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All functions

antibody_model_biphasic()
Biphasic antibody boosting-waning model
antibody_model_monophasic()
Monophasic antibody boosting-waning model
antibody_model_typhoid()
Power law antibody boosting and waning
biomarker_protection()
Function to calculate the risk of infection at a given biomarker quantity
convert_indices_matrix_to_vector()
Convert 2D indexing to 1D indexing
draw_parameters_fixed_fx()
Draw parameters with fixed effects
draw_parameters_fixed_fx_biomarker_dep()
Draw parameters fixed effects with biomarker-quantity-dependent boosting
draw_parameters_random_fx()
Draw parameters with random effects
draw_parameters_random_fx_biomarker_dep()
Draw parameters random effects with biomarker-quantity-dependent boosting
example_biomarker_map
Example biomarker map
example_biomarker_map_numeric
Example numeric biomarker map
example_biomarker_states
Example biomarker states
example_biomarker_states_wide
Example biomarker states (wide)
example_demography
Example demography tibble
example_exposure_force
Example force of exposure
example_exposure_histories
Example exposure histories
example_exposure_histories_wide
Example exposure histories (wide)
example_exposure_probabilities
Example exposure probability
example_foe_pars
Example force of exposure parameters (foe_pars)
example_model_pars
Example model parameters (model_pars)
example_model_pars_biphasic
Example model parameters for biphasic waning model
example_model_pars_numeric
Example numeric model parameters (model_pars)
example_model_pars_typhoid
Example model parameters for typhoid model (model_pars_typhoid)
example_observed_biomarker_states
Example observed biomarker states
exposure_model_dem_mod()
Exposure Model Modified By Relevant Demographic Elements
exposure_model_fixed()
Fixed probability of exposure
exposure_model_gaussian_process()
Gaussian process model
exposure_model_indiv_fixed()
Known individual-level probability of exposure
exposure_model_simple_FOE()
Exposure Model Simple- Force of Exposure (FOE)
exposure_model_sir()
SIR Exposure Model
generate_pop_demography()
Generate population demography dataset
immunity_model_all_successful()
Null immunity model
immunity_model_ifxn_biomarker_prot()
Immunity model for infection with biomarker-quantity-mediated protection
immunity_model_vacc_ifxn_biomarker_prot()
Immunity model for vaccination and infection events with biomarker-quantity-mediated protection
immunity_model_vacc_ifxn_simple()
Simple immunity model for vaccination and infection events
immunity_model_vacc_only()
Vaccine-mediated immunity model
normal_to_lognormal_mean()
Convert normal distributions to log-normal distributions and return mean
normal_to_lognormal_sd()
Convert normal distributions to log-normal distributions and return standard deviation
observation_model_continuous()
Observation model for continuous assays with no added noise
observation_model_continuous_bounded()
Observation model for continuous assays with detection limits and no added noise
observation_model_continuous_bounded_noise()
Observation model for continuous assays with detection limits and added noise
observation_model_continuous_noise()
Observation model for continuous assays with no detection limits and added noise
observation_model_discrete()
Observation model for discrete assays with no added noise
observation_model_discrete_noise()
Observation Model For Discrete Assays With Added Noise
plot_antibody_model()
Plots example trajectories of the provided antibody kinetics model
plot_biomarker_dependent_boosting()
Generate a plot displaying proportion of full boost received at each starting biomarker quantity
plot_biomarker_mediated_protection()
Plot biomarker mediated protection graphs for each pathogen
plot_biomarker_quantity()
Plot biomarker quantities across time for all individuals and biomarkers
plot_exposure_force()
Plot individual exposure probabilities across time for all individuals and exposure events
plot_exposure_histories()
Plot individual exposure histories
plot_exposure_model()
Plots the probability of exposure over time for the provided exposure models
plot_exposure_prob()
Plot probability of a successful exposure event for all individuals and exposure events
plot_obs_biomarkers_one_sample()
Plot Observed Biomarker Quantities For One Observation Time
plot_obs_biomarkers_paired_sample()
Plot biomarker quantities for multiple observation times and paired samples
plot_subset_individuals_history()
Plot biomarker states and exposure histories for a subset of individuals
precomputation_checks()
Pre-compute exposure probabilities
reformat_biomarker_map()
Reformat biomarker_map or model_pars exposure and biomarker variables
runserosim()
Main simulation function for serosim
simulate_birth_times()
Simulate random birth times
simulate_gaussian_process()
Simulate incidence curve using Gaussian Process
simulate_removal_times()
Simulate removal times for individuals
update()
runserosim function update message