Package index • serodynamics

Simulate case data

sim_case_data(): Simulate longitudinal case follow-up data from a homogeneous population

Prepare data for analysis

serodynamics_example(): Get path to an example file
load_data(): load and format data
as_case_data(): Convert data into case_data
prep_data(): prepare data for JAGs

Visualize data

autoplot(<case_data>): Plot case data

Prepare auxiliary JAGS inputs

prep_priors(): Prepare priors
initsfunction(): JAGS chain initialization function

Model seroreponse

run_mod(): Run Jags Model

Model diagnostics

plot_jags_dens(): Density Plot Diagnostics
plot_jags_Rhat(): Rhat Plot Diagnostics
plot_jags_trace(): Trace Plot Diagnostics
plot_jags_effect(): Plot Effective Sample Size Diagnostics
plot_predicted_curve(): Generate Predicted Antibody Response Curves (Median + 95% CI)

Postprocess JAGS output

postprocess_jags_output(): Postprocess JAGS output

Summarize seroresponse model estimates

post_summ(): Summary Table of Jags Posterior Estimates
print(<sr_model>): Default print for run_mod() output object of class sr_model

Example data sets

serodynamics_example(): Get path to an example file
nepal_sees: SEES Typhoid data
nepal_sees_jags_output: SEES Typhoid run_mod jags output