Package index • serocalculator

Prepare data

as_pop_data(): Load a cross-sectional antibody survey data set

load_pop_data(): Load a cross-sectional antibody survey data set

as_curve_params(): Load antibody decay curve parameter

load_curve_params(): Load antibody decay curve 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 from an object

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 curve

graph_loglik(): Graph log-likelihood of data

log_likelihood(): Calculate log-likelihood

Estimate seroconversion incidence rates

est.incidence(): Find the maximum likelihood estimate of the incidence rate parameter

est.incidence.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

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