DSIR: Data Science Infrastructure for Global Health in R

Description

A small, opinionated toolkit for global health data analysis. It bundles a publication-ready ggplot2 theme (theme_dsi()), sensible flextable defaults (dsi_flextable_defaults()), a quick pie chart helper (ggpie()), regional country-code datasets (wpro_cty), and thin clients for the WHO Global Health Observatory API (gho_indicators(), gho_data(), gho_dimensions()) and the UN Sustainable Development Goals API (sdg_goals(), sdg_targets(), sdg_indicators(), sdg_areas(), sdg_data()).

Author(s)

Maintainer: Shanlong WHO dings@who.int

See Also

Useful links:

• https://github.com/shanlong-who/DSIR

• Report bugs at https://github.com/shanlong-who/DSIR/issues

Set DSIR Flextable Defaults

Description

Applies a consistent set of flextable formatting defaults for publication-ready tables (booktabs theme, bold headers, modest padding). Pick any font you like — the default "" leaves the flextable default in place so the call is safe on systems where Cambria is not installed.

Usage

dsi_flextable_defaults(
  font_size = 12,
  font_family = "",
  font_color = "#333333",
  border_color = "black",
  padding = c(3, 3, 4, 4)
)

Arguments

Value

Invisibly returns NULL. Called for its side effect of mutating the flextable global defaults via flextable::set_flextable_defaults().

Examples

dsi_flextable_defaults()

Create a Pie Chart with ggplot2

Description

Builds a pie chart from a data frame using one categorical column and one numeric column. Slices are labeled with the category name and percentage share.

Usage

ggpie(
  df,
  .x,
  .y,
  .offset = 1,
  .color = "white",
  .legend = FALSE,
  .label = TRUE,
  .label_size = 3.5
)

Arguments

Value

A ggplot object.

Examples

df <- data.frame(
  category = c("A", "B", "C"),
  value = c(40, 35, 25)
)
ggpie(df, "category", "value")

Fetch GHO Data

Description

Retrieves observations for a specific indicator from the WHO GHO OData API, with optional filters by spatial level, country / region and year range.

Usage

gho_data(
  indicator,
  spatial_type = NULL,
  area = NULL,
  year_from = NULL,
  year_to = NULL
)

Arguments

Value

A data frame of indicator observations, or an empty data frame when the service is unreachable.

See Also

gho_indicators(), gho_dimensions().

Examples

## Not run: 
# Country-level data for one indicator
gho_data("NCDMORT3070", spatial_type = "country")

# Specific countries and years
gho_data("WHOSIS_000001", area = c("FRA", "DEU"), year_from = 2015)

## End(Not run)

List Dimensions of a GHO Indicator

Description

Returns the unique values of a given dimension across all observations of a GHO indicator. Useful for discovering which ages, sexes, regions, or other breakdowns are available before calling gho_data().

Usage

gho_dimensions(indicator, dimension = "SpatialDimType")

Arguments

Value

A character vector of unique, sorted dimension values, or an empty character vector when the service is unreachable or the dimension is missing.

See Also

gho_data(), gho_indicators().

Examples

## Not run: 
gho_dimensions("NCDMORT3070")
gho_dimensions("NCDMORT3070", dimension = "Dim1")

## End(Not run)

List GHO Indicators

Description

Fetches the catalog of indicators from the WHO Global Health Observatory (GHO) OData API.

Usage

gho_indicators(search = NULL)

Arguments

Value

A data frame with columns IndicatorCode, IndicatorName and Language. Returns an empty data frame (with a message) when the service is unreachable.

See Also

gho_data(), gho_dimensions().

Examples

## Not run: 
# All indicators
inds <- gho_indicators()

# Search by keyword
gho_indicators("mortality")

## End(Not run)

List SDG Geographic Areas

Description

Fetches the list of geographic areas available from the UN SDG database.

Usage

sdg_areas()

Value

A data frame with area codes and names, or NULL when the service is unreachable.

See Also

sdg_data().

Examples

## Not run: 
sdg_areas()

## End(Not run)

Fetch SDG Data

Description

Retrieves data for one or more SDG indicators from the UN SDG API, with optional filters by area and year.

Usage

sdg_data(
  indicator,
  area = NULL,
  year_from = NULL,
  year_to = NULL,
  page_size = 1000L
)

Arguments

Value

A data frame of indicator observations, or an empty data frame when the service is unreachable or there are no matching rows.

See Also

sdg_indicators(), sdg_areas().

Examples

## Not run: 
# All data for indicator 1.1.1
sdg_data("1.1.1")

# Specific area and year range
sdg_data("3.2.1", area = "156", year_from = 2015, year_to = 2023)

## End(Not run)

List SDG Goals

Description

Fetches the list of Sustainable Development Goals from the UN SDG API.

Usage

sdg_goals(include_children = FALSE)

Arguments

Value

A list (or data frame) of SDG goals, or NULL when the service is unreachable.

See Also

sdg_targets(), sdg_indicators(), sdg_data().

Examples

## Not run: 
sdg_goals()
sdg_goals(include_children = TRUE)

## End(Not run)

List SDG Indicators

Description

Fetches the list of SDG indicators from the UN SDG API.

Usage

sdg_indicators()

Value

A list (or data frame) of SDG indicators, or NULL when the service is unreachable.

See Also

sdg_targets(), sdg_data().

Examples

## Not run: 
sdg_indicators()

## End(Not run)

List SDG Targets

Description

Fetches the list of SDG targets from the UN SDG API.

Usage

sdg_targets(include_children = FALSE)

Arguments

Value

A list (or data frame) of SDG targets, or NULL when the service is unreachable.

See Also

sdg_goals(), sdg_indicators().

Examples

## Not run: 
sdg_targets()

## End(Not run)

DSIR ggplot2 Theme

Description

A clean, publication-ready ggplot2 theme based on ggplot2::theme_minimal() with a consistent color accent and bordered panels.

Usage

theme_dsi(
  base_size = 12,
  base_family = "",
  color = "steelblue",
  grid_color = "grey85"
)

Arguments

Details

The default base_family = "" uses the graphics device's default font so the theme works on any system (including CRAN's Linux test machines). For the original DSIR look, pass base_family = "Cambria" on a system where that font is installed and registered with R (see grDevices::postscriptFonts() or the systemfonts package).

Value

A ggplot2 theme object that can be added to a plot with +.

Examples

library(ggplot2)
ggplot(women, aes(height, weight)) +
  geom_point(color = "steelblue") +
  theme_dsi()

WPRO Member States (ISO 3166-1 alpha-3)

Description

A character vector of ISO3 codes for countries and areas in the WHO Western Pacific Region.

Usage

wpro_cty

Format

A character vector of length N.