Plot TB Burden by Country

Plot 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 plot them (by default plots all countries). Various other options are available for tuning the plot further.

plot_tb_burden(
  df = NULL,
  dict = NULL,
  metric = "e_inc_100k",
  metric_label = NULL,
  smooth = FALSE,
  conf = c("_lo", "_hi"),
  countries = NULL,
  years = NULL,
  compare_to_region = FALSE,
  facet = NULL,
  legend = "none",
  annual_change = FALSE,
  trans = "identity",
  scales = "fixed",
  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.
smooth	Logical, defaults to `FALSE`. Should the data be smoothed (using `ggplot2::geom_smooth`) prior to plotting. If set to `TRUE` then the confidence intervals shown are derived from the smooth and do not represent the underlying uncertainty in the data.
conf	Character vector specifying the name variations to use to specify the upper and lower confidence intervals. Defaults to c("_lo", "_hi"), if set to `NULL` then no confidence intervals are shown. When `annual_change = TRUE` the confidence intervals represent the annual percentage change in the metrics confidence intervals.
countries	A character string specifying the countries to target.
years	Numeric vector of years. Defaults to `NULL` which includes all years in the data.
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 `"none"`. Position of the legend see `?ggplot2::theme` for defaults but known options are: `"none"`, `"top"`, `"right"` and `"bottom"`.
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`.
scales	Character string, see ?ggplot2::facet_wrap for details. Defaults to "fixed", alternatives are "free_y", "free_x", or "free".
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


## Get the WHO TB burden data and the data dictionary
tb_burden <- get_tb_burden()
dict <- get_data_dict()

## Get a random sample of 9 countries
sample_countries <- sample(unique(tb_burden$country), 9)

## Plot incidence rates in these countries
plot_tb_burden(df = tb_burden, dict = dict, facet = "country", countries = sample_countries)
if (FALSE) {
## Plot smoothed incidence rates in these countries
plot_tb_burden(
  df = tb_burden, dict = dict, facet = "country", smooth = TRUE,
  countries = sample_countries
)
## Use data caching to plot incidence rates with free y scales
plot_tb_burden(facet = "country", countries = sample_countries, scales = "free_y")

## Plot annual percentage change in incidence rates in selected countries
plot_tb_burden(
  df = tb_burden, dict = dict, facet = "country", scales = "free_y",
  countries = sample_countries, annual_change = TRUE, conf = NULL
)

## Find variables relating to mortality in the WHO dataset
search_data_dict(def = "mortality")
## Plot mortality rates (exc HIV) - without progress messages
plot_tb_burden(
  metric = "e_mort_exc_tbhiv_100k", facet = "country",
  countries = sample_countries, scales = "free_y"
)
}

Arguments

Value

See also

Examples