This data set was presented first in Symons, Grimson, and Yuan (1983), analysed with reference to the spatial nature of the data in Cressie and Read (1985), expanded in Cressie and Chan (1989), and used in detail in Cressie (1991). It is for the 100 counties of North Carolina, and includes counts of numbers of live births (also non-white live births) and numbers of sudden infant deaths, for the July 1, 1974 to June 30, 1978 and July 1, 1979 to June 30, 1984 periods. In Cressie and Read (1985), a listing of county neighbours based on shared boundaries (contiguity) is given, and in Cressie and Chan (1989), and in Cressie (1991, 386–89), a different listing based on the criterion of distance between county seats, with a cutoff at 30 miles. The county seat location coordinates are given in miles in a local (unknown) coordinate reference system. The data are also used to exemplify a range of functions in the spatial statistics module user’s manual (Kaluzny et al. 1996).

We will be using the **spdep** and
**spreg** packages, here version: spdep, version 1.3-6,
2024-08-31, the **sf** package and the
**tmap** package. The data from the sources referred to
above is documented in the help page for the `nc.sids`

data
set in **spData**. The actual data, included in a shapefile
of the county boundaries for North Carolina were made available in the
**maptools** package ^{1}. These data are known to be geographical
coordinates (longitude-latitude in decimal degrees) and are assumed to
use the NAD27 datum. The ESRI Shapefile is deprecated, and was replaced
here by a GeoPackage, written from reading the original files in
**spData** 2.3.1:

```
library(spdep)
nc <- st_read(system.file("shapes/sids.gpkg", package="spData")[1], quiet=TRUE)
#st_crs(nc) <- "EPSG:4267"
row.names(nc) <- as.character(nc$FIPSNO)
```

The shapefile format presupposed that you had three files with
extensions `.shp`

, `.shx`

, and `.dbf`

,
where the first contains the geometry data, the second the spatial
index, and the third the attribute data. They were required to have the
same name apart from the extension, and were read here using
`sf::st_read()`

into the `sf`

object
`nc`

; the class is defined in **sf**. The
centroids of the largest polygon in each county are available using the
`st_centroid`

method from **sf** as an
**sfc** POINT object, and can be used to place labels after
the extraction of the coordinate matrix:

```
sf_use_s2(TRUE)
plot(st_geometry(nc), axes=TRUE)
text(st_coordinates(st_centroid(st_geometry(nc), of_largest_polygon=TRUE)), label=nc$FIPSNO, cex=0.5)
```

We can examine the names of the columns of the data frame to see what it contains — in fact some of the same columns that we will be examining below, and some others which will be useful in cleaning the data set.

`names(nc)`

```
## [1] "CNTY_ID" "AREA" "PERIMETER" "CNTY_" "NAME" "FIPS" "FIPSNO"
## [8] "CRESS_ID" "BIR74" "SID74" "NWBIR74" "BIR79" "SID79" "NWBIR79"
## [15] "east" "north" "x" "y" "lon" "lat" "L_id"
## [22] "M_id" "geom"
```

