Changes in version 0.4.23 - add in 'trackvt' (track time since vaccination) version of xpvwrh - which separates V and R into two strata each, and individuals in the second V and R strata are vaccine eligible Changes in version 0.4.22 - percentage cases averted and cumulative inc. asymptomatic and symptomatic diagnoses are output from compare_baseline_xpvwrh Changes in version 0.4.21 - person years exposed from the point of view of a non-screening RCT (U, I, A, S, AND T) added Changes in version 0.4.20 - person-years exposed both from the point of view of an RCT (U, I, A, S) and in the true sense (U only) are output from the model rather than calculated in post Changes in version 0.4.19 - partner notification and vaccination on notification added into population-level model Changes in version 0.4.18 - diagnoses history in a trial is recorded at the point of receiving treatment and whether a trial records asymptomatic infections or not can be switched on or off Changes in version 0.4.17 - ved acts on duration of asymptomatic infection rather than the rate of asymptomatic natural clearance Changes in version 0.4.16 - Expose demographic_params in run function to facilitate adaptation to non-UK contexts Changes in version 0.4.15 - the maximum effective rate of natural clearance in the presence of ved is now capped at the value for the rate of care seeking Changes in version 0.4.14 - extracting diagnoses and vaccination by stratum type now possible with n_erlang > 1, and symptomatic and asymptomatic diagnoses by vaccine-protected vs non-vaccine-protected can be extracted against (adjusted) baseline Changes in version 0.4.13 - model updated to include diagnosis history (i.e. the number of times individuals have been diagnosed in last Y years) at n_diag_rec = 1, the model is the same as previous versions tested to work for n_diag_rec > 1 with xpvwrh tested to work with n_diag_rec = 1 for all other strategies Changes in version 0.4.12 - model_trial_stochastic updated so that total number of individuals exiting each state drawn first, then the specific transitions made drawn after #gonovax 0.4.11 - deterministic version of the xvw_trial model can now have parallel strata that account for diagnosis history Changes in version 0.4.10 - stochastic version of the xvw_trial model can now have parallel strata that account for diagnosis history Changes in version 0.4.9 - package now also includes a stochastic version of the xvw_trial model Changes in version 0.4.8 - model XPVWRH and XVW_trial can now have 'n' transitions between entering a vaccine-protected stratum and waning to no protection (erlang compartments) Changes in version 0.4.7 - model outputs present value of cumulative cases averted in a model run compared with baseline transmission in the absence of vaccination Changes in version 0.4.6 - model outputs level of population vaccine protection (number vaccinated weighted by efficacy). Tests also added to check number of individuals vaccinated is being performed correctly Changes in version 0.4.5 - model outputs annual number of individuals and proportion of the population experiencing vaccine protection (not just the number vaccinated) Changes in version 0.4.4 - added incremental costs calculation for £35 and £70 per dose Changes in version 0.4.3 - new downstream functions generate meaningful output metrics for branching model Changes in version 0.4.2 - new model structure where primary vaccination can either be partial or full depending on 1 or 2 doses, with primary vaccination waning to unvaccinated and an immunologically naive state, and full vaccination waning with some immunological memory. Partial vaccination with one dose can now provide an assigned level of protection. Individuals with one dose who visit the clinic can receive their second dose. Changes in version 0.4.1 - calculate and return incremental vaccination costs for £9 per dose Changes in version 0.4.0 - calculate and return annual and cumulative # individuals receiving primary and booster vaccination separately and annual and cumulative number of primary and booster doses administered Changes in version 0.3.12 - calculate and return # doses wasted. Outputs incremental costs for intermediate price (£50) Changes in version 0.3.11 - output the cumulative number offered vaccination Changes in version 0.3.10 - document and export compare_baseline function Changes in version 0.3.9 - allows