
Function reference
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antibody_model_biphasic()
- Biphasic antibody boosting-waning model
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antibody_model_monophasic()
- Monophasic antibody boosting-waning model
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antibody_model_typhoid()
- Power law antibody boosting and waning
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biomarker_protection()
- Function to calculate the risk of infection at a given biomarker quantity
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convert_indices_matrix_to_vector()
- Convert 2D indexing to 1D indexing
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draw_parameters_fixed_fx()
- Draw parameters with fixed effects
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draw_parameters_fixed_fx_biomarker_dep()
- Draw parameters fixed effects with biomarker-quantity-dependent boosting
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draw_parameters_random_fx()
- Draw parameters with random effects
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draw_parameters_random_fx_biomarker_dep()
- Draw parameters random effects with biomarker-quantity-dependent boosting
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example_biomarker_map
- Example biomarker map
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example_biomarker_map_numeric
- Example numeric biomarker map
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example_biomarker_states
- Example biomarker states
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example_biomarker_states_wide
- Example biomarker states (wide)
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example_demography
- Example demography tibble
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example_exposure_force
- Example force of exposure
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example_exposure_histories
- Example exposure histories
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example_exposure_histories_wide
- Example exposure histories (wide)
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example_exposure_probabilities
- Example exposure probability
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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
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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
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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
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observation_model_discrete()
- Observation model for discrete assays with no added noise
-
observation_model_discrete_noise()
- Observation Model For Discrete Assays With Added Noise
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plot_antibody_model()
- Plots example trajectories of the provided antibody kinetics model
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plot_biomarker_dependent_boosting()
- Generate a plot displaying proportion of full boost received at each starting biomarker quantity
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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
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plot_exposure_force()
- Plot individual exposure probabilities across time for all individuals and exposure events
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plot_exposure_histories()
- Plot individual exposure histories
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plot_exposure_model()
- Plots the probability of exposure over time for the provided exposure models
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plot_exposure_prob()
- Plot probability of a successful exposure event for all individuals and exposure events
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plot_obs_biomarkers_one_sample()
- Plot Observed Biomarker Quantities For One Observation Time
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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
ormodel_pars
exposure and biomarker variables
-
runserosim()
- Main simulation function for serosim
-
simulate_birth_times()
- Simulate random birth times
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simulate_gaussian_process()
- Simulate incidence curve using Gaussian Process
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simulate_removal_times()
- Simulate removal times for individuals
-
update()
- runserosim function update message