R: Estimating Infection Rates from Serological Data

# Estimating Infection Rates from Serological Data

## Documentation for package ‘serocalculator’ version 1.4.1

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

analyze_sims | Analyze simulation results
as_noise_params | Load noise parameters
as_pop_data | Load a cross-sectional antibody survey data set
as_sr_params | Load longitudinal seroresponse parameters
autoplot.curve_params | Graph antibody decay curves by antigen isotype
autoplot.pop_data | Plot distribution of antibodies
autoplot.seroincidence | Plot the log-likelihood curve for the incidence rate estimate
autoplot.seroincidence.by | Plot 'seroincidence.by' log-likelihoods
autoplot.sim_results | Plot simulation results 'autoplot()' method for 'sim_results' objects
autoplot.summary.seroincidence.by | Plot method for 'summary.seroincidence.by' objects
check_pop_data | Check the formatting of a cross-sectional antibody survey dataset.
compare_seroincidence | Compare seroincidence rates between two groups
compare_seroincidence.seroincidence | Compare seroincidence rates between two groups
compare_seroincidence.seroincidence.by | Compare seroincidence rates between two groups
est_seroincidence | Find the maximum likelihood estimate of the incidence rate parameter
est_seroincidence_by | Estimate Seroincidence
example_noise_params_pk | Small example of noise parameters for typhoid
example_noise_params_sees | Small example of noise parameters for typhoid
get_biomarker_levels | Extract biomarker levels
get_biomarker_names_var | Get biomarker variable name
get_values | Get antibody measurement values
get_values_var | Extract antibody measurement values
graph.curve.params | Graph estimated antibody decay curves
graph_loglik | Graph log-likelihood of data
load_noise_params | Load noise parameters
load_pop_data | Load a cross-sectional antibody survey data set
load_sr_params | Load longitudinal seroresponse parameter samples
log_likelihood | Calculate log-likelihood
sees_pop_data_100 | Small example cross-sectional data set
sees_pop_data_pk_100 | Small example cross-sectional data set
sees_typhoid_ests_strat | Example '"seroincidence.by"' object
serocalculator_example | Get path to an example file
sim_pop_data | Simulate a cross-sectional serosurvey with noise
sim_pop_data_multi | Simulate multiple data sets
strata | Extract 'Strata' metadata from an object
summary.seroincidence | Summarizing fitted seroincidence models
summary.seroincidence.by | Summary Method for '"seroincidence.by"' Objects
typhoid_curves_nostrat_100 | Small example of antibody response curve parameters for typhoid