Man pages for sbfnk/dynmod
Dynamic models

age.distributionCalculate age distribution in equilibrium age groups to lower age limits.
age.likelihoodLog-likelihood for a model run of an age-structured childhood...
backcalc.populationCalculate previous states of a population, using a...
brownianGenerate a trajectory of brownian motion
clean_countriesClean country names
combine.compartmentsCombine compartments that have been split up to get an Erlang...
cpx.age.wallingaChickenpox age distribution of cases from the Wallinga (2004)...
cpx.init.priorChickenpox prior for initial conditions
cpx.priorEvaluate parameters under a prior distribution for chickenpox
df_to_tsConvert a 'data.frame' into a 'ts' time series object
endemic.age.distcalculates the age distribution in an endemic setting using...
epidemic.age.distcalculates the age distribution in an epidemic setting using...
estimate.immunity.mmrEstimate vaccine-induced immunity in the population from...
estimateMMRImmunityEstimate immunity from MMR and case data
estimate.uptake.mmrEstimate vaccine uptake by age group in the population from...
fit.chickenpox.wallingaFit the chickenpox data
fit.measles.wallingaFit the measles data
fit.polymodFit POLYMOD matrix and age population to target distribution...
forward.initial.conditionsUpdate initial conditions to the start of the actual run (not...
gen.initGenerate initial conditions for measles or chickenpox from...
homogeneous.mixing.matrixGenerate a homogeneous mixing matrix from a social contact...
initSIRInitial conditions for the SIR model
interpolate.serologyInterpolate serology lower age limits to age groups.
loadBryanDataLoad measles England & Wales data
loadChickenpoxEWAgeLoad Chickenpox England & Wales age data
loadChickenpoxSerologyLoad Chickenpox serology data
loadCopenhagenDiseaseLoad Copenhagen disease data
loadDemographicsEWLoad demographic England & Wales data
loadEuropeanMapsLoad European maps
loadMeaslesEuropeLoad measles Europe data
loadMeaslesEWAgeLoad age-specific measles England & Wales data
loadMeaslesEWConfirmationLoad Measles England & Wales confirmation data
loadMeaslesSerologyLoad measles serology data
loadMeaslesSerologyFine1950Load measles serology data from Fine(1950)
loadMeaslesWHOLoad measles WHO data
loadMMREuropeTimingsLoad MMR European timing data
loadMMREWLoad MMR England & Wales data
loadMMRWorldLoad MMR world data
loadPolymodLoad POLYMOD data
loadPopulationEuropeLoad population Europe data
loadPopulationEWAgeLoad population England & Wales age data
loadPopulationWorldAgeLoad population world data
loadRVCVaccinationDataLoad SIA data
loadSIADataLoad SIA data
loadWorldMeaslesDataLoad measles world data
loadWorldPopulationProspectDataLoad worldwide serology data lower to upper age limits
melt.trajectoryMelt a trajectory in terms of time and age groups
ms.age.structure.wallingaMeasles age distribution of cases from the Wallinga (2004)...
ms.priorEvaluate parameters under a prior distribution for measles
pad.zeroesFormat a number padded with zeroes
piecewise.linearGenerate a piecewise linear trajectory
plotChickenpoxEWBeforeAfterRatiosPlot England & Wales chickenpox before/after ratios
plotChickenpoxEWDataPlot England & Wales chickenpox data
plotChickenpoxSerologyPlot chickenpox serology
plotDemographicEWDataPlot England & Wales demographic data
plotMeaslesEuropeanMapsPlot European measles maps
plotMeaslesEWConfDataPlot England & Wales measles confirmation data
plotMeaslesEWDataPlot England & Wales measles data
plotMeaslesSerologyPlot measles serology
plotMeaslesWHODataPlot WHO measles data
plot_mixing_vacc_agesPlot age distributions for measles and chickenpox according...
plotMMRDataPlot MMR data
plot.model.dataPlot a model and data
plotMSCPXEWDataPlot England and Wales measles and chicknepox data
plot.sampled.runPlot a sampled run and data
pop.parametersGet population parameters for England & Wales
rcpp_hello_worldSimple function using Rcpp
runSIRRuns an SIR model
sample.initRandomly sample initial conditions for measles or chickenpox...
sample.posteriorTake random samples from the posterior
sample.priorSample parameters from a prior distribution for measles or...
scan.age.distScan a range of q values
seir.mcmcRun MCMC on the SEIR model
seir.stochasticcalculates a stochastic trajectory of the S(E)IR model
tsir-packageSimulate the gravity TSIR model for infectious disease... year and week to date.
sbfnk/dynmod documentation built on May 29, 2019, 3:21 p.m.