serocalculator (version 1.3.0)

autoplot.summary.seroincidence.by: Plot method for summary.seroincidence.by objects

Description

Plot method for summary.seroincidence.by objects

Usage

# S3 method for summary.seroincidence.by
autoplot(object, xvar, alpha = 0.7, shape = 1, width = 0.001, ...)

Value

a ggplot2::ggplot() object

Arguments

object

a summary.seroincidence.by object (generated by applying the summary() method to the output of est.incidence.by()).

xvar

the name of a stratifying variable in object

alpha

transparency for the points in the graph (1 = no transparency, 0 = fully transparent)

shape

shape argument for geom_point()

width

width for jitter

...

unused

Examples

library(dplyr)
library(ggplot2)

xs_data <-
  sees_pop_data_pk_100

curve <-
  typhoid_curves_nostrat_100 %>%
  filter(antigen_iso %in% c("HlyE_IgA", "HlyE_IgG"))

noise <-
  example_noise_params_pk

est2 <- est.incidence.by(
  strata = c("catchment"),
  pop_data = xs_data,
  curve_params = curve,
  noise_params = noise,
  antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
  #num_cores = 8 #Allow for parallel processing to decrease run time
)

est2sum <- summary(est2)

autoplot(est2sum, "catchment")