Man pages for jameshay218/zikaProj
zikaInfer

average_bucketsAverages a vector based on bucket sizes
b.calcBite rate calculation
calc_devianceDeviance
calc_post_meanPosterior mean
calc_post_varPosterior variance
calculate_ARAttack rate
calculate_BICBIC calculation
calculate_DICDIC
calculate_gamma_modeGamma mode
combine_chainsCombine MCMC chains
convert_name_to_locationLocation conversion
convert_name_to_location_factorConvert name to factor
createLocationParTableMCMC location-specific parameter table creation
createParTableMCMC parameter table creation
create_posteriorSimplify posterior call
cumul_trueCumulative true
density.calcDensity calculation
density_plot_funcMicrocephaly parameter density plot
density_plot_statePosterior density plot
exampleParTabExample parameter table
extra_microceph_calculationsPost calculations
find_peak_timesFind peak times
forecast_CRSModel function for CRS prediction
forecast_microcephMicrocephaly incidence forecast
fromUnitScaleConverts to linear scale
generateAllowableParamsGenerate allowable starting parameters
generate_foiFOI calculation
generate_micro_curveGenerate microceph curve
generate_multiple_dataSimulation multi-state microcephaly and incidence data
generate_plot_date_labelsGenerate date labels
generate_probMTime varying microcephaly risk
generate_probM_auxTime varying microcephaly risk AUX
generate_probM_forecastTime varying microcephaly risk not aborted
generate_probM_forecast_OLDTime varying microcephaly risk AUX
generate_riskIRisk of infection
generate_riskSCumulative susceptible probability
generateStartingParTabMCMC start parTab
generate_y0sGenerates y0s
get_best_parsBest pars
get_correct_orderLocation order
getDaysPerMonthGet days per month of the year
get_epidemic_locationsSubset epidemic locations
get_index_parsIndex pars
get_lower_micro_boundLower microcephaly risk bound
get_max_microMax micro risk
get_max_micro_dayMax micro risk day
get_microceph_rangeMicrocephaly risk range
get_upper_micro_boundUpper microbound
incidence_likelihoodIncidence likelihood (binomial)
incidence_likelihood_normIncidence likelihood (normal)
isolate_locationIsolate location from chain
likelihood_probMLikelihood function for time-varying microcephaly
likelihood_probM_normLikelihood function for time-varying microcephaly
load_mcmc_chainsLoad MCMC chains
locationInfoLocation information table
make_micro_datFormat MCMC chain
median.quantileMedian and quantiles
microceph_v1Microcephaly risk V1
microceph_v2Microcephaly risk V2
microceph_v3Microcephaly risk V3
microceph_v4Microcephaly risk V4
mvr_proposalMultivariate proposal function
parTabSetupParameter setup
parTabSetup_auxMCMC parameter setup
plot_best_trajectory_multiPlot all best trajectoroes
plot_best_trajectory_singlePlot single best trajectory
plot_MCMCPlot MCMC chains
plot_micro_boundsPlot microcephaly curves with bounds
plot_random_microceph_curvesPlot microceph curves
plot_setup_dataGet plot data
posterior_complex_bucketsPosterior function for the simple SEIR model with bucketed...
posterior_CRSPosterior function for CRS prediction
posterior_incPosterior function for the simple SEIR model with incidence...
posterior_known_incPosterior function for forecast
posterior_known_inc_seirPosterior function for forecasting analysis
posterior_simple_bucketsPosterior function for the simple SEIR model with bucketed...
print_version_namesRisk window names
proposalfunctionMCMC proposal function
r0.calcR0 calculation
r0.vectorR0 vector calculation
read_all_dataRead all data
read_iniparsRead partab
rm_scaleStep size scaler
run_metropolis_MCMCAdaptive Metropolis-within-Gibbs Random Walk Algorithm.
scaletuningScale step sizes
setupListParsDefault parameter list setup
setupLocationParTableSetup location specific parameter table
setupParsLongDefault simulation parameters
setupParsODEDefaults ODE parameters
simeqAttack rate simeq
solveSEIRModelSolve simple SEIR model
solveSEIRModel_lsodaSolve simple SEIR model (lsoda)
solveSEIRModel_rlsodaSolve simple SEIR model (rlsoda)
sum_bucketsSums a vector based on bucket sizes
summarise_chainSummarise MCMC chain
sum_n_vectorSums nth elements
to.pngPNG - Rich's function to print to device without potential...
to.svgSVG - Rich's function to print to device without potential...
toUnitScaleConverts to unit scale
zikaInferzikaInfer
jameshay218/zikaProj documentation built on Oct. 3, 2018, 3:40 a.m.