Package index

Prepare data, kinetics models, and noise parameters for analysis

• as_pop_data() — Load a cross-sectional antibody survey data set
• load_pop_data() — Load a cross-sectional antibody survey data set
• as_sr_params() — Load longitudinal seroresponse parameters
• load_sr_params() — Load longitudinal seroresponse parameter samples
• as_noise_params() — Load noise parameters
• load_noise_params() — Load noise parameters
• check_pop_data() — Check the formatting of a cross-sectional antibody survey dataset.
• strata() — Extract Strata metadata from an object

Extract information from data, seroresponse models, and noise parameters

• get_biomarker_levels() — Extract biomarker levels
• get_biomarker_names_var() — Get biomarker variable name
• get_values_var() — Extract antibody measurement values
• get_values() — Get antibody measurement values

Visualize data

• autoplot.pop_data — Plot distribution of antibodies
• autoplot.curve_params — Graph antibody decay curves by antigen isotype
• graph.curve.params() — Graph estimated antibody decay curves
• graph_loglik() — Graph log-likelihood of data
• log_likelihood() — Calculate log-likelihood
• antibody_decay_curve() — Antibody decay curve with natural parameters
• pathogen_decay_curve() — Pathogen decay curve
• plot_decay_curve() — Plot a decay function
• curve_app() — Launch the interactive Shiny app for the antigen-antibody kinetics model
• t1f() — Calculate time to end of active infection
• y1f() — Calculate peak antibody concentration

Estimate seroconversion incidence rates

• est_seroincidence() — Find the maximum likelihood estimate of the incidence rate parameter
• est_seroincidence_by() — Estimate Seroincidence

Summarize seroconversion incidence rate estimates

• summary.seroincidence — Summarizing fitted seroincidence models
• summary.seroincidence.by — Summary Method for "seroincidence.by" Objects

Visualize seroconversion incidence rate estimates

• autoplot.seroincidence — Plot the log-likelihood curve for the incidence rate estimate
• autoplot.seroincidence.by — Plot seroincidence.by log-likelihoods
• autoplot.summary.seroincidence.by — Plot method for summary.seroincidence.by objects

Compare seroconversion incidence rates

• compare_seroincidence() — Compare seroincidence rates between two groups

Example data sets

• sees_pop_data_100 — Small example cross-sectional data set
• sees_pop_data_pk_100 — Small example cross-sectional data set
• typhoid_curves_nostrat_100 — Small example of antibody response curve parameters for typhoid
• example_noise_params_sees — Small example of noise parameters for typhoid
• example_noise_params_pk — Small example of noise parameters for typhoid
• sees_typhoid_ests_strat — Example "seroincidence.by" object
• serocalculator_example() — Get path to an example file

Simulate data sets

• sim_pop_data() — Simulate a cross-sectional serosurvey with noise
• sim_pop_data_multi() — Simulate multiple data sets
• analyze_sims() — Analyze simulation results
• autoplot.sim_results — Plot simulation results autoplot() method for sim_results objects

Other

• est_seroincidence_by_cached() — Estimate seroincidence by stratum, caching the result on disk
• sim_pop_data_multi_cached() — Simulate multiple data sets, caching the result on disk