compare_baseline_xpvwrh: compare model runs with vaccination to a baseline run for the...

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

compare model runs with vaccination to a baseline run for the branching XPVWRH model where both partial and full vaccination have a given level of efficacy

Description

compare model runs with vaccination to a baseline run for the branching XPVWRH model where both partial and full vaccination have a given level of efficacy

Usage

compare_baseline_xpvwrh(
  y,
  baseline,
  uptake_first_dose,
  uptake_second_dose,
  cost_params,
  disc_rate,
  vea,
  vea_p
)

Arguments

y	list of model runs, e.g. created by 'run_onevax_xpvwrh', each list entry refers to a different parameter set
baseline	list of baseline runs e.g. created by 'run_onevax_xpvwrh'. Should be same length as 'y'
uptake_first_dose	numeric (0-1) either length 1 or same as 'y'
uptake_second_dose	numeric (0-1) either length 1 or same as 'y'
cost_params	list of cost effectiveness parameters, containing entries 'qaly_loss_per_diag_s', 'unit_cost_manage_symptomatic', 'unit_cost_manage_asymptomatic', 'unit_cost_screen_uninfected'. Each entry length 1 or same as 'y'
disc_rate	discount rate for cost-effectiveness output per annum, default = 0
vea	= scalar indicating efficacy of full vaccination against aquisition (between 0-1)
vea_p	scalar indicating efficacy of partial vaccination against acquisition (between 0-1)

