Package: gonovax 0.4.23

Lilith Whittles

gonovax: Deterministic Compartmental Model of Gonorrhoea with Vaccination

Model for gonorrhoea vaccination, using odin.

Authors:Lilith Whittles [aut, cre], Dariya Nikitin [aut], Trystan Leng [aut]

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gonovax.pdf |gonovax.html✨
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NEWS

# Install 'gonovax' in R:
install.packages('gonovax', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrc-ide/gonovax/issues

On CRAN:

Conda:

4.56 score 3 stars 57 exports 38 dependencies

Last updated 14 days agofrom:4b02b30855 (on master). Checks:1 OK, 11 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 28 2025
R-4.5-win-x86_64NOTEMar 28 2025
R-4.5-mac-x86_64NOTEMar 28 2025
R-4.5-mac-aarch64NOTEMar 28 2025
R-4.5-linux-x86_64NOTEMar 28 2025
R-4.4-win-x86_64NOTEMar 28 2025
R-4.4-mac-x86_64NOTEMar 28 2025
R-4.4-mac-aarch64NOTEMar 28 2025
R-4.4-linux-x86_64NOTEMar 28 2025
R-4.3-win-x86_64NOTEMar 28 2025
R-4.3-mac-x86_64NOTEMar 28 2025
R-4.3-mac-aarch64NOTEMar 28 2025

Exports:adjust_baselineaggregatecomparecompare_baselinecompare_baseline_xpvwrhdbetabinomextract_flowsextract_flows_trialextract_flows_xpvwrhgen_erlang_labelsgen_erlang_labels_trackvtgen_labelsgen_trial_labelsgono_paramsgono_params_trialgonovax_datagonovax_yeargonovax_year_as_yearinitial_paramsinitial_params_trialinitial_params_xpvwrhinitial_params_xpvwrh_trackvtinitial_params_xvwinitial_params_xvw_trialinitial_params_xvwrhmcmcmcmc_combinemcmc_samplemcmc_thinmodelmodel_paramsmodel_params_trialmodel_params_xpvwrhmodel_params_xpvwrh_trackvtrestart_hesrestart_paramsrunrun_gridrun_onevax_xpvwrhrun_onevax_xpvwrh_trackvtrun_onevax_xvwrun_onevax_xvw_trialrun_onevax_xvwrrun_onevax_xvwrhrun_onevax_xvwvrun_trialset_protectionset_protection_trackvtstratum_index_xpvwrhstratum_index_xpvwrh_trackvtstratum_index_xvwstratum_index_xvw_trialstratum_index_xvwrstratum_index_xvwrhstratum_index_xvwvtransformtransform_fixed

Dependencies:callrcinterpolateclicodetoolscpp11crayonddedescdeSolvedigestdustfsfurrrfutureglobalsgluehmsjsonlitelifecyclelistenvmagrittrmcstateodinparallellypkgbuildpkgconfigpkgloadprettyunitsprocessxprogresspspurrrR6ringrlangrprojrootvctrswithr

Getting started

Lilith Whittles

Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Mar 28 2025.