`summary(nc)`

```
## CNTY_ID AREA PERIMETER CNTY_ NAME
## Min. :1825 Min. :0.0420 Min. :0.999 Min. :1825 Length:100
## 1st Qu.:1902 1st Qu.:0.0910 1st Qu.:1.324 1st Qu.:1902 Class :character
## Median :1982 Median :0.1205 Median :1.609 Median :1982 Mode :character
## Mean :1986 Mean :0.1263 Mean :1.673 Mean :1986
## 3rd Qu.:2067 3rd Qu.:0.1542 3rd Qu.:1.859 3rd Qu.:2067
## Max. :2241 Max. :0.2410 Max. :3.640 Max. :2241
## FIPS FIPSNO CRESS_ID BIR74 SID74
## Length:100 Min. :37001 Min. : 1.00 Min. : 248 Min. : 0.00
## Class :character 1st Qu.:37050 1st Qu.: 25.75 1st Qu.: 1077 1st Qu.: 2.00
## Mode :character Median :37100 Median : 50.50 Median : 2180 Median : 4.00
## Mean :37100 Mean : 50.50 Mean : 3300 Mean : 6.67
## 3rd Qu.:37150 3rd Qu.: 75.25 3rd Qu.: 3936 3rd Qu.: 8.25
## Max. :37199 Max. :100.00 Max. :21588 Max. :44.00
## NWBIR74 BIR79 SID79 NWBIR79 east
## Min. : 1.0 Min. : 319 Min. : 0.00 Min. : 3.0 Min. : 19.0
## 1st Qu.: 190.0 1st Qu.: 1336 1st Qu.: 2.00 1st Qu.: 250.5 1st Qu.:178.8
## Median : 697.5 Median : 2636 Median : 5.00 Median : 874.5 Median :285.0
## Mean :1051.0 Mean : 4224 Mean : 8.36 Mean : 1352.8 Mean :271.3
## 3rd Qu.:1168.5 3rd Qu.: 4889 3rd Qu.:10.25 3rd Qu.: 1406.8 3rd Qu.:361.2
## Max. :8027.0 Max. :30757 Max. :57.00 Max. :11631.0 Max. :482.0
## north x y lon lat
## Min. : 6.0 Min. :-328.04 Min. :3757 Min. :-84.08 Min. :33.92
## 1st Qu.: 97.0 1st Qu.: -60.55 1st Qu.:3920 1st Qu.:-81.20 1st Qu.:35.26
## Median :125.5 Median : 114.38 Median :3963 Median :-79.26 Median :35.68
## Mean :122.1 Mean : 91.46 Mean :3953 Mean :-79.51 Mean :35.62
## 3rd Qu.:151.5 3rd Qu.: 240.03 3rd Qu.:4000 3rd Qu.:-77.87 3rd Qu.:36.05
## Max. :182.0 Max. : 439.65 Max. :4060 Max. :-75.67 Max. :36.52
## L_id M_id geom
## Min. :1.00 Min. :1.00 MULTIPOLYGON :100
## 1st Qu.:1.00 1st Qu.:2.00 epsg:4267 : 0
## Median :2.00 Median :3.00 +proj=long...: 0
## Mean :2.12 Mean :2.67
## 3rd Qu.:3.00 3rd Qu.:3.25
## Max. :4.00 Max. :4.00
```

Let’s check the different versions of the data against each other -
**sf** and **spData** have NC SIDS files, as
does GeoDa Center in two forms:

```
library(sf)
nc_sf <- st_read(system.file("shape/nc.shp", package="sf"),
quiet=TRUE)
st_crs(nc_sf)
```

```
## Coordinate Reference System:
## User input: NAD27
## wkt:
## GEOGCRS["NAD27",
## DATUM["North American Datum 1927",
## ELLIPSOID["Clarke 1866",6378206.4,294.978698213898,
## LENGTHUNIT["metre",1]]],
## PRIMEM["Greenwich",0,
## ANGLEUNIT["degree",0.0174532925199433]],
## CS[ellipsoidal,2],
## AXIS["latitude",north,
## ORDER[1],
## ANGLEUNIT["degree",0.0174532925199433]],
## AXIS["longitude",east,
## ORDER[2],
## ANGLEUNIT["degree",0.0174532925199433]],
## ID["EPSG",4267]]
```

```
nc <- st_read(system.file("shapes/sids.shp",
package="spData"), quiet=TRUE)
st_crs(nc)
```

`## Coordinate Reference System: NA`

As the actual CRS is unknown, **spData** reports
missing, although it may very well be
`+proj=longlat +datum=NAD27`

`st_crs(nc) <- "+proj=longlat +datum=NAD27"`

Next, are the geometries the same? `sf::st_equals`

returns
a logical matrix, so we’ll check that the diagonal values are all
`TRUE`

, and that only those values are `TRUE`

by
summing and recalling that `n`

is `100`

:

```
suppressWarnings(st_crs(nc_sf) <- st_crs(nc))
xx <- st_equals(nc, nc_sf, sparse=FALSE)
all(diag(xx)) && sum(xx) == 100L
```

`## [1] TRUE`

Next, let’s download the GeoDa files and repeat the comparisons:

```
td <- tempdir()
#download.file("https://geodacenter.github.io/data-and-lab//data/sids.zip", file.path(td, "sids.zip"), quiet=TRUE)
# local copy (2020-10-22) as repository sometimes offline
file.copy(system.file("etc/misc/sids.zip", package="spdep"), td)
```

