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, width = 0.001, ...)

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

Value

a ggplot2::ggplot() object

Examples

library(dplyr)
library(ggplot2)

xs_data <- load_pop_data("https://osf.io/download//n6cp3/")

curve <- load_curve_params("https://osf.io/download/rtw5k/") %>%
  filter(antigen_iso %in% c("HlyE_IgA", "HlyE_IgG")) %>%
  slice(1:100, .by = antigen_iso) # Reduce dataset for the purposes of this example

noise <- load_noise_params("https://osf.io/download//hqy4v/")

est2 <- est.incidence.by(
  strata = c("catchment"),
  pop_data = xs_data %>% filter(Country == "Pakistan"),
  curve_params = curve,
  noise_params = noise %>% filter(Country == "Pakistan"),
  antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
  #num_cores = 8 #Allow for parallel processing to decrease run time
)
#> Warning: curve_params is missing all strata variables, and will be used unstratified.
#> 
#> To avoid this warning, specify the desired set of stratifying variables in the `curve_strata_varnames` and `noise_strata_varnames` arguments to `est.incidence.by()`.
#> Warning: noise_params is missing all strata variables, and will be used unstratified.
#> 
#> To avoid this warning, specify the desired set of stratifying variables in the `curve_strata_varnames` and `noise_strata_varnames` arguments to `est.incidence.by()`.

est2sum <- summary(est2)

autoplot(est2sum, "catchment")