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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gonovax/json (API)

# 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:

3.90 score 4 stars 1 scripts 57 exports 39 dependencies

Last updated from:4b02b30855 (on master). Checks:11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	809
linux-devel-x86_64	NOTE	814
source / vignettes	OK	210
linux-release-arm64	NOTE	799
linux-release-x86_64	NOTE	854
macos-release-arm64	NOTE	586
macos-release-x86_64	NOTE	838
macos-oldrel-arm64	NOTE	594
macos-oldrel-x86_64	NOTE	831
windows-devel	NOTE	624
windows-release	NOTE	627
windows-oldrel	NOTE	619
wasm-release	OK	122

Exports:adjust_baseline aggregate compare compare_baseline compare_baseline_xpvwrh dbetabinom extract_flows extract_flows_trial extract_flows_xpvwrh gen_erlang_labels gen_erlang_labels_trackvt gen_labels gen_trial_labels gono_params gono_params_trial gonovax_data gonovax_year gonovax_year_as_year initial_params initial_params_trial initial_params_xpvwrh initial_params_xpvwrh_trackvt initial_params_xvw initial_params_xvw_trial initial_params_xvwrh mcmc mcmc_combine mcmc_sample mcmc_thin model model_params model_params_trial model_params_xpvwrh model_params_xpvwrh_trackvt restart_hes restart_params run run_grid run_onevax_xpvwrh run_onevax_xpvwrh_trackvt run_onevax_xvw run_onevax_xvw_trial run_onevax_xvwr run_onevax_xvwrh run_onevax_xvwv run_trial set_protection set_protection_trackvt stratum_index_xpvwrh stratum_index_xpvwrh_trackvt stratum_index_xvw stratum_index_xvw_trial stratum_index_xvwr stratum_index_xvwrh stratum_index_xvwv transform transform_fixed

Dependencies:callr cinterpolate cli codetools cpp11 crayon dde desc deSolve digest dust fs furrr future globals glue hms jsonlite lifecycle listenv magrittr mcstate odin otel parallelly pkgbuild pkgconfig pkgload prettyunits processx progress ps purrr R6 ring rlang rprojroot vctrs withr

Getting started

Running the model without vaccination | Running the model with vaccination | Graphical representations of results

Rendered fromgetting_started.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 vaccination	adjust_baseline
aggregate model runs by vaccination group x vaccine strata	aggregate
Calculate the log likelihood of the data given the parameters diagnoses and attendances lhoods are negative binomial p_symp lhood is betabinomial	compare
compare model runs with vaccination to a baseline runs	compare_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 efficacy	compare_baseline_xpvwrh
Calculate the log likelihood of the data given the parameters	compare_basic
Create mapping for movement between strata due to diagnosis waning	create_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 vaccination	create_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 waning	create_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 xpvwrh	create_waning_map_branching
Create mapping for movement between strata due to vaccine waning in a vaccine trial with erlang compartments	create_waning_map_trial
pdf of a betabinomial parametrised in terms of probability and over-dispersion	dbetabinom
extract flows used for run_grid	extract_flows
extract flows for the XVW trial model	extract_flows_trial
extract flows used for run_grid when the branching xpvwrh model has been run	extract_flows_xpvwrh
generates the appropriate strata labels for the number of strata in the model, which depends on the value given to n_erlang	gen_erlang_labels
generates the appropriate strata labels for the number of strata in the model, which depends on the value given to n_erlang	gen_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 history	gono_params
Posterior parameters of gonorrhoea natural history	gono_params_trial
Get gonovax data	gonovax_data
Convert a year into the number of years after 2009	gonovax_year
Convert a gonovax year into calendar years	gonovax_year_as_year
Initial conditions for the model	initial_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 model	initial_params_xpvwrh
Initial conditions for the model	initial_params_xpvwrh_trackvt
Initial conditions for the model in a vaccine trial	initial_params_xvw_trial
Initial conditions for the model	initial_params_xvwrh
Run a mcmc sampler	mcmc
Combine mcmc samples	mcmc_combine
Thin a mcmc chain	mcmc_sample mcmc_thin
Model of gonorrhoea with dual vaccines This is an odin model.	model
Parameters for the dualvax model	model_params
Parameters for the vaccination trial model	model_params_trial
Parameters for the dualvax model	model_params_xpvwrh
Parameters for the xpvrwrh model tracking time since vaccination	model_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 run	restart_params
Run odin model of gonorrhoea with or without vaccination	run
run model from equilibrium with single vaccine at the input efficacy / duration grid locations for n parameter sets	run_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 stratum	run_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 stratum	run_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 compartment	run_onevax_xvwv
Run odin model of gonorrhoea vaccine trial with or without vaccination	run_trial
Run odin model of gonorrhoea with or without vaccination	run_xpvwrh
Run odin model of gonorrhoea with or without vaccination	run_xpvwrh_trackvt
generates vector which tells the model which strata are under vaccine protection and what the value of protection for that strata is	set_protection
generates vector which tells the model which strata are under vaccine protection and what the value of protection for that strata is	set_protection_trackvt
Translate each named vaccine strategy into a format interpretable by `create_vax_map`	set_strategy
Generate the indices of all xpvwrh strata	stratum_index_xpvwrh
Generate the indices of all xpvwrh strata trcaking time since vacc	stratum_index_xpvwrh_trackvt
Generate the indices of all xvwv trial strata	stratum_index_xvw
Generate the indices of all xvw trial strata	stratum_index_xvw_trial
Generate the indices of all xvwr trial strata	stratum_index_xvwr
Generate the indices of all xvwrh trial strata	stratum_index_xvwrh
Generate the indices of all xvwv trial strata	stratum_index_xvwv
Transform fitted parameters into gonovax params	transform
Transform fitted parameters into non-time-varying gonovax params	transform_fixed
create vaccination parameters for use in onevax_xpvwrh model	vax_params_xpvwrh
create vaccination parameters for use in onevax_xpvwrh model	vax_params_xpvwrh_trackvt
Create vaccination parameters for use in onevax_xvw model	vax_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 model	vax_params_xvwr
create vaccination parameters for use in onevax_xvwrh model	vax_params_xvwrh
create vaccination parameters for use in onevax_xvwv model	vax_params_xvwv
create vaccination parameters for use in novax model (null)	vax_params0