Last update: 2024-07-02
Started: 2021-06-16

Readme and manuals

Help Manual

Help pageTopics
adjust model run in absence of vaccination so diagnoses are spread across vaccine protected and non-vaccine protected strata as if the rate of movement was the same as in an equivalent model run in the presence of vaccinationadjust_baseline
aggregate model runs by vaccination group x vaccine strataaggregate
Calculate the log likelihood of the data given the parameters diagnoses and attendances lhoods are negative binomial p_symp lhood is betabinomialcompare
compare model runs with vaccination to a baseline runscompare_baseline
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 efficacycompare_baseline_xpvwrh
Calculate the log likelihood of the data given the parameterscompare_basic
Create mapping for movement between strata due to diagnosis waningcreate_diagnosis_waning_map
Creates uptake mapping array with dimensions n_group x n_vax x n_vax and assigns the relevant primary uptake and booster uptake values defined by the user.create_uptake_map
Creates uptake mapping for the branching XPVWRH model where individuals can move from unvaccinated (X) to vaccinated (V) or partially vaccinated (P) as well as revaccinated from waned (W) to (R) and, and partially vaccinated (P) to fully vaccianted (V). The former reflects the specific indices which are chosen for assigning uptakes.create_uptake_map_xpvwrh
Creates uptake mapping for the branching XPVWRH model where individuals can move from unvaccinated (X) to vaccinated (V) or partially vaccinated (P) as well as revaccinated from waned (W) to (R) and, and partially vaccinated (P) to fully vaccianted (V). The former reflects the specific indices which are chosen for assigning uptakes.create_uptake_map_xpvwrh_trackvt
Creates uptake mapping array with dimensions n_group x n_vax x n_vax and assigns the relevant primary uptake and booster uptake values defined by the user.create_uptake_map_xvw
Creates uptake mapping array with dimensions n_group x n_vax x n_vax and assigns the relevant primary uptake and booster uptake values defined by the user.create_uptake_map_xvwr
Creates uptake mapping array with dimensions n_group x n_vax x n_vax and assigns the relevant primary uptake and booster uptake values defined by the user.create_uptake_map_xvwv
Create mapping for movement between strata due to vaccinationcreate_vax_map
Create mapping for movement between strata due to vaccination where vaccination uptake splits off into two types (partial and full) from the naive population (X). Different to create_vax_map as this function specifically maps vbe to V (3) than P(2)create_vax_map_branching
Create mapping for movement between strata due to vaccine waningcreate_waning_map
Create mapping for movement between strata due to vaccine waning where waning from the partially vaccinated stratum (P) moves individuals back to a naive unvaccinated state (X), and waning from fully vaccinated stratum (V) moves individuals into a separate waned stratum (W) Note, this structure is specific to xpvwrhcreate_waning_map_branching
Create mapping for movement between strata due to vaccine waning in a vaccine trial with erlang compartmentscreate_waning_map_trial
pdf of a betabinomial parametrised in terms of probability and over-dispersiondbetabinom
extract flows used for run_gridextract_flows
extract flows for the XVW trial modelextract_flows_trial
extract flows used for run_grid when the branching xpvwrh model has been runextract_flows_xpvwrh
generates the appropriate strata labels for the number of strata in the model, which depends on the value given to n_erlanggen_erlang_labels
generates the appropriate strata labels for the number of strata in the model, which depends on the value given to n_erlanggen_erlang_labels_trackvt
generates the appropriate strata labels for the number of strata in the model, which depends on the value given to n_erlang and diagnosis history levels desired (n_diag_rec)gen_labels
generates the appropriate strata labels for the number of strata in the model, which depends on the value given to n_erlang and diagnosis history levels desired (n_diag_rec)gen_trial_labels
Posterior parameters of gonorrhoea natural historygono_params
Posterior parameters of gonorrhoea natural historygono_params_trial
Get gonovax datagonovax_data
Convert a year into the number of years after 2009gonovax_year
Convert a gonovax year into calendar yearsgonovax_year_as_year
Initial conditions for the modelinitial_params initial_params_xvw
Initial conditions for the model trial where the entire cohort is in the high sexual activity group.initial_params_trial
Initial conditions for the modelinitial_params_xpvwrh
Initial conditions for the modelinitial_params_xpvwrh_trackvt
