037d5ada8e556e12ad96818984 *man/summarise_results.Rd
c4a306523fce0d9bd212f82555833b4a *man/summary.epinow.Rd
4528e2681155801f2c775042f670a4eb *man/summary.estimate_infections.Rd
9bb389bb704e90715e09f2a2360a239b *man/theme_map.Rd
cb8f1c0e3ec6f82c01724c66f043d724 *man/trunc_opts.Rd
5f2d0ba833fc9acfe2a89614e6ec365b *man/tune_inv_gamma.Rd
3059f0dbd7d6d8b64f97783d114b80b0 *man/update_horizon.Rd
241ca7b7ccef5039dbda565d20d80c8f *man/update_list.Rd
134064746a7d56ea77961ec7b5fb3b19 *src/Makevars
5c907fbecdd9b89552a08d0ec58deb61 *src/Makevars.win
f4ede6263dd853319fd7fdf8595b47f0 *src/RcppExports.cpp
0baa6f69735ee186e27e556a4737a72e *src/stanExports_estimate_infections.cc
108d5b9abd18636ab6bc2726d80ca74a *src/stanExports_estimate_infections.h
427242c3dbbcfb46c7b844e7cbb91e0c *src/stanExports_estimate_secondary.cc
95894107445847dc251cae230181a281 *src/stanExports_estimate_secondary.h
dec49c73d7fc32c50a80db9506413d21 *src/stanExports_estimate_truncation.cc
09c04854d4d0db980c8b5466444d2b8c *src/stanExports_estimate_truncation.h
fcdc275e01dfdea9f7ed4e9bafe6e780 *src/stanExports_exp.cc
b5844f96ca644bfb9b0d2be26a6c4d8e *src/stanExports_exp.h
e827f0d0f45e87fe6e35a8dab42fa749 *src/stanExports_gamma.cc
684e0ba22b01e3a45c8d73224fe84034 *src/stanExports_gamma.h
efd0614f139864691a73bec46f10e740 *src/stanExports_lnorm.cc
801e54c83ca3425000918a3b56960926 *src/stanExports_lnorm.h
de07eb60fdfe50b2d4b93d22979d6a8c *src/stanExports_simulate_infections.cc
93f6904479589b26e0e747c5cf5c0a6c *src/stanExports_simulate_infections.h
86f357ead9f9043bd4dfd94b2db557e8 *src/stanExports_simulate_secondary.cc
7ae04df9e17cdaad6165f21cab313940 *src/stanExports_simulate_secondary.h
2272c40e6bb5f7f6f54f184d1c0476fe *src/stanExports_tune_inv_gamma.cc
adc38c0876d082a237c995fc382e1978 *src/stanExports_tune_inv_gamma.h
0622a97a2aaa3c342f09636052c2d7f5 *tests/spelling.R
f65b8ec7e0a25841a2d066a29d170a7b *tests/testthat.R
08c8c9336b09f03ec3986231a60862cc *tests/testthat/test-calc_CrI.R
678374ae01a948296c1e29f7ae917ae5 *tests/testthat/test-calc_CrIs.R
0f629c4f8d62f615593fe011bfa3a962 *tests/testthat/test-calc_summary_measures.R
0863e355d3f3831717a90473a548a960 *tests/testthat/test-calc_summary_stats.R
ede46b2881004cbc3214e402f1adaa57 *tests/testthat/test-create_future-rt.R
a964009097ec9f9d9f65f772ece722e4 *tests/testthat/test-create_stan_args.R
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_CrI_default.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_CrI_grouping.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_CrIs_custom_CrI.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_CrIs_default.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_CrIs_grouping.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_summary_measures_custom_CrI.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_summary_measures_default.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_summary_measures_grouping.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_summary_stats_default.rds
d41d8cd98f00b204e9800998ecf8427e *tests/testthat/test-data/calc_summary_stats_grouping.rds
51744f8e009561c0b9dea2a6734032a4 *tests/testthat/test-epinow.R
191b9446b60099d9cea8ad14e2743cc1 *tests/testthat/test-estimate_infections.R
99e8bfcbdc868e24724914669645028f *tests/testthat/test-extract_CrIs.R
d874d1226b212a88995b21b7627ae0a4 *tests/testthat/test-get_dist.R
f6efc322937f715cd8b06b3973d72254 *tests/testthat/test-match_output_arguments.R
0f75271efd0c9f04d7fefcdec1670fdb *tests/testthat/test-regional_epinow.R
11ab7a70ad25e5d805617f0d768e8b58 *tests/testthat/test-regional_runtimes.R
babe4197f56d4c97e358490b5f30dd13 *tests/testthat/test-setup_future.R
2d1f8831ce2fc81e3313385ba7d563d9 *tests/testthat/test-simulate_infections.R
4a221c474a08fed5a2cddc66ee3cf9f9 *tests/testthat/test-stan-infections.R
87f58ad7c56c43dea0746e4c2844a863 *tests/testthat/test-stan-rt.R
42cef65c0d4aa6ff7e0256e7c3e47e54 *tests/testthat/test-stan-secondary.R
