Files in ImperialCollegeLondon/epidemia
Modeling of Epidemics using Hierarchical Bayesian Models
.Rbuildignore
.covrignore
.github/.gitignore
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/additional_priors.R
R/as.matrix.epimodel.R
R/autocor.R
R/data.R
R/epidemia-package.R
R/epiformula.R
R/epiinf.R
R/epim.R
R/epimodel-methods.R
R/epimodel-objects.R
R/epimodel.R
R/epiobs-methods.R
R/epiobs.R
R/epirt.R
R/forecasting.R
R/geom_stepribbon.R
R/get_samps.R
R/helpers.R
R/misc.R
R/parse_mm.R
R/plots.R
R/plots_epi.R
R/posterior_latents.R
R/posterior_linpred.R
R/posterior_predict.R
R/posterior_sims.R
R/pp_eta.R
R/print.R
R/prior_summary.R
R/stan_data.R
R/standata_reg.R
R/stanmodels.R
R/summary.R
R/utilities.R
README.md
_pkgdown.yml
configure
configure.win
data/EnglandNewCases.RData
data/EuropeCovid.RData
data/EuropeCovid2.RData
index.md
inst/CITATION
inst/REFERENCES.bib
inst/include/csr_matrix_times_vector2.hpp
inst/include/stan_meta_header.hpp
inst/include/tests.cpp
inst/stan/data/NKX.stan
inst/stan/data/data_ac.stan
inst/stan/data/data_glm.stan
inst/stan/data/data_indices.stan
inst/stan/data/data_inf.stan
inst/stan/data/data_model.stan
inst/stan/data/data_obs.stan
inst/stan/data/data_obs_mm.stan
inst/stan/data/glmer_stuff.stan
inst/stan/data/glmer_stuff2.stan
inst/stan/data/hyperparameters.stan
inst/stan/epidemia_base.stan
inst/stan/epidemia_pp_base.stan
inst/stan/functions/common_functions.stan
inst/stan/functions/continuous_likelihoods.stan
inst/stan/functions/linkinv.stan
inst/stan/functions/reverse.stan
inst/stan/functions/trunc_normal.stan
inst/stan/generated_quantities/gen_infections_pp.stan
inst/stan/include/license.stan
inst/stan/model/priors_ac.stan
inst/stan/model/priors_glm.stan
inst/stan/model/priors_inf.stan
inst/stan/model/priors_obs.stan
inst/stan/parameters/parameters_ac.stan
inst/stan/parameters/parameters_glm.stan
inst/stan/parameters/parameters_inf.stan
inst/stan/parameters/parameters_obs.stan
inst/stan/tdata/tdata_glm.stan
inst/stan/tdata/tdata_reverse.stan
inst/stan/tparameters/eta_add_Zb.stan
inst/stan/tparameters/eta_add_ac.stan
inst/stan/tparameters/eta_no_intercept.stan
inst/stan/tparameters/gen_eobs.stan
inst/stan/tparameters/gen_infections.stan
inst/stan/tparameters/infections_rt.stan
inst/stan/tparameters/make_eta.stan
inst/stan/tparameters/make_oeta.stan
inst/stan/tparameters/tparameters_ac.stan
inst/stan/tparameters/tparameters_glm.stan
inst/stan/tparameters/tparameters_obs.stan
man-roxygen/args-epimodel-object.R
man-roxygen/args-epiobs-object.R
man-roxygen/args-epirt-object.R
man/EnglandNewCases.Rd
man/EuropeCovid.Rd
man/EuropeCovid2.Rd
man/all_obs_types.Rd
man/as.matrix.epimodel.Rd
man/epidemia-package.Rd
man/epiinf.Rd
man/epim.Rd
man/epimodel-objects.Rd
man/epiobs.Rd
man/epirt.Rd
man/evaluate_forecast.Rd
man/figures/favicon.ico
man/figures/logo.png
man/figures/logo_big.png
man/figures/logo_padded.png
man/formula.epimodel.Rd
man/get_samps.Rd
man/get_x.Rd
man/hexp.Rd
man/model.frame.epimodel.Rd
man/ngrps.mixed.Rd
man/pairs.epimodel.Rd
man/plot.epimodel.Rd
man/plot_coverage.Rd
man/plot_infections.Rd
man/plot_infectious.Rd
man/plot_linpred.Rd
man/plot_metrics.Rd
man/plot_obs.Rd
man/plot_rt.Rd
man/posterior_coverage.Rd
man/posterior_infections.Rd
man/posterior_infectious.Rd
man/posterior_latent.Rd
man/posterior_linpred.Rd
man/posterior_metrics.Rd
man/posterior_predict.epimodel.Rd
man/posterior_rt.Rd
man/posterior_sample_size.Rd
man/print.epimodel.Rd
man/print.prior_summary.epimodel.Rd
man/print.prior_summary_reg.epimodel.Rd
man/prior_summary.epimodel.Rd
man/reexports.Rd
man/rw.Rd
man/scaled_logit.Rd
man/shifted_gamma.Rd
man/summary.epimodel.Rd
man/terms.epimodel.Rd
man/terms_rw.Rd
pkgdown/extra.css
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
src/Makevars
src/Makevars.win
src/RcppExports.cpp
tests/data/NYWA.RData
tests/data/NYWA2.RData
tests/data/fm-uk.rds
tests/data/forecast-test-data.rds
tests/data/plot_test_fit.RData
tests/data/plot_test_fit.rds
tests/testthat.R
tests/testthat/test-FE-priors.R
tests/testthat/test-FE-stan_data.R
tests/testthat/test-Model-stan_data.R
tests/testthat/test-RE-stan_data.R
tests/testthat/test-autocor.R
tests/testthat/test-data.R
tests/testthat/test-epiinf.R
tests/testthat/test-epim-args.R
tests/testthat/test-epim.R
tests/testthat/test-epiobs.R
tests/testthat/test-epiobs_.R
tests/testthat/test-epirt.R
tests/testthat/test-forecasts.R
tests/testthat/test-intercepts.R
tests/testthat/test-make-names.R
tests/testthat/test-newdata.R
tests/testthat/test-obs-autocor.R
tests/testthat/test-parse-data.R
tests/testthat/test-plotting.R
tests/testthat/test-standata_data.R
tests/testthat/test-standata_inf.R
vignettes/europe-covid.Rmd
vignettes/flu.Rmd
vignettes/install.Rmd
vignettes/model-description.Rmd
vignettes/model-implementation.Rmd
vignettes/model-introduction.Rmd
vignettes/model-schematic.Rmd
vignettes/multiple-obs.Rmd
vignettes/partial-pooling.Rmd
vignettes/priors.Rmd
