Description Usage Arguments Value See Also Examples
View source: R/plot_tb_burden.R
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | 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,
...
)
|
df |
Dataframe of TB burden data, as sourced by |
dict |
A tibble of the data dictionary. See |
metric |
Character string specifying the metric to plot |
metric_label |
Character string specifying the metric label to use. |
smooth |
Logical, defaults to |
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 |
countries |
A character string specifying the countries to target. |
years |
Numeric vector of years. Defaults to |
compare_to_region |
Logical, defaults to |
facet |
Character string, the name of the variable to facet by. |
legend |
Character string, defaults to |
annual_change |
Logical, defaults to |
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 |
scales |
Character string, see ?ggplot2::facet_wrap for details. Defaults to "fixed", alternatives are "free_y", "free_x", or "free". |
interactive |
Logical, defaults to |
download_data |
Logical, defaults to |
save |
Logical, should the data be saved for reuse during the current R session. Defaults to
|
viridis_palette |
Character string indicating the |
viridis_direction |
Numeric, indicating the direction for the colour palette (1 or -1), defaults to -1.
See |
viridis_end |
Numeric between 0 and 1, defaults to 0.9. The end point of the viridis scale to use.
#' See |
verbose |
Logical, defaults to |
... |
Additional arguments to pass to |
A plot of TB Incidence Rates by Country
get_tb_burden search_data_dict
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | ## 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)
## Not run:
## 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"
)
## End(Not run)
|
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