Map TB Burden

Map measures of TB burden by country by specifying a metric from the TB burden data. Specify a country or vector of countries in order to map them (the default is to map all countries). Various other options are available for tuning the plot further.

map_tb_burden(
  df = NULL,
  dict = NULL,
  metric = "e_inc_100k",
  metric_label = NULL,
  fill_var_type = NULL,
  countries = NULL,
  compare_to_region = FALSE,
  facet = NULL,
  legend = "bottom",
  year = NULL,
  annual_change = FALSE,
  trans = "identity",
  interactive = FALSE,
  download_data = TRUE,
  save = TRUE,
  viridis_palette = "viridis",
  viridis_direction = -1,
  viridis_end = 0.9,
  verbose = FALSE,
  ...
)

Arguments

df	Dataframe of TB burden data, as sourced by `get_tb_burden`. If not specified then will source the WHO TB burden data, either locally if available or directly from the WHO (if `download_data = TRUE`).
dict	A tibble of the data dictionary. See `get_data_dict` for details. If not supplied the function will attempt to load a saved version of the dictionary. If this fails and `download_data = TRUE` then the dictionary will be downloaded.
metric	Character string specifying the metric to plot
metric_label	Character string specifying the metric label to use.
fill_var_type	A character string, defaults to `NULL`. To set the fill variable type to be discrete use "discrete" and to be continuous use "continuous".
countries	A character string specifying the countries to target.
compare_to_region	Logical, defaults to `FALSE`. If `TRUE` all countries that share a region with those listed in `countries` will be plotted. Note that this will override settings for `facet`, unless it is set to "country".
facet	Character string, the name of the variable to facet by.
legend	Character string, defaults to `"bottom"`. Position of the legend see `?ggplot2::theme` for defaults but known options are: `"none"`, `"top"`, `"right"` and `"bottom"`.
year	Numeric, indicating the year of data to map. Defaults to the latest year in the data. If `interactive = TRUE` then multiple years may be passed as a vector, the result will then be animated over years.
annual_change	Logical, defaults to `FALSE`. If `TRUE` then the percentage annual change is computed for the specified metric.
trans	A character string specifying the transform to use on the specified metric. Defaults to no transform ("identity"). Other options include log scaling ("log") and log base 10 scaling ("log10"). For a complete list of options see `ggplot2::continous_scale`.
interactive	Logical, defaults to `FALSE`. If `TRUE` then an interactive plot is returned.
download_data	Logical, defaults to `TRUE`. If not found locally should the data be downloaded from the specified URL?
save	Logical, should the data be saved for reuse during the current R session. Defaults to `TRUE`. If `TRUE` then the data is saved to the temporary directory specified by `tempdir`.
viridis_palette	Character string indicating the `viridis` colour palette to use. Defaults to "viridis". Options include "cividis", "magma", "inferno", "plasma", and "viridis". For additional details see `viridis_pal` for additional details.
viridis_direction	Numeric, indicating the direction for the colour palette (1 or -1), defaults to -1. See `scale_color_viridis` for additional details.
viridis_end	Numeric between 0 and 1, defaults to 0.9. The end point of the viridis scale to use. #' See `scale_color_viridis` for additional details.
verbose	Logical, defaults to `FALSE`. Should additional status and progress messages be displayed.
...	Additional arguments to pass to `get_tb_burden`.

Value

A plot of TB Incidence Rates by Country

Examples


## Map raw incidence rates
map_tb_burden()
if (FALSE) {
#' ## Map raw incidence rates
map_tb_burden(year = 2014:2017, facet = "year")

## Map log10 scaled incidence rates
map_tb_burden(trans = "log10")

## Map percentage annual change in incidence rates
map_tb_burden(annual_change = TRUE)

## Find variables relating to mortality in the WHO dataset
search_data_dict(def = "mortality")

## Map mortality rates (exc HIV) - without progress messages
map_tb_burden(metric = "e_mort_exc_tbhiv_100k", verbose = FALSE)

## Can also use a discrete metric if one is available
map_tb_burden(metric = "g_whoregion", metric_label = "WHO world region")
}

Arguments

Value

See also

Examples