{ "_id": "6a1f2cdbb401979e73426297", "Package": "gonovax", "Title": "Deterministic Compartmental Model of Gonorrhoea with Vaccination", "Version": "0.4.23", "Authors@R": "c( person(given = \"Lilith\",\nfamily = \"Whittles\",\nrole = c(\"aut\", \"cre\"),\nemail = \"l.whittles@imperial.ac.uk\"),\nperson(given = \"Dariya\",\nfamily = \"Nikitin\",\nrole = c(\"aut\"),\nemail = \"d.nikitin20@imperial.ac.uk\"),\nperson(given = \"Trystan\",\nfamily = \"Leng\",\nrole = c(\"aut\"),\nemail = \"trystan.leng@imperial.ac.uk\"))", "Description": "Model for gonorrhoea vaccination, using odin.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Language": "en-GB", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Remotes": [ "mrc-ide/odin", "mrc-ide/dde", "mrc-ide/mcstate" ], "Config/pak/sysreqs": "cmake make libuv1-dev", "Repository": "https://mrc-ide.r-universe.dev", "Date/Publication": "2025-03-14 12:59:52 UTC", "RemoteUrl": "https://github.com/mrc-ide/gonovax", "RemoteRef": "master", "RemoteSha": "4b02b30855ddd7fbaee03a7ccbf0a3b3f305dd7b", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-15 09:44:16 UTC", "User": "root" }, "Author": "Lilith Whittles [aut, cre],\nDariya Nikitin [aut],\nTrystan Leng [aut]", "Maintainer": "Lilith Whittles ", "MD5sum": "2728ab66a7c64485b7ccba9079246336", "_user": "mrc-ide", "_type": "src", "_file": "gonovax_0.4.23.tar.gz", "_fileid": "4d416d03bac24fa89a5a4ab433b80037e56ef5a2fcc28489f01b0a1618dbf28f", "_filesize": 3517080, "_sha256": "4d416d03bac24fa89a5a4ab433b80037e56ef5a2fcc28489f01b0a1618dbf28f", "_created": "2026-05-15T09:44:16.000Z", "_published": "2026-06-02T19:19:55.708Z", "_distro": "noble", "_jobs": [ { "job": 79152975873, "time": 824, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7014570045" }, { "job": 79152975693, "time": 847, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7014576849" }, { "job": 79152975827, "time": 794, "config": "linux-release-arm64", 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actions/cache@v4 (required to pass R-CMD-checks in pull requests)\n\n* Update R/onevax_xpvwrh_trackvt.R\r\n\r\namend comment to reflect actual model structure\n\nCo-authored-by: Lilith Whittles \n\n* lintr change to comment\n\n---------\n\nCo-authored-by: Lilith Whittles ", "time": 1741957192 }, "_maintainer": { "name": "Lilith Whittles", "email": "l.whittles@imperial.ac.uk" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "odin", "version": ">= 1.1.0", "role": "Imports" }, { "package": "dde", "version": ">= 1.0.1", "role": "Imports" }, { "package": "furrr", "role": "Imports" }, { "package": "progress", "version": ">= 1.2.0", "role": "Imports" }, { "package": "mcstate", "version": ">= 0.2.13", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "mrc-ide", "_selfowned": true, "_usedby": 0, "_updates": 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"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" ], "_help": [ { "page": "adjust_baseline", "title": "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", "topics": [ "adjust_baseline" ] }, { "page": "aggregate", "title": "aggregate model runs by vaccination group x vaccine strata", "topics": [ "aggregate" ] }, { "page": "compare", "title": "Calculate the log likelihood of the data given the parameters diagnoses and attendances lhoods are negative binomial p_symp lhood is betabinomial", "topics": [ "compare" ] }, { "page": "compare_baseline", "title": "compare model runs with vaccination to a baseline runs", "topics": [ "compare_baseline" ] }, { "page": "compare_baseline_xpvwrh", "title": "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", "topics": [ "compare_baseline_xpvwrh" ] }, { "page": "compare_basic", "title": "Calculate the log likelihood of the data given the parameters", "topics": [ "compare_basic" ] }, { "page": "create_diagnosis_waning_map", "title": "Create mapping for movement between strata due to diagnosis waning", "topics": [ "create_diagnosis_waning_map" ] }, { "page": "create_uptake_map", "title": "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.", "topics": [ "create_uptake_map" ] }, { "page": "create_uptake_map_xpvwrh", "title": "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.", "topics": [ "create_uptake_map_xpvwrh" ] }, { "page": "create_uptake_map_xpvwrh_trackvt", "title": "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.", "topics": [ "create_uptake_map_xpvwrh_trackvt" ] }, { "page": "create_uptake_map_xvw", "title": "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.", "topics": [ "create_uptake_map_xvw" ] }, { "page": "create_uptake_map_xvwr", "title": "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.", "topics": [ "create_uptake_map_xvwr" ] }, { "page": "create_uptake_map_xvwv", "title": "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.", "topics": [ "create_uptake_map_xvwv" ] }, { "page": "create_vax_map", "title": "Create mapping for movement between strata due to vaccination", "topics": [ "create_vax_map" ] }, { "page": "create_vax_map_branching", "title": "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)", "topics": [ "create_vax_map_branching" ] }, { "page": "create_waning_map", "title": "Create mapping for movement between strata due to vaccine waning", "topics": [ "create_waning_map" ] }, { "page": "create_waning_map_branching", "title": "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", "topics": [ "create_waning_map_branching" ] }, { "page": "create_waning_map_trial", "title": "Create mapping for movement between strata due to vaccine waning in a vaccine trial with erlang compartments", "topics": [ "create_waning_map_trial" ] }, { "page": "dbetabinom", "title": "pdf of a betabinomial parametrised in terms of probability and over-dispersion", "topics": [ "dbetabinom" ] }, { "page": "extract_flows", "title": "extract flows used for run_grid", "topics": [ "extract_flows" ] }, { "page": "extract_flows_trial", "title": "extract flows for the XVW trial model", "topics": [ "extract_flows_trial" ] }, { "page": "extract_flows_xpvwrh", "title": "extract flows used for run_grid when the branching xpvwrh model has been run", "topics": [ "extract_flows_xpvwrh" ] }, { "page": "gen_erlang_labels", "title": "generates the appropriate strata labels for the number of strata in the model, which depends on the value given to n_erlang", "topics": [ "gen_erlang_labels" ] }, { "page": "gen_erlang_labels_trackvt", "title": "generates the appropriate strata labels for the number of strata in the model, which depends on the value given to n_erlang", "topics": [ "gen_erlang_labels_trackvt" ] }, { "page": "gen_labels", "title": "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)", "topics": [ "gen_labels" ] }, { "page": "gen_trial_labels", "title": "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)", "topics": [ "gen_trial_labels" ] }, { "page": "gono_params", "title": "Posterior parameters of gonorrhoea natural history", "topics": [ "gono_params" ] }, { "page": "gono_params_trial", "title": "Posterior parameters of gonorrhoea natural history", "topics": [ "gono_params_trial" ] }, { "page": "gonovax_data", "title": "Get gonovax data", "topics": [ "gonovax_data" ] }, { "page": "gonovax_year", "title": "Convert a year into the number of years after 2009", "topics": [ "gonovax_year" ] }, { "page": "gonovax_year_as_year", "title": "Convert a gonovax year into calendar years", "topics": [ "gonovax_year_as_year" ] }, { "page": "initial_params", "title": "Initial conditions for the model", "topics": [ "initial_params", "initial_params_xvw" ] }, { "page": "initial_params_trial", "title": "Initial conditions for the model trial where the entire cohort is in the high sexual activity group.", "topics": [ "initial_params_trial" ] }, { "page": "initial_params_xpvwrh", "title": "Initial conditions for the model", "topics": [ "initial_params_xpvwrh" ] }, { "page": "initial_params_xpvwrh_trackvt", "title": "Initial conditions for the model", "topics": [ "initial_params_xpvwrh_trackvt" ] }, { "page": "initial_params_xvw_trial", "title": "Initial conditions for the model in a vaccine trial", "topics": [ "initial_params_xvw_trial" ] }, { "page": "initial_params_xvwrh", "title": "Initial conditions for the model", "topics": [ "initial_params_xvwrh" ] }, { "page": "mcmc", "title": "Run a mcmc sampler", "topics": [ "mcmc" ] }, { "page": "mcmc_combine", "title": "Combine mcmc samples", "topics": [ "mcmc_combine" ] }, { "page": "mcmc_thin", "title": "Thin a mcmc chain", "topics": [ "mcmc_sample", "mcmc_thin" ] }, { "page": "model", "title": "Model of gonorrhoea with dual vaccines This is an odin model.", "topics": [ "model" ] }, { "page": "model_params", "title": "Parameters for the dualvax model", "topics": [ "model_params" ] }, { "page": "model_params_trial", "title": "Parameters for the vaccination trial model", "topics": [ "model_params_trial" ] }, { "page": "model_params_xpvwrh", "title": "Parameters