Bayesian Estimation of the Force of Infection from Serological Data
Simulate serosurvey data based on a time-varying Force-of-Infection (F...
Adds age group marker to serosurvey
Builds stan data for sampling depending on the selected model
Check min and max age consistency for validation purposes
Extracts central estimates from stan_fit object for specified paramete...
Runs specified stan model for the Force-of-Infection (FoI)
Generates Force-of-Infection indexes for heterogeneous age groups
Generate seropositivity counts by bin given the probability and sample...
Generate probabilities of seropositivity by age based on an age-varyin...
Generate probabilities of seropositivity by age based on an age-and-ti...
Generate probabilities of seropositivity by age based on model choice.
Generate probabilities of seropositivity by age based on a general For...
Generate probabilities of seropositivity by age based on a time-varyin...
Computes the probability of being seropositive when Forces-of-Infectio...
Computes the probability of being seropositive when Forces-of-Infectio...
The 'serofoi' package.
Sets initialization function for sampling
Set stan data defaults for sampling
Sets Cauchy distribution parameters for sampling
Sets empty prior distribution
Sets normal distribution parameters for sampling
Sets uniform distribution parameters for sampling
Simulate serosurvey data based on an age-and-time-varying Force-of-Inf...
Simulate serosurvey data based on an age-varying Force-of-Infection (F...
Simulate serosurvey data based on general serocatalytic model.
Prepares serosurvey for plotting
Helper function to validate consistency between the FoI and the survey...
Helper function to validate consistency between the FoI and the survey...
Plots model summary
Plots Force-of-Infection central estimates
Plot r-hats convergence criteria for the specified model
Visualise results of the provided model
Plot seroprevalence estimates on top of the serosurvey
Plots seroprevalence from the given serosurvey
Helper function to validate serosurvey features for simulation
Simulate serosurvey data based on various Force-of-Infection (FoI) mod...
Summarise central estimate
Extract specified loo estimate
Summarise specified model
Helper function to validate FoI structure for simulation
Helper function to validate FoI index consistency
Helper function to validate whether the current plot corresponds to a ...
Helper function to validate seroreversion rate properties for simulati...
Helper function to validate serosurvey structure
Estimating the force of infection from time varying, age varying, or constant serocatalytic models from population based seroprevalence studies using a Bayesian framework, including data simulation functions enabling the generation of serological surveys based on this models. This tool also provides a flexible prior specification syntax for the force of infection and the seroreversion rate, as well as methods to assess model convergence and comparison criteria along with useful visualisation functions.
Useful links