`## [1] TRUE`

```
unzip(file.path(td, "sids.zip"), c("sids/sids.dbf", "sids/sids.prj", "sids/sids.shp", "sids/sids.shx"), exdir=td)
sids_sf <- st_read(file.path(td, "sids/sids.shp"), quiet=TRUE)
#download.file("https://geodacenter.github.io/data-and-lab//data/sids2.zip", file.path(td, "sids2.zip"), quiet=TRUE)
file.copy(system.file("etc/misc/sids2.zip", package="spdep"), td)
```

`## [1] TRUE`

```
unzip(file.path(td, "sids2.zip"), c("sids2/sids2.dbf", "sids2/sids2.prj", "sids2/sids2.shp", "sids2/sids2.shx"), exdir=td)
sids2_sf <- st_read(file.path(td, "sids2/sids2.shp"), quiet=TRUE)
```

`st_crs(sids_sf)`

```
## Coordinate Reference System:
## User input: WGS 84
## wkt:
## GEOGCRS["WGS 84",
## DATUM["World Geodetic System 1984",
## ELLIPSOID["WGS 84",6378137,298.257223563,
## LENGTHUNIT["metre",1]]],
## PRIMEM["Greenwich",0,
## ANGLEUNIT["degree",0.0174532925199433]],
## CS[ellipsoidal,2],
## AXIS["latitude",north,
## ORDER[1],
## ANGLEUNIT["degree",0.0174532925199433]],
## AXIS["longitude",east,
## ORDER[2],
## ANGLEUNIT["degree",0.0174532925199433]],
## ID["EPSG",4326]]
```

`st_crs(sids2_sf)`

```
## Coordinate Reference System:
## User input: WGS 84
## wkt:
## GEOGCRS["WGS 84",
## DATUM["World Geodetic System 1984",
## ELLIPSOID["WGS 84",6378137,298.257223563,
## LENGTHUNIT["metre",1]]],
## PRIMEM["Greenwich",0,
## ANGLEUNIT["degree",0.0174532925199433]],
## CS[ellipsoidal,2],
## AXIS["latitude",north,
## ORDER[1],
## ANGLEUNIT["degree",0.0174532925199433]],
## AXIS["longitude",east,
## ORDER[2],
## ANGLEUNIT["degree",0.0174532925199433]],
## ID["EPSG",4326]]
```

It looks as though the external files are assuming WGS84/NAD83 for the datum, but also contain the same geometries.

```
suppressWarnings(st_crs(sids_sf) <- st_crs(nc_sf))
xx <- st_equals(sids_sf, nc_sf, sparse=FALSE)
all(diag(xx)) && sum(xx) == 100L
```

`## [1] FALSE`

```
suppressWarnings(st_crs(sids2_sf) <- st_crs(nc_sf))
xx <- st_equals(sids2_sf, nc_sf, sparse=FALSE)
all(diag(xx)) && sum(xx) == 100L
```

`## [1] FALSE`

Now for the contents of the files - `sids2`

also contains
rates, while the file in `spData`

contains the coordinates as
given in Cressie (1991), and the parcels
of contiguous counties on p. 554, and the aggregations used for median
polishing.

`all.equal(as.data.frame(nc_sf)[,1:14], as.data.frame(sids_sf)[,1:14])`

```
## [1] "Names: 12 string mismatches"
## [2] "Component 4: Modes: numeric, character"
## [3] "Component 4: target is numeric, current is character"
## [4] "Component 5: 100 string mismatches"
## [5] "Component 6: Modes: character, numeric"
## [6] "Component 6: target is character, current is numeric"
## [7] "Component 7: Mean relative difference: 0.9986388"
## [8] "Component 8: Mean relative difference: 64.33901"
## [9] "Component 9: Mean relative difference: 0.9979786"
## [10] "Component 10: Mean relative difference: 156.5427"
## [11] "Component 11: Mean relative difference: 3.01968"
## [12] "Component 12: Mean relative difference: 0.9980208"
## [13] "Component 13: Mean relative difference: 160.8194"
## [14] "Component 14: Modes: numeric, list"
## [15] "Component 14: Attributes: < target is NULL, current is list >"
## [16] "Component 14: target is numeric, current is sfc_MULTIPOLYGON"
```