for the dualvax model", "topics": [ "model_params_xpvwrh" ] }, { "page": "model_params_xpvwrh_trackvt", "title": "Parameters for the xpvrwrh model tracking time since vaccination", "topics": [ "model_params_xpvwrh_trackvt" ] }, { "page": "restart_hes", "title": "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.", "topics": [ "restart_hes" ] }, { "page": "restart_params", "title": "Create initial conditions to start the model from the end of a run", "topics": [ "restart_params" ] }, { "page": "run", "title": "Run odin model of gonorrhoea with or without vaccination", "topics": [ "run" ] }, { "page": "run_grid", "title": "run model from equilibrium with single vaccine at the input efficacy / duration grid locations for n parameter sets", "topics": [ "run_grid" ] }, { "page": "run_onevax_xpvwrh", "title": "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.", "topics": [ "run_onevax_xpvwrh" ] }, { "page": "run_onevax_xpvwrh_trackvt", "title": "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.", "topics": [ "run_onevax_xpvwrh_trackvt" ] }, { "page": "run_onevax_xvw", "title": "Run model with single vaccine for input parameter sets, either from initialisation or from equilibrium, those with waned vaccines are not eligible for revaccination.", "topics": [ "run_onevax_xvw" ] }, { "page": "run_onevax_xvw_trial", "title": "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.", "topics": [ "run_onevax_xvw_trial" ] }, { "page": "run_onevax_xvwr", "title": "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", "topics": [ "run_onevax_xvwr" ] }, { "page": "run_onevax_xvwrh", "title": "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", "topics": [ "run_onevax_xvwrh" ] }, { "page": "run_onevax_xvwv", "title": "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", "topics": [ "run_onevax_xvwv" ] }, { "page": "run_trial", "title": "Run odin model of gonorrhoea vaccine trial with or without vaccination", "topics": [ "run_trial" ] }, { "page": "run_xpvwrh", "title": "Run odin model of gonorrhoea with or without vaccination", "topics": [ "run_xpvwrh" ] }, { "page": "run_xpvwrh_trackvt", "title": "Run odin model of gonorrhoea with or without vaccination", "topics": [ "run_xpvwrh_trackvt" ] }, { "page": "set_protection", "title": "generates vector which tells the model which strata are under vaccine protection and what the value of protection for that strata is", "topics": [ "set_protection" ] }, { "page": "set_protection_trackvt", "title": "generates vector which tells the model which strata are under vaccine protection and what the value of protection for that strata is", "topics": [ "set_protection_trackvt" ] }, { "page": "set_strategy", "title": "Translate each named vaccine strategy into a format interpretable by `create_vax_map`", "topics": [ "set_strategy" ] }, { "page": "stratum_index_xpvwrh", "title": "Generate the indices of all xpvwrh strata", "topics": [ "stratum_index_xpvwrh" ] }, { "page": "stratum_index_xpvwrh_trackvt", "title": "Generate the indices of all xpvwrh strata trcaking time since vacc", "topics": [ "stratum_index_xpvwrh_trackvt" ] }, { "page": "stratum_index_xvw", "title": "Generate the indices of all xvwv trial strata", "topics": [ "stratum_index_xvw" ] }, { "page": "stratum_index_xvw_trial", "title": "Generate the indices of all xvw trial strata", "topics": [ "stratum_index_xvw_trial" ] }, { "page": "stratum_index_xvwr", "title": "Generate the indices of all xvwr trial strata", "topics": [ "stratum_index_xvwr" ] }, { "page": "stratum_index_xvwrh", "title": "Generate the indices of all xvwrh trial strata", "topics": [ "stratum_index_xvwrh" ] }, { "page": "stratum_index_xvwv", "title": "Generate the indices of all xvwv trial strata", "topics": [ "stratum_index_xvwv" ] }, { "page": "transform", "title": "Transform fitted parameters into gonovax params", "topics": [ "transform" ] }, { "page": "transform_fixed", "title": "Transform fitted parameters into non-time-varying gonovax params", "topics": [ "transform_fixed" ] }, { "page": "vax_params_xpvwrh", "title": "create vaccination parameters for use in onevax_xpvwrh model", "topics": [ "vax_params_xpvwrh" ] }, { "page": "vax_params_xpvwrh_trackvt", "title": "create vaccination parameters for use in onevax_xpvwrh model", "topics": [ "vax_params_xpvwrh_trackvt" ] }, { "page": "vax_params_xvw", "title": "Create vaccination parameters for 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