Package index • serocalculator

All functions

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.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 serocalculator-package: 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

`[`(<seroincidence.by>): Extract or replace parts of a seroincidence.by object

summary(<pop_data>) print(<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