Package index • serocalculator

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

Summarize data

summary(<pop_data>) print(<summary.pop_data>): Summarize cross-sectional antibody survey data

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

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

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