Function reference • serosim

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