Man pages for sbfnk/dynmod
Dynamic models
| age.distribution | Calculate age distribution in equilibrium |
| agegroups.to.limits | Convert age groups to lower age limits. |
| age.likelihood | Log-likelihood for a model run of an age-structured childhood... |
| backcalc.population | Calculate previous states of a population, using a... |
| brownian | Generate a trajectory of brownian motion |
| clean_countries | Clean country names |
| combine.compartments | Combine compartments that have been split up to get an Erlang... |
| cpx.age.wallinga | Chickenpox age distribution of cases from the Wallinga (2004)... |
| cpx.init.prior | Chickenpox prior for initial conditions |
| cpx.prior | Evaluate parameters under a prior distribution for chickenpox |
| df_to_ts | Convert a 'data.frame' into a 'ts' time series object |
| endemic.age.dist | calculates the age distribution in an endemic setting using... |
| epidemic.age.dist | calculates the age distribution in an epidemic setting using... |
| estimate.immunity.mmr | Estimate vaccine-induced immunity in the population from... |
| estimateMMRImmunity | Estimate immunity from MMR and case data |
| estimate.uptake.mmr | Estimate vaccine uptake by age group in the population from... |
| fit.chickenpox.wallinga | Fit the chickenpox data |
| fit.measles.wallinga | Fit the measles data |
| fit.polymod | Fit POLYMOD matrix and age population to target distribution... |
| forward.initial.conditions | Update initial conditions to the start of the actual run (not... |
| gen.init | Generate initial conditions for measles or chickenpox from... |
| homogeneous.mixing.matrix | Generate a homogeneous mixing matrix from a social contact... |
| initSIR | Initial conditions for the SIR model |
| interpolate.serology | Interpolate serology |
| limits.to.agegroups | Convert lower age limits to age groups. |
| loadBryanData | Load measles England & Wales data |
| loadChickenpoxEWAge | Load Chickenpox England & Wales age data |
| loadChickenpoxSerology | Load Chickenpox serology data |
| loadCopenhagenDisease | Load Copenhagen disease data |
| loadDemographicsEW | Load demographic England & Wales data |
| loadEuropeanMaps | Load European maps |
| loadMeaslesEurope | Load measles Europe data |
| loadMeaslesEWAge | Load age-specific measles England & Wales data |
| loadMeaslesEWConfirmation | Load Measles England & Wales confirmation data |
| loadMeaslesSerology | Load measles serology data |
| loadMeaslesSerologyFine1950 | Load measles serology data from Fine(1950) |
| loadMeaslesWHO | Load measles WHO data |
| loadMMREuropeTimings | Load MMR European timing data |
| loadMMREW | Load MMR England & Wales data |
| loadMMRWorld | Load MMR world data |
| loadPolymod | Load POLYMOD data |
| loadPopulationEurope | Load population Europe data |
| loadPopulationEWAge | Load population England & Wales age data |
| loadPopulationWorldAge | Load population world data |
| loadRVCVaccinationData | Load SIA data |
| loadSIAData | Load SIA data |
| loadWorldMeaslesData | Load measles world data |
| loadWorldPopulationProspectData | Load worldwide serology data |
| lower.to.upper.limits | Convert lower to upper age limits |
| melt.trajectory | Melt a trajectory in terms of time and age groups |
| ms.age.structure.wallinga | Measles age distribution of cases from the Wallinga (2004)... |
| ms.prior | Evaluate parameters under a prior distribution for measles |
| pad.zeroes | Format a number padded with zeroes |
| piecewise.linear | Generate a piecewise linear trajectory |
| plotChickenpoxEWBeforeAfterRatios | Plot England & Wales chickenpox before/after ratios |
| plotChickenpoxEWData | Plot England & Wales chickenpox data |
| plotChickenpoxSerology | Plot chickenpox serology |
| plotDemographicEWData | Plot England & Wales demographic data |
| plotMeaslesEuropeanMaps | Plot European measles maps |
| plotMeaslesEWConfData | Plot England & Wales measles confirmation data |
| plotMeaslesEWData | Plot England & Wales measles data |
| plotMeaslesSerology | Plot measles serology |
| plotMeaslesWHOData | Plot WHO measles data |
| plot_mixing_vacc_ages | Plot age distributions for measles and chickenpox according... |
| plotMMRData | Plot MMR data |
| plot.model.data | Plot a model and data |
| plotMSCPXEWData | Plot England and Wales measles and chicknepox data |
| plot.sampled.run | Plot a sampled run and data |
| pop.parameters | Get population parameters for England & Wales |
| rcpp_hello_world | Simple function using Rcpp |
| runSIR | Runs an SIR model |
| sample.init | Randomly sample initial conditions for measles or chickenpox... |
| sample.posterior | Take random samples from the posterior |
| sample.prior | Sample parameters from a prior distribution for measles or... |
| scan.age.dist | Scan a range of q values |
| seir.mcmc | Run MCMC on the SEIR model |
| seir.stochastic | calculates a stochastic trajectory of the S(E)IR model |
| tsir-package | Simulate the gravity TSIR model for infectious disease... |
| year.week.to.date | Convert year and week to date. |
