Estimating Infection Rates from Serological Data

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Documentation for package ‘serocalculator’ version 1.3.0

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serocalculator-package Estimating Infection Rates from Serological Data
ab kinetics of the antibody (ab) response (power function decay)
as_curve_params Load antibody decay curve parameter
as_noise_params Load noise parameters
as_pop_data Load a cross-sectional antibody survey data set
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.summary.seroincidence.by Plot method for 'summary.seroincidence.by' objects
check_pop_data Check the formatting of a cross-sectional antibody survey dataset.
est.incidence Find the maximum likelihood estimate of the incidence rate parameter
est.incidence.by Estimate Seroincidence
example_noise_params_pk Small example of noise parameters for typhoid
graph.curve.params Graph estimated antibody decay curve
graph_loglik Graph log-likelihood of data
load_curve_params Load antibody decay curve parameter samples
load_noise_params Load noise parameters
load_pop_data Load a cross-sectional antibody survey data set
log_likelihood Calculate log-likelihood
mk_baseline generate random sample from baseline distribution
plot_curve_params_one_ab Graph an antibody decay curve model
print.seroincidence Print Method for 'seroincidence' Object
print.seroincidence.by Print Method for 'seroincidence.by' Object
print.summary.pop_data Summarize cross-sectional antibody survey data
print.summary.seroincidence.by Print Method for Seroincidence Summary Object
row_longitudinal_parameter extract a row from longitudinal parameter set
sees_pop_data_pk_100 Small example cross-sectional data set
sees_pop_data_pk_100_old_names Small example cross-sectional data set
serocalculator Estimating Infection Rates from Serological Data
serocalculator_example Get path to an example file
sim.cs Simulate a cross-sectional serosurvey with noise
sim.cs.multi Simulate multiple data sets
simcs.tinf collect cross-sectional data
simresp.tinf simulate antibody kinetics of y over a time interval
strata Extract strata from an object
strata.seroincidence.by Extract the 'Strata' attribute from an object, if present
summary.pop_data Summarize cross-sectional antibody survey data
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
warn.missing.strata Warn about missing stratifying variables in a dataset
[.seroincidence.by Extract or replace parts of a 'seroincidence.by' object