seroprevalence.fit: Plot the fit of the seroprevalence vs. age

In nathoze/Rsero: Estimate the annual force of infection using serological data

Plot the fit of the seroprevalence vs. age

Description

Plot the mean and credible interval of the posterior of the seroprevalence, given an object of the class FOIfit. See function seroprevalence for plotting the seroprevalence from the data. The function returns graphical objects that can be further modified.

Usage

seroprevalence.fit(
  FOIfit,
  individual_samples = 0,
  age_class = 10,
  YLIM = 1,
  ...
)

Arguments

FOIfit	The FOIfit object to be plotted.
individual_samples	Integer. Number of individual samples to be plotted additionally to the mean and the credible interval of the force of infection. The indivual_samples samples are randomly chosen in the chains. Default = 0.
age_class	Integer. Length of the age groups (in years). Used if show_data = TRUE. Default = 10.
YLIM	Upper limit of the y-axis. Default = 1. The lower limit is set to 0.
show_data	Boolean. If TRUE, shows the fraction of seropositive as well. By default, ages are associated in groups of age_class years. Default = TRUE.

Value

A list of ggplot2 objects.

Author(s)

Nathanael Hoze [e-mail]

Examples

data <- simulate_SeroData( max_age = 50, epidemic_years = c(1976,1992), foi = c(0.2,0.3))
model <- FOImodel(type='outbreak', background=TRUE, K = 2)

Fit <- fit(model = model, data = data)

# plot the fraction of seropositive, with 2 individual samples
p <- seroprevalence.fit(Fit,  individual_samples = 2,YLIM=0.2)

nathoze/Rsero documentation built on Dec. 1, 2024, 6:39 p.m.