NEWS.md

In mrc-ide/gonovax: Deterministic Compartmental Model of Gonorrhoea with Vaccination

gonovax 0.4.22

• percentage cases averted and cumulative inc. asymptomatic and symptomatic diagnoses are output from compare_baseline_xpvwrh

gonovax 0.4.21

• person years exposed from the point of view of a non-screening RCT (U, I, A, S, AND T) added

gonovax 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

gonovax 0.4.19

• partner notification and vaccination on notification added into population-level model

gonovax 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

gonovax 0.4.17

• ved acts on duration of asymptomatic infection rather than the rate of asymptomatic natural clearance

gonovax 0.4.16

• Expose demographic_params in run function to facilitate adaptation to non-UK contexts

gonovax 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

gonovax 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

gonovax 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

gonovax 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

gonovax 0.4.10

• stochastic version of the xvw_trial model can now have parallel strata that account for diagnosis history

gonovax 0.4.9

• package now also includes a stochastic version of the xvw_trial model

gonovax 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)

gonovax 0.4.7

• model outputs present value of cumulative cases averted in a model run compared with baseline transmission in the absence of vaccination

gonovax 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

gonovax 0.4.5

• model outputs annual number of individuals and proportion of the population experiencing vaccine protection (not just the number vaccinated)

gonovax 0.4.4

• added incremental costs calculation for £35 and £70 per dose

gonovax 0.4.3

• new downstream functions generate meaningful output metrics for branching model

gonovax 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.

gonovax 0.4.1

• calculate and return incremental vaccination costs for £9 per dose

gonovax 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

gonovax 0.3.12

• calculate and return # doses wasted. Outputs incremental costs for intermediate price (£50)

gonovax 0.3.11

• output the cumulative number offered vaccination

gonovax 0.3.10

• document and export compare_baseline function

gonovax 0.3.9

• allows proportion of population to be vaccine hesitant, allows primary and booster vaccination uptakes to be different proportions

gonovax 0.3.8

• add vaccination of trial cohort

gonovax 0.3.7

• Output costs and benefits separately to allow ICER calculation

gonovax 0.3.6

• Assume two doses for adolescent vaccination

gonovax 0.3.5

• output incremental cumulative vaccine doses given

gonovax 0.3.4

• allow setting of initial coverage in XVW model

gonovax 0.3.3

• improve tests and add checks for bad parameter inputs

gonovax 0.3.2

• add three-stratum waning model with no re-vaccination: X -> V -> W

gonovax 0.3.1

• add vignette
• add fixed parameter transform function

gonovax 0.3.0

• add vaccine effects vea (acquisition), vei (infectiousness), ved (duration of infection), ves (symptoms)
• rename ve -> vbe to avoid confusion

gonovax 0.2.9

• reduce input size from run_grid

gonovax 0.2.8

• rename strategies

gonovax 0.2.7

• fix bug QALY cost bug

gonovax 0.2.6

• move transform function into package

gonovax 0.2.5

• run_grid uses length of baseline to determine time horizon

gonovax 0.2.4

• Allow efficacy to be varied in run_onevax

gonovax 0.2.3

• move compare function used in paper into package

gonovax 0.2.2

• refactor to run based on strategy
• allow XVWR model to have two different vaccines (i.e. eff / dur profile)

gonovax 0.2.1

• add four-stratum waning model: X -> V -> W <-> R

gonovax 0.2.0

• move globals into package

gonovax 0.1.24

• allow model restart from a future point (necessary for time-varying params)

gonovax 0.1.23

• add GRASP 2020 data

gonovax 0.1.22

• add varying screening rate by group

gonovax 0.1.21

• data starts in 2010
• add beta binomial function

gonovax 0.1.20

• add time-varying beta and eta
• add option to change compare function

gonovax 0.1.19

• add GRASP % symptomatic data
• export data easily
• add user function for running novax

gonovax 0.1.18

• add mcmc thinning and sampling tools

gonovax 0.1.17

• add mcmc fitting method to gumcad data

gonovax 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

gonovax 0.1.15

• output vaccination and revaccination separately
• use parsimonious numbers of compartments in waning model

gonovax 0.1.14

• output full time series in run_grid()
• extend baseline to 30 years

gonovax 0.1.13

• add time-varying vaccination parameter

gonovax 0.1.12

• export aggregate()
• export set_strategy()

gonovax 0.1.11

• output asymptomatic and symptomatic diagnoses

gonovax 0.1.10

• extend baseline to 20 years
• take plot method out of package
• export format_grid

gonovax 0.1.9

• allow vaccination of activity groups at differing rates

gonovax 0.1.8

• add onevax_waning model

gonovax 0.1.7

• remove n_par index as running multiple parameter sets in vectorised mode is inefficient in ode solver.

gonovax 0.1.6

• add option to output full results in grid_search()
• add ability to input baseline in grid_search()

gonovax 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

gonovax 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

gonovax 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

gonovax 0.1.2

• add novax_equilib() which returns the cached equilibrium compartments for all parameters in gono_params()

gonovax 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

gonovax 0.1.0

• initial version of the model tested with Bexsero only

mrc-ide/gonovax documentation built on Dec. 15, 2024, 11:02 a.m.