Value

A list of matrices with rows = time point and columns = parameter set list entries are: 'cum_treated' = cumulative number treated in model run 'cum_vaccinated' = cumulative vaccinated treated in model run 'diag_a' = annual number of asymptomatic diagnoses in model run 'diag_s' = annual number of symptomatic diagnoses in model run 'treated' = annual number treated in model run 'screened' = annual number screened in model run 'vaccinated' = annual number vaccinated in model run (includes those getting vbe and boosters) 'vbe' = annual number vaccinated before entry in model run 'revaccinated' = annual number receiving booster in model run 'inc_cum_treated' = cumulative number treated compared to baseline 'pv_cases_averted' = cumulative number treated when discounting applied compared to baseline 'inc_cum_vaccinated' = cumulative number vaccinated compared to baseline 'inc_diag_a' = annual number of asymptomatic diagnoses compared to baseline 'inc_diag_s' = annual number of symptomatic diagnoses compared to baseline 'inc_treated' = annual number treated compared to baseline 'inc_screened' = annual number screened compared to baseline 'inc_vaccinated' = annual number vaccinated compared to baseline (includes those getting vbe and boosters) 'inc_vbe' = annual number vaccinated before entry compared to baseline 'inc_revaccinated' = annual number receiving booster compared to baseline 'inc_cum_revaccinated' = cumulative number revaccinated by recieving booster compared to baseline 'inc_primary' = annual number receiving primary vaccination (full or partial) compared to baseline (does not include vbe) 'inc_cum_primary' = cumulative number of individuals receiving primary vaccination (full or partial) compared to baseline (does not include vbe) 'inc_part_to_full'= annual number of individuals who have already received their 1st dose, who receive their 2nd dose compared to baseline 'inc_cum_part_to_full' = cumulative number of individuals who have already received their 1st dose, who receive their 2nd dose compared to baseline 'inc_doses' = number of doses compared to baseline (per year). Assumes primary vaccination uses 2 doses, booster uses 1 dose. 'inc_cum_doses' = cumulative number of doses compared to baseline. Assumes primary vaccination uses 2 doses, booster uses 1 dose. 'inc_primary_part_doses' = annual number of 1st doses administered as part of primary vaccination which were not followed by a 2nd dose compared to baseline. 'inc_cum_primary_part_doses' = cumulative number of 1st doses administered as part of primary vaccination which were not followed by a 2nd dose compared to baseline. 'inc_primary_full_doses' = annual number 1st and 2nd doses administered together as part of primary vaccination compared to baseline. 'inc_cum_primary_full_doses' = cumulative number of 1st and 2nd doses administered together as part of primary vaccination compared to baseline. 'inc_primary_total_doses' = annual number of primary doses administered compared to baseline. Includes doses contributing to partial and full vaccination 'inc_cum_primary_total_doses' = cumulative number of primary doses administered compared to baseline. Includes doses contributing to partial and full vaccination. 'inc_booster_doses' = annual number of booster doses administered to waned individuals for revaccination compared to baseline, where 1 dose is needed for full protection. 'inc_cum_booster_doses' = cumulative number of booster doses administered to waned individuals for revaccination compared to baseline, where 1 dose is needed for full protection. 'inc_vbe_doses' = annual number of vaccinations given before entry, where 2 doses give full protection. 'inc_cum_vbe_doses' = cumulative number of vaccinations given before entry, where 2 doses give full protection. 'cases_averted_per_dose' = cumulative number of cases (i.e. diagnoses) averted per dose of vaccine 'cases_averted_per_dose_pv' = present value of cases_averted_per_dose (i.e. sum of annual numbers discounted at rate 'disc_rate' to time 0) 'pv_inc_doses' = present value of number of doses compared to baseline (i.e. sum of annual numbers discounted at rate 'disc_rate' to time 0) 'pv_red_net_cost' = present value of the reduction in net costs compared to baseline (i.e. sum of annual reduction in costs discounted at rate 'disc_rate' to time 0) 'pv_qaly_gain' = present value of the QALYs gained due to vaccination compared to baseline (i.e. QALYs gained each year discounted at rate 'disc_rate' to time 0, and summed) 'cet_20k' = cost effectiveness threshold (i.e. £ value per dose at which vaccination becomes cost-effective) calculated using £20,000 / QALY. (pv_red_net_cost + pv_qaly_gain * £20,000) / pv_inc_doses 'cet_30k' = cost effectiveness threshold (i.e. £ value per dose at which vaccination becomes cost-effective) calculated using £30,000 / QALY (pv_red_net_cost + pv_qaly_gain * £30,000) / pv_inc_doses 'inc_costs_9' = present value of incremental costs assuming £9 / dose. Incremental costs are calculated as: pv_inc_doses * £9 - pv_red_net_cost 'inc_costs_18' = present value of incremental costs assuming £18 / dose. Incremental costs are calculated as: pv_inc_doses * £18 - pv_red_net_cost 'inc_costs_35' = present value of incremental costs assuming £35 / dose. Incremental costs are calculated as: pv_inc_doses * £35 - pv_red_net_cost 'inc_costs_50' = present value of incremental costs assuming £50 / dose. Incremental costs are calculated as: pv_inc_doses * £50 - pv_red_net_cost 'inc_costs_70' = present value of incremental costs assuming £70 / dose. Incremental costs are calculated as: pv_inc_doses * £70 - pv_red_net_cost 'inc_costs_85' = present value of incremental costs assuming £85 / dose Incremental costs are calculated as: pv_inc_doses * £85 - pv_red_net_cost 'vacprotec_full' = number of fully vaccine protected individuals in the population at a given timepoint 'vacprotec_part' = number of partially vaccine protected individuals in the population at a given timepoint 'vacprotec_total' = total number of vaccine protected individuals in the population (both partially and fully vaccinated) at a given timepoint 'vacprotec_full_prop' = proportion of the population experiencing full vaccine protection at a given timepoint 'vacprotec_part_prop' = proportion of the population experiencing partial vaccine protection at a given timepoint 'vacprotec_total_prop' = total proportion of the population experiencing some form of vaccine protection at a given timepoint 'level_vacprotec' = the level of vaccine protection in the population at a given timepoint. Given as the sum of the products of the number of partially and fully vaccinated individuals and the one dose and two dose vaccine efficacies respectively. 'inc_diag_a_xwh' = annual number of asymptomatic diagnoses in non- vaccine protected strata compared to an adjusted baseline 'inc_diag_s_xwh' = annual number of symptomatic diagnoses in non- vaccine protected strata compared to an adjusted baseline 'inc_diag_t_xwh' = annual number of total diagnoses in non-vaccine protected strata compared to an adjusted baseline 'inc_diag_a_pvr' = annual number of asymptomatic diagnoses in vaccine protected strata compared to an adjusted baseline 'inc_diag_s_pvr' = annual number of symptomatic diagnoses in vaccine protected strata compared to an adjusted baseline 'inc_diag_t_pvr' = annual number of total diagnoses in vaccine protected strata compared to an adjusted baseline 'inc_cum_diag_a_xwh' = cumulative number of asymptomatic diagnoses in non- vaccine protected strata compared to an adjusted baseline 'inc_cum_diag_s_xwh' = cumulative number of symptomatic diagnoses in non- vaccine protected strata compared to an adjusted baseline 'inc_cum_diag_t_xwh' = cumulative number of total diagnoses in non-vaccine protected strata compared to an adjusted baseline 'inc_cum_diag_a_pvr' = cumulative number of asymptomatic diagnoses in vaccine protected strata compared to an adjusted baseline 'inc_cum_diag_s_pvr' = cumulative number of symptomatic diagnoses in vaccine protected strata compared to an adjusted baseline 'inc_cum_diag_t_pvr' = cumulative number of total diagnoses in vaccine protected strata compared to an adjusted baseline 'percentage_cases_avert' = percentage of cases avoided in each time-point compared to a baseline of no vaccination when cases are counted as successful treatment 'cum_percentage_cases_avert'= percentage of cases avoided cumulatively across all timepoints compared to a baseline of no vaccination when cases are counted as successful treatment 'percentage_diag_avert' = percentage of cases avoided in each time-point compared to a baseline of no vaccination when cases are counted as the sum of all diagnoses 'cum_percentage_diags_avert'= percentage of cases avoided cumulatively across all timepoints compared to a baseline of no vaccination when cases are counted as the sum of all diagnoses 'inc_diag_t' = total number of diagnoses in each time point 'inc_cum_diag_t' = cumulative total number of diagnoses over time 'inc_cum_diag_a' = cumulative number of asymptomatic diagnoses over time 'inc_cum_diag_s' = cumulative number of symptomatic diagnoses over time 'pv_num_vaccinations' = present value cumulative number of vaccinations

mrc-ide/gonovax documentation built on April 17, 2025, 8:33 p.m.