Plot Time Series of Malaria Incidence (Raw and Transformed)

This function creates time series plots for malaria incidence, optionally including transformed incidence values (e.g., for observation models). Also supports plotting climate covariates, with faceting and overlay options.

Usage

plot_time_series(
  results,
  met = NULL,
  plot_title = "Malaria Incidence Time Series",
  incidence_y_label = "Malaria Incidence",
  climate_y_label = "Climate",
  climate_facet = FALSE,
  select_incidence = c(">=5", "<5", "total"),
  select_climate = c("temp", "cumrain"),
  incidence_colors = c(`>=5` = "blue", `<5` = "red", total = "green", `transformed_>=5` =
    "skyblue", `transformed_<5` = "orange", transformed_total = "darkgreen"),
  climate_colors = c(temp = "orange", cumrain = "purple"),
  climate_alpha = 0.7,
  base_size = 15
)

Arguments

results

A data frame from data_sim() containing columns like inc_C, inc_A, inc_C_transformed, inc_A_transformed, and date_ymd.

met

Optional data frame of climate covariates.

plot_title

Title of the plot.

incidence_y_label

Y-axis label for incidence.

climate_y_label

Y-axis label for climate plot.

climate_facet

Whether to facet incidence and climate plots.

select_incidence

Vector of incidence types to include. Options: "<5", ">=5", "total", "transformed_<5", "transformed_>=5", "transformed_total".

select_climate

Climate vars to include (e.g., "temp", "cumrain").

incidence_colors

Named vector of colors for incidence types.

climate_colors

Named vector of colors for climate vars.

climate_alpha

Transparency for climate lines.

base_size

Base font size.

Value

A ggplot or grid of ggplots