`all.equal(as.data.frame(nc_sf)[,1:14], as.data.frame(sids2_sf)[,1:14])`

```
## [1] "Names: 12 string mismatches"
## [2] "Component 4: Modes: numeric, character"
## [3] "Component 4: target is numeric, current is character"
## [4] "Component 5: 100 string mismatches"
## [5] "Component 6: Modes: character, numeric"
## [6] "Component 6: target is character, current is numeric"
## [7] "Component 7: Mean relative difference: 0.9986388"
## [8] "Component 8: Mean relative difference: 64.33901"
## [9] "Component 9: Mean relative difference: 0.9979786"
## [10] "Component 10: Mean relative difference: 156.5427"
## [11] "Component 11: Mean relative difference: 3.01968"
## [12] "Component 12: Mean relative difference: 0.9980208"
## [13] "Component 13: Mean relative difference: 160.8194"
## [14] "Component 14: Mean relative difference: 0.9984879"
```

The **spData** data set has some columns reordered and a
surprise:

`all.equal(as.data.frame(nc_sf)[,1:14], as.data.frame(nc)[,c(2,3,4,1,5:14)])`

`## [1] "Component \"NWBIR74\": Mean relative difference: 0.04891304"`

so a difference in `NWBIR74`

:

`which(!(nc_sf$NWBIR74 == nc$NWBIR74))`

`## [1] 21`

`c(nc$NWBIR74[21], nc_sf$NWBIR74[21])`

`## [1] 386 368`

where **spData** follows Cressie
(1991) and **sf** and Geoda follow Cressie and Chan (1989) for NWBIR74 in Chowan
county.

We will now examine the data set reproduced from Cressie and
collaborators, included in **spData** (formerly in
**spdep**), and add the neighbour relationships used in
Cressie and Chan (1989) to the background
map as a graph shown in Figure \(\ref{plot-CC89.nb}\):

```
gal_file <- system.file("weights/ncCR85.gal", package="spData")[1]
ncCR85 <- read.gal(gal_file, region.id=nc$FIPSNO)
ncCR85
```

```
## Neighbour list object:
## Number of regions: 100
## Number of nonzero links: 492
## Percentage nonzero weights: 4.92
## Average number of links: 4.92
```

```
gal_file <- system.file("weights/ncCC89.gal", package="spData")[1]
ncCC89 <- read.gal(gal_file, region.id=nc$FIPSNO)
ncCC89
```

```
## Neighbour list object:
## Number of regions: 100
## Number of nonzero links: 394
## Percentage nonzero weights: 3.94
## Average number of links: 3.94
## 2 regions with no links:
## 37055, 37095
## 3 disjoint connected subgraphs
```

```
plot(st_geometry(nc), border="grey")
plot(ncCC89, st_centroid(st_geometry(nc), of_largest_polygon), add=TRUE, col="blue")
```

Printing the neighbour object shows that it is a neighbour list
object, with a very sparse structure — if displayed as a matrix, only
3.94% of cells would be filled. Objects of class
`nb`

contain a list as long as the number of
counties; each component of the list is a vector with the index numbers
of the neighbours of the county in question, so that the neighbours of
the county with `region.id`

of
`37001`

can be retreived by matching against the
indices. More information can be obtained by using
`summary()`

on an `nb`

object. Finally, we associate a vector of names with the neighbour list,
through the `row.names`

argument. The names
should be unique, as with data frame row names.

```
r.id <- attr(ncCC89, "region.id")
ncCC89[[match("37001", r.id)]]
```

`## [1] 11 26 29 30 48`

`r.id[ncCC89[[match("37001", r.id)]]]`

`## [1] 37033 37081 37135 37063 37037`

The neighbour list object records neighbours by their order in
relation to the list itself, so the neighbours list for the county with
`region.id`

“37001” are the seventeenth,
nineteenth, thirty-second, forty-first and sixty-eighth in the list. We
can retreive their codes by looking them up in the
`region.id`

attribute.

`as.character(nc$NAME)[card(ncCC89) == 0]`

`## [1] "Dare" "Hyde"`

We should also note that this neighbour criterion generates two
counties with no neighbours, Dare and Hyde, whose county seats were more
than 30 miles from their nearest neighbours. The
`card()`

function returns the cardinality of the
neighbour set. We need to return to methods for handling no-neighbour
objects later on. We will also show how new neighbours lists may be
constructed in , and compare these with those from the literature.

