Plot method for summary.seroincidence.by objects

Plot method for summary.seroincidence.by objects

Usage

# S3 method for class 'summary.seroincidence.by'
autoplot(
  object,
  xvar,
  alpha = 0.7,
  shape = 1,
  dodge_width = 0.001,
  CIs = FALSE,
  ...
)

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()

dodge_width

width for jitter

CIs

logical, if TRUE, add CI error bars

...

unused

Value

a ggplot2::ggplot() object

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,
  curve_strata_varnames= NULL,
  noise_strata_varnames = NULL,
  antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
  num_cores = 2 # Allow for parallel processing to decrease run time
)

est2sum <- summary(est2)

autoplot(est2sum, "catchment")