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Primary biliary cirrhosis incidence in North East England

Source: R/data.R
liver.Rd

A real aggregated disease-count dataset: incident primary biliary cirrhosis (a chronic liver disease) cases by Lower-layer Super Output Area (LSOA) in the Newcastle and Gateshead area of North East England, with population and area deprivation covariates. This is the case study of Johnson et al. (2019) and a realistic test bed for the spatial model: cases ~ deprivation + offset(log(pop)).

Usage

liver

Format

An sf object of 545 LSOA polygons (British National Grid, EPSG:27700) with columns:

lsoa

LSOA 2004 census code.

cases

observed incident case count in the LSOA.

pop

population at risk (the offset; use offset(log(pop))).

IMD

Index of Multiple Deprivation score (higher = more deprived).

Income

income-deprivation score.

Employment

employment-deprivation score.

geometry

the LSOA polygon.

Source

Johnson, O., Diggle, P. and Giorgi, E. (2019), "A spatially discrete approximation to log-Gaussian Cox processes for modelling aggregated disease count data", Statistics in Medicine, 38(24), 4871-4884. doi:10.1002/sim.8339 . Population and area-deprivation covariates are from the 2004 English indices of deprivation (Lower-layer Super Output Area level). See data-raw/liver.R in the package sources.

See also

sdalgcp_data for a small simulated example.

Examples

data(liver)
summary(liver$cases)
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#>  0.0000  0.0000  1.0000  0.7615  1.0000  7.0000 
plot(liver["IMD"])