serocalculator-package |
Estimating Infection Rates from Serological Data |
ab |
kinetics of the antibody (ab) response (power function decay) |
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. |
clean_pop_data |
Reformat a cross-sectional antibody survey dataset |
df_to_array |
Convert a data.frame (or tibble) into a multidimensional array |
est.incidence |
Find the maximum likelihood estimate of the incidence rate parameter |
est.incidence.by |
Estimate Seroincidence |
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 |
serocalculator |
Estimating Infection Rates from Serological Data |
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 a cross-sectional antibody survey data set |
summary.seroincidence |
Summarizing fitted seroincidence models |
summary.seroincidence.by |
Summary Method for '"seroincidence.by"' Objects |
warn.missing.strata |
Warn about missing stratifying variables in a dataset |
[.seroincidence.by |
Extract or replace parts of a 'seroincidence.by' object |