getTBinR (version 0.7.1)

map_tb_burden: Map TB Burden

Description

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.

Usage

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

See Also

plot_tb_burden plot_tb_burden_overview get_tb_burden search_data_dict

Examples

# NOT RUN {
## Map raw incidence rates
map_tb_burden()
# }
# NOT RUN {
#' ## 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")
# }