proportion of population to be vaccine hesitant, allows primary and booster vaccination uptakes to be different proportions Changes in version 0.3.8 - add vaccination of trial cohort Changes in version 0.3.7 - Output costs and benefits separately to allow ICER calculation Changes in version 0.3.6 - Assume two doses for adolescent vaccination Changes in version 0.3.5 - output incremental cumulative vaccine doses given Changes in version 0.3.4 - allow setting of initial coverage in XVW model Changes in version 0.3.3 - improve tests and add checks for bad parameter inputs Changes in version 0.3.2 - add three-stratum waning model with no re-vaccination: X -> V -> W Changes in version 0.3.1 - add vignette - add fixed parameter transform function Changes in version 0.3.0 - add vaccine effects vea (acquisition), vei (infectiousness), ved (duration of infection), ves (symptoms) - rename ve -> vbe to avoid confusion Changes in version 0.2.9 - reduce input size from run_grid Changes in version 0.2.8 - rename strategies Changes in version 0.2.7 - fix bug QALY cost bug Changes in version 0.2.6 - move transform function into package Changes in version 0.2.5 - run_grid uses length of baseline to determine time horizon Changes in version 0.2.4 - Allow efficacy to be varied in run_onevax Changes in version 0.2.3 - move compare function used in paper into package Changes in version 0.2.2 - refactor to run based on strategy - allow XVWR model to have two different vaccines (i.e. eff / dur profile) Changes in version 0.2.1 - add four-stratum waning model: X -> V -> W <-> R Changes in version 0.2.0 - move globals into package Changes in version 0.1.24 - allow model restart from a future point (necessary for time-varying params) Changes in version 0.1.23 - add GRASP 2020 data Changes in version 0.1.22 - add varying screening rate by group Changes in version 0.1.21 - data starts in 2010 - add beta binomial function Changes in version 0.1.20 - add time-varying beta and eta - add option to change compare function Changes in version 0.1.19 - add GRASP % symptomatic data - export data easily - add user function for running novax Changes in version 0.1.18 - add mcmc thinning and sampling tools Changes in version 0.1.17 - add mcmc fitting method to gumcad data Changes in version 0.1.16 - bug-fix: extract flows now correctly attributes vaccination / re-vaccination - re-code model so treatment of VbE is now the same structure as VoD / VoA Changes in version 0.1.15 - output vaccination and revaccination separately - use parsimonious numbers of compartments in waning model Changes in version 0.1.14 - output full time series in run_grid() - extend baseline to 30 years Changes in version 0.1.13 - add time-varying vaccination parameter Changes in version 0.1.12 - export aggregate() - export set_strategy() Changes in version 0.1.11 - output asymptomatic and symptomatic diagnoses Changes in version 0.1.10 - extend baseline to 20 years - take plot method out of package - export format_grid Changes in version 0.1.9 - allow vaccination of activity groups at differing rates Changes in version 0.1.8 - add onevax_waning model Changes in version 0.1.7 - remove n_par index as running multiple parameter sets in vectorised mode is inefficient in ode solver. Changes in version 0.1.6 - add option to output full results in grid_search() - add ability to input baseline in grid_search() Changes in version 0.1.5 - fix bug in novax_baseline() - fix model bug that caused people to go missing in VoD - update plot method to avoid ggplot2 warnings Changes in version 0.1.4 - cache baseline (novax) incidence parameters - add run_grid_onevax() which run the model with cached parameters across an eff x dur vaccination grid - add plot methods for grid objects Changes in version 0.1.3 - rename model to separate novax, onevax (and in future, dualvax / dualvax_wane) - add run_novax() and run_onevax() which run the model with cached parameters from equilibrium if specified - add VbE to vaccination output Changes in version 0.1.2 - add novax_equilib() which returns the cached equilibrium compartments for all parameters in gono_params() Changes in version 0.1.1 - export gono_params() and allow selection of specific parameter sets - export dualvax_initial() - add dualvax_restart() for restarting the model from a previous position Changes in version 0.1.0 - initial version of the model tested with Bexsero only