Initial conditions for the model in a vaccine trialinitial_params_xvw_trial
Initial conditions for the modelinitial_params_xvwrh
Run a mcmc samplermcmc
Combine mcmc samplesmcmc_combine
Thin a mcmc chainmcmc_sample mcmc_thin
Model of gonorrhoea with dual vaccines This is an odin model.model
Parameters for the dualvax modelmodel_params
Parameters for the vaccination trial modelmodel_params_trial
Parameters for the dualvax modelmodel_params_xpvwrh
Parameters for the xpvrwrh model tracking time since vaccinationmodel_params_xpvwrh_trackvt
uses XPVWRH model run in the absence of vaccination or hesitancy. Saves down the number of individuals in each compartment, and moves a given proportion (hes) of them from the X to the H strata to generate new initial conditions in the presence of hesitancy.restart_hes
Create initial conditions to start the model from the end of a runrestart_params
Run odin model of gonorrhoea with or without vaccinationrun
run model from equilibrium with single vaccine at the input efficacy / duration grid locations for n parameter setsrun_grid
run model with a two-dose vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are eligible for revaccination (R), and return to the R stratum, those with waned partial vaccines return to the unvaccinated stratum (X) and considered immunologically naive. A user defined proportion of the population is vaccine hesitant and is never vaccinated. Full acciantion (V) with 2 doses gives maximum protection whereas partial vaccination with 1 dose (P) gives less. Individuals can get 2 doses either by committing in X or upon visiting a clinic in P.run_onevax_xpvwrh
run model with a two-dose vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are eligible for revaccination (R), and return to the R stratum, those with waned partial vaccines return to the unvaccinated stratum (X) and considered immunologically naive. A user defined proportion of the population is vaccine hesitant and is never vaccinated. Full acciantion (V) with 2 doses gives maximum protection whereas partial vaccination with 1 dose (P) gives less. Individuals can get 2 doses either by committing in X or upon visiting a clinic in P.run_onevax_xpvwrh_trackvt
Run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are not eligible for revaccination.run_onevax_xvw
Run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are not eligible for re-vaccination.run_onevax_xvw_trial
run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are eligible for revaccination (R), and return to the R stratumrun_onevax_xvwr
run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are eligible for revaccination (R), and return to the R stratumrun_onevax_xvwrh
run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are eligible for revaccination, and return to the V compartmentrun_onevax_xvwv
Run odin model of gonorrhoea vaccine trial with or without vaccinationrun_trial
Run odin model of gonorrhoea with or without vaccinationrun_xpvwrh
Run odin model of gonorrhoea with or without vaccinationrun_xpvwrh_trackvt
generates vector which tells the model which strata are under vaccine protection and what the value of protection for that strata isset_protection
generates vector which tells the model which strata are under vaccine protection and what the value of protection for that strata isset_protection_trackvt
Translate each named vaccine strategy into a format interpretable by `create_vax_map`set_strategy
Generate the indices of all xpvwrh stratastratum_index_xpvwrh
Generate the indices of all xpvwrh strata trcaking time since vaccstratum_index_xpvwrh_trackvt
Generate the indices of all xvwv trial stratastratum_index_xvw
Generate the indices of all xvw trial stratastratum_index_xvw_trial
Generate the indices of all xvwr trial stratastratum_index_xvwr
Generate the indices of all xvwrh trial stratastratum_index_xvwrh
Generate the indices of all xvwv trial stratastratum_index_xvwv
Transform fitted parameters into gonovax paramstransform
Transform fitted parameters into non-time-varying gonovax paramstransform_fixed
create vaccination parameters for use in onevax_xpvwrh modelvax_params_xpvwrh
create vaccination parameters for use in onevax_xpvwrh modelvax_params_xpvwrh_trackvt
Create vaccination parameters for use in onevax_xvw modelvax_params_xvw
Create vaccination parameters for use in onevax_xvw_trial model, assign who experiences vaccine effects, and how waning occurs.vax_params_xvw_trial
create vaccination parameters for use in onevax_xvwr modelvax_params_xvwr
create vaccination parameters for use in onevax_xvwrh modelvax_params_xvwrh
create vaccination parameters for use in onevax_xvwv modelvax_params_xvwv
create vaccination parameters for use in novax model (null)vax_params0