Description Usage Arguments Value Examples
View source: R/summarise_tb_burden.R
Summarise TB burden metrics by region, globally, and for custom groupings. For variables with uncertainty represented by confidence intervals bootstrapping can be used (assuming a normal distribution) to include this in any estimated summary measures. Currently two statistics are supported; the mean (with 95\
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | summarise_tb_burden(
df = NULL,
dict = NULL,
metric = "e_inc_num",
metric_label = NULL,
conf = c("_lo", "_hi"),
years = NULL,
samples = 1000,
countries = NULL,
compare_to_region = FALSE,
compare_to_world = TRUE,
custom_compare = NULL,
compare_all_regions = TRUE,
stat = "rate",
denom = "e_pop_num",
rate_scale = 1e+05,
truncate_at_zero = TRUE,
annual_change = FALSE,
download_data = TRUE,
save = TRUE,
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. |
conf |
Character vector specifying the name variations to use to specify the upper
and lower confidence intervals. Defaults to |
years |
Numeric vector of years. Defaults to |
samples |
Numeric, the number of samples to use to generate confidence
intervals (only used when |
countries |
A character string specifying the countries to target. |
compare_to_region |
Logical, defaults to |
compare_to_world |
Logical, defaults to |
custom_compare |
Logical, defaults to |
compare_all_regions |
Logical, defaults to |
stat |
Character string, defaults to |
denom |
Character string defaulting to |
rate_scale |
Numeric defaults to 100,000. The scaling to use for rates. If |
truncate_at_zero |
Logical, defaults to |
annual_change |
Logical, defaults to |
download_data |
Logical, defaults to |
save |
Logical, should the data be saved for reuse during the current R session. Defaults to
|
verbose |
Logical, defaults to |
... |
Additional arguments to pass to |
A tibble containing summarised values (with 95% confidence intervals) for the metric of choice stratified by area and year.
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 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | ## Get the most recent year of data
tb_burden <- get_tb_burden()
most_recent_year <- max(tb_burden$year)
## Get summary of the e_mdr_pct_rr_new cases
summarise_tb_burden(
metric = "e_mdr_pct_rr_new",
years = most_recent_year,
stat = "mean",
samples = 100,
compare_all_regions = TRUE,
compare_to_world = TRUE,
verbose = TRUE
)
## Not run:
## Get median (with 95% IQR) of the case fatality rate for regions and the world
## Boostrapping uncertainty in country measures
summarise_tb_burden(
metric = "cfr",
years = most_recent_year,
samples = 100,
stat = "median",
compare_all_regions = TRUE,
compare_to_world = TRUE,
verbose = FALSE
)
## Get summary data for the UK, Europe and the world
## Bootstrapping CI's
summarise_tb_burden(
metric = "e_inc_num",
samples = 100,
stat = "median",
countries = "United Kingdom",
compare_to_world = TRUE,
compare_to_region = TRUE,
verbose = FALSE
)
## Get an overview of incidence rates regionally and globally compared to the UK
summarise_tb_burden(
metric = "e_inc_num",
stat = "rate",
countries = "United Kingdom",
compare_to_world = TRUE,
compare_to_region = TRUE,
verbose = FALSE
)
## End(Not run)
|
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