Files in epichains

Simulating and Analysing Transmission Chain Statistics Using Branching Process Models

NEWS.md README.md R/stat_likelihoods.R R/likelihood.R R/simulate.R R/checks.R R/epichains.R R/epichains-package.R R/borel.R R/helpers.R R/utils.R R/covid19_sa.R inst/doc/interventions.Rmd inst/doc/projecting_incidence.Rmd inst/doc/epichains.Rmd inst/doc/branching_process_literature.R inst/doc/epichains.R inst/doc/interventions.R inst/doc/design-principles.R inst/doc/projecting_incidence.R inst/doc/theoretical_background.R inst/doc/design-principles.Rmd inst/doc/theoretical_background.Rmd inst/doc/branching_process_literature.Rmd tests/testthat.R tests/spelling.R tests/testthat/test-utils.R tests/testthat/tests-borel.r tests/testthat/test-simulate.R tests/testthat/test-stat_likelihoods.R tests/testthat/setup-options.R tests/testthat/test-helpers.R tests/testthat/test-checks.R tests/testthat/helper-state.R tests/testthat/test-likelihood.R tests/testthat/test-epichains.R tests/testthat/_snaps/simulate.md tests/testthat/_snaps/epichains.md vignettes/interventions.Rmd vignettes/projecting_incidence.Rmd vignettes/epichains.Rmd vignettes/design-principles.Rmd vignettes/theoretical_background.Rmd vignettes/branching_process_literature.Rmd man/dot-nbinom_size_ll.Rd man/simulate_chain_stats.Rd man/dot-complementary_logprob.Rd man/dot-validate_epichains.Rd man/rgborel.Rd man/dot-epichains.Rd man/dot-check_sim_args.Rd man/dot-validate_epichains_summary.Rd man/dot-get_statistic_func.Rd man/dot-is_epichains.Rd man/summary.epichains_summary.Rd man/rborel.Rd man/dot-offspring_ll.Rd man/print.epichains_summary.Rd man/dot-check_generation_time_valid.Rd man/dot-epichains_summary.Rd man/dot-get_susceptible_offspring.Rd man/dot-update_chain_stat.Rd man/dot-rgen_length.Rd man/dot-geom_length_ll.Rd man/dot-init_susc_pop.Rd man/print.epichains.Rd man/covid19_sa.Rd man/likelihood.Rd man/dot-check_offspring_func_valid.Rd man/epichains-package.Rd man/dot-check_statistic_args.Rd man/head.epichains.Rd man/dborel.Rd man/dot-check_time_args.Rd man/dot-new_epichains.Rd man/summary.epichains.Rd man/dot-gborel_size_ll.Rd man/dot-sample_possible_offspring.Rd man/dot-adjust_next_gen.Rd man/dot-pois_length_ll.Rd man/dot-pois_size_ll.Rd man/dot-is_epichains_summary.Rd man/dot-rbinom_size.Rd man/dot-new_epichains_summary.Rd man/simulate_chains.Rd man/aggregate.epichains.Rd