Man pages for seroanalytics/serosolver
Inference Framework for Serological Data

add_measurement_shiftsAdd measurement shifts to predictions
add_noiseAdd noise
bb_meanBeta binomial mean
bb_varBeta binomial variance
calc_phi_probsCalculate FOI log probability
calc_phi_probs_indivCalculate FOI log probability vector
calc_phi_probs_splineCalculate FOI from spline - INACTIVE
calculate_infection_history_statisticsGet posterior information infection histories
check_attack_ratesChecks the attack_rates supplied in simulate_data
check_dataChecks the entries of data used in run_MCMC
check_inf_histCheck infection history matrix
check_par_tabCheck par_tab for simulate_data
check_proposalsChecks if the multivariate proposal is being used with the...
create_age_maskCreate age mask
create_cross_reactivity_vectorConvert melted antigenic map to cross reactivity
create_posterior_funcPosterior function pointer
create_prior_muCreate strain specific bias prior
create_prob_shiftsMeasurement shift creation
create_strain_maskCreate strain mask
cs1_chains_realMCMC chains case study 1, real
cs1_chains_real_bMCMC chains case study 1, real, for sim
cs1_chains_simMCMC chains case study 1, sim
cs2_chains_realMCMC chains case study 2, real
cs2_chains_real_bMCMC chains case study 2, real, for sim
cs2_chains_simMCMC chains case study 2, sim
dbBeta prior on an infection
dbbBeta binomial density
dbb_priorBeta binomial prior used here (no choose constant)
density_beta_binomBeta binomial density
describe_priorsDescribe infection history priors
estimate_modeEstimate vector mode
example_antigenic_mapExample antigenic map
example_inf_chainExample MCMC chain for infection histories
example_inf_histExample infection history matrix
example_par_tabExample parameter table
example_theta_chainExample MCMC chain for kinetics parameters
example_titre_datExample titre data
expand_summary_inf_chainExpands default MCMC saved inf_chain
expand_summary_infChainExpand sparse infection history matrix
Fast-observation-error-function-continuousFast observation error function continuous Calculate the...
find_bb_2Beta binomial parameter match
find_beta_prior_modeFind Beta distribution parameters with mode
find_beta_prior_with_meanFind beta parameters with maximum variance
find_beta_prior_with_mean_varFind beta parameters for mean and variance
find_prior_alpha_betaBeta binomial parameters
fit_beta_priorFit beta distribution to MCMC output
fit_normal_priorFit normal distribution to MCMC output
fromUnitScaleConvert from unit scale to original scale
generate_antigenic_mapGenerate antigenic map
generate_antigenic_map_flexibleGenerate antigenic map, flexible
generate_ar_annualGenerates attack rates from an SIR model with fixed...
generate_cumulative_inf_plotsPlot cumulative and per time posterior infection probability...
generate_phisGenerate FOI phis - INACTIVE
generate_quantilesFormatted quantiles
generate_start_tabGenerate starting parameter table
gen_spline_yGenerates a spline for 'generate_phis' - INACTIVE
get_best_parsBest pars
get_DOBsGet DOBs
get_index_parsIndex pars
get_n_aliveGet number alive
get_n_alive_groupGet number alive by location
get_titre_predictionsGenerate titre credible intervals
get_total_number_infectionsGet total number of infections
hist_rbbBeta binomial histogram
infection_history_priorBeta binomial infection history prior
infection_history_symmetricBrute force infection history proposal
inf_hist_prop_prior_v2_and_v4Infection history gibbs proposal
inf_hist_prop_prior_v3Fast infection history proposal function
inf_hist_swapSwap infection history years
inf_hist_swap_phiSwap infection history years with phi term
inf_mat_priorInfection history prior R
inf_mat_prior_cppMarginal prior probability (p(Z)) of a particular infection...
inf_mat_prior_cpp_vectorMarginal prior probability (p(Z)) of a particular infection...
inf_mat_prior_group_cppMarginal prior probability (p(Z)) of infection history matrix...
inf_mat_prior_group_cpp_vectorMarginal prior probability (p(Z)) of a particular infection...
inf_mat_prior_total_group_cppMarginal prior probability (p(Z)) of a particular infection...
likelihood_func_fastFast observation error function Calculate the probability of...
load_antigenic_map_fileRead in antigenic_map
load_infection_chainsLoad MCMC chains for infection histories
load_mcmc_chainsCombine theta and infection history chains
load_start_tabRead in start_tab
load_theta_chainsLoad MCMC chains for theta
load_titre_datRead in titre_dat
melt_antigenic_coordsCreate useable antigenic map
mvr_proposalMultivariate proposal function
pad_alphas_and_betasPad par_tab with alpha and betas
pad_inf_chainPad infection history chain
pbbBeta binomial distribution function
plot_attack_ratesPlot historical attack rates
plot_attack_rates_monthlyPlot historical attack rates monthly
plot_dataUseful plot for looking at simulated data
plot_infection_historiesPlots infection histories and titre model fits
plot_infection_histories_longPlots infection histories and titre model fits longitudinal
plot_infection_history_chains_indivPlot MCMC trace for infections per individual
plot_infection_history_chains_timePlot MCMC trace for infections per year
plot_number_infectionsPlot point range number infections per individual
plot_posteriors_infhistPlot inferred posteriors infection histories
plot_posteriors_thetaPlot inferred posteriors theta
plot_samples_distancesPlot time between serum samples
plot_total_number_infectionsTotal number of infections
prob_musPrior probability of strain specific boosting
prob_shiftsPrior on measurement shifts
protectProtect function
qbbBeta binomial quantile function
rbbBeta binomial random generation
r_likelihoodLikelihood function given discrete data (normal)
r_likelihood_continuousLikelihood function given continuous data (normal)
rm_scaleRobins and Monro scaler, thanks to Michael White
run_MCMCAdaptive Metropolis-within-Gibbs/Metropolis Hastings Random...
save_infection_history_to_diskWrite given infection history to disk
scaletuningScale step sizes
setup_infection_historiesPropose initial infection histories
setup_infection_histories_oldPropose initial infection histories - OLD VERSION
setup_infection_histories_titrePropose initial infection histories based on titres - use...
setup_infection_histories_totalInitial infection history prior on total
setup_titredat_for_posterior_funcSetup titre data indices
simulate_attack_ratesSimulate attack rates
simulate_cross_sectionalSimulates multiple cohorts in a cross-sectional framework.
simulate_dataSimulate full data set
simulate_groupSimulate group data
simulate_individualSimulate individual data
simulate_individual_fasterSimulate individual data quickly
simulate_infection_historiesSimulate infection histories
subset_nullable_vectorTakes a subset of a Nullable NumericVector, but only if it...
sum_bucketsSums a vector based on bucket sizes
sum_infections_by_groupCount infections by group and time
sum_likelihoodsSum likelihoods into buckets
titre_data_fastOverall model function, fast implementation
titre_dependent_boosting_plotTitre dependent boosting relationship
to.pdfPDF - Rich's function to print to device without potential...
to.pngPNG - Rich's function to print to device without potential...
to.svgSVG - Rich's function to print to device without potential...
toUnitScaleConvert to unit scale
univ_proposalMCMC proposal function
wane_functionFunction to calculate non-linear waning All additional...
seroanalytics/serosolver documentation built on July 19, 2023, 5:10 a.m.