Rather than review functions for measuring and modelling spatial
dependence in the **spdep** package, we will focus on
probability mapping for disease rates data. Typically, we have counts of
the incidence of some disease by spatial unit, associated with counts of
populations at risk. The task is then to try to establish whether any
spatial units seem to be characterised by higher or lower counts of
cases than might have been expected in general terms (Bailey and Gatrell 1995).

An early approach by Choynowski (1959),
described by Cressie and Read (1985) and
Bailey and Gatrell (1995), assumes, given
that the true rate for the spatial units is small, that as the
population at risk increases to infinity, the spatial unit case counts
are Poisson with mean value equal to the population at risk times the
rate for the study area as a whole. Choynowski’s approach folds the two
tails of the measured probabilities together, so that small values, for
a chosen \(\alpha\), occur for spatial
units with either unusually high or low rates. For this reason, the high
and low counties are plotted separately below. Note that
`cut`

returns a `factor`

labeled with cut
intervals.

```
ch <- choynowski(nc$SID74, nc$BIR74)
nc$ch_pmap_low <- ifelse(ch$type, ch$pmap, NA)
nc$ch_pmap_high <- ifelse(!ch$type, ch$pmap, NA)
prbs <- c(0,.001,.01,.05,.1,1)
nc$high = cut(nc$ch_pmap_high, prbs)
nc$low = cut(nc$ch_pmap_low,prbs )
```

```
is_tmap <- FALSE
if (require(tmap, quietly=TRUE)) is_tmap <- TRUE
is_tmap
```

`## [1] TRUE`

```
library(tmap)
tmap4 <- packageVersion("tmap") >= "3.99"
if (tmap4) {
tm_shape(nc) + tm_polygons(fill=c("low", "high"), fill.scale = tm_scale(values="brewer.set1"), fill.legend = tm_legend("p-values", frame=FALSE, item.r = 0), fill.free=FALSE, lwd=0.01) + tm_layout(panel.labels=c("low", "high"))
} else {
tm_shape(nc) + tm_fill(c("low", "high"), palette="Set1", title="p-values") +
tm_facets(free.scales=FALSE) + tm_layout(panel.labels=c("low", "high"))
}
```

For more complicated thematic maps, it may be helpful to use
ColorBrewer (https://colorbrewer2.org) colour palettes. Here we use
palettes accessed through **tmap**, available in R in the
**RColorBrewer** package.

While the `choynowski()`

function only
provides the probability map values required, the
`probmap()`

function returns raw (crude) rates,
expected counts (assuming a constant rate across the study area),
relative risks, and Poisson probability map values calculated using the
standard cumulative distribution function
`ppois()`

. This does not fold the tails
together, so that counties with lower observed counts than expected,
based on population size, have values in the lower tail, and those with
higher observed counts than expected have values in the upper tail, as
we can see.

```
pmap <- probmap(nc$SID74, nc$BIR74)
nc$pmap <- pmap$pmap
```

```
brks <- c(0,0.001,0.01,0.025,0.05,0.95,0.975,0.99,0.999,1)
if (tmap4) {
tm_shape(nc) + tm_polygons(fill="pmap", fill.scale = tm_scale(values="brewer.rd_bu", midpoint=0.5, breaks=brks), fill.legend = tm_legend(frame=FALSE, item.r = 0, position = tm_pos_out("right", "center")), lwd=0.01) + tm_layout(component.autoscale=FALSE)
} else {
tm_shape(nc) + tm_fill("pmap", breaks=brks, midpoint=0.5, palette="RdBu") + tm_layout(legend.outside=TRUE)
}
```

Marilia Carvalho (personal communication) and Virgilio Gómez Rubio (Gómez-Rubio, Ferrándiz-Ferragud, and López-Quílez 2005) have pointed to the unusual shape of the distribution of the Poisson probability values (histogram below), repeating the doubts about probability mapping voiced by Cressie (1991, 392): “an extreme value \(\ldots\) may be more due to its lack of fit to the Poisson model than to its deviation from the constant rate assumption”. There are many more high values than one would have expected, suggesting perhaps overdispersion, that is that the ratio of the variance and mean is larger than unity.

`hist(nc$pmap, main="")`