Help for package sabre

Version:

0.4.3

Title:

Spatial Association Between Regionalizations

Description:

Calculates a degree of spatial association between regionalizations or categorical maps using the information-theoretical V-measure (Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>). It also offers an R implementation of the MapCurve method (Hargrove et al. (2006) <doi:10.1007/s10109-006-0025-x>).

License:

MIT + file LICENSE

Encoding:

UTF-8

LazyData:

true

ByteCompile:

true

Suggests:

testthat, covr, knitr, rmarkdown, methods

RoxygenNote:

7.2.1

Depends:

R (≥ 3.3.0)

Imports:

dplyr, entropy, raster, rlang, sf, tibble, tidyr

Enhances:

stars, terra

VignetteBuilder:

knitr

URL:

https://jakubnowosad.com/sabre/

BugReports:

https://github.com/Nowosad/sabre/issues

NeedsCompilation:

Packaged:

2022-08-17 09:01:55 UTC; jn

Author:

Jakub Nowosad

[aut, cre], Tomasz Stepinski [aut], Space Informatics Lab [cph]

Maintainer:

Jakub Nowosad <nowosad.jakub@gmail.com>

Repository:

CRAN

Date/Publication:

2022-08-17 09:30:02 UTC

sabre: Spatial Association Between Regionalizations

Description

Calculates a degree of spatial association between regionalizations or categorical maps using the information-theoretical V-measure (Nowosad and Stepinski (2018) doi: 10.1080/13658816.2018.1511794). It also offers an R implementation of the MapCurve method (Hargrove et al. (2006) doi: 10.1007/s10109-006-0025-x).

Author(s)

Maintainer: Jakub Nowosad nowosad.jakub@gmail.com (ORCID)

Authors:

Tomasz Stepinski

Other contributors:

Space Informatics Lab [copyright holder]

Ecoregions of the United States

Description

Bailey's Ecoregions of the Conterminous United States

Usage

eco_us

Format

An object of class sf (inherits from data.frame) with 330 rows and 5 columns.

Source

https://www.sciencebase.gov/catalog/item/54244abde4b037b608f9e23d

Mapcurves

Description

Mapcurves: a quantitative method for comparing categorical maps.

Usage

mapcurves(x, y, z = NULL)

Arguments

x

A numeric vector, representing a categorical values.

y

A numeric vector, representing a categorical values.

z

A numeric matrix. The goodness of fit (GOF) value for each pair of classes in x and y. By default this argument is set to NULL, and the value of z is calculated based on x and y.

Value

A list with two elements:

"ref_map" - the map to be used as reference ("x" or "y")
"gof" - the Mapcurves's goodness of fit value

References

Hargrove, William W., Forrest M. Hoffman, and Paul F. Hessburg. "Mapcurves: a quantitative method for comparing categorical maps." Journal of Geographical Systems 8.2 (2006): 187.

Examples

set.seed(2018-03-21)
A = floor(matrix(runif(100, 0, 9), 10))
B = floor(matrix(runif(100, 0, 9), 10))
mapcurves(A, B)

Mapcurves calculation

Description

It calculates the Mapcurves's goodness-of-fit (GOF)

Usage

mapcurves_calc(x, y, x_name, y_name, precision = NULL)

## S3 method for class 'sf'
mapcurves_calc(x, y, x_name, y_name, precision = NULL)

## S3 method for class 'stars'
mapcurves_calc(x, y, x_name = NULL, y_name = NULL, precision = NULL)

## S3 method for class 'SpatRaster'
mapcurves_calc(x, y, x_name = NULL, y_name = NULL, precision = NULL)

## S3 method for class 'RasterLayer'
mapcurves_calc(x, y, x_name = NULL, y_name = NULL, precision = NULL)

Arguments

x

An object of class sf with a POLYGON or MULTIPOLYGON geometry type or a spatial raster object of class RasterLayer, SpatRaster, or stars.

y

An object of class sf with a POLYGON or MULTIPOLYGON geometry type or a spatial raster object of class RasterLayer, SpatRaster, or stars.

x_name

A name of the column with regions/clusters names.

y_name

A name of the column with regions/clusters names.

precision

numeric, or object of class units with distance units (but see details); see st_as_binary for how to do this.

Value

A list with four elements:

"map1" - the sf object containing the first map used for calculation of GOF
"map2" - the sf object containing the second map used for calculation of GOF
"ref_map" - the map used as a reference ("x" or "y")
"gof" - the Mapcurves's goodness of fit value

References

Hargrove, William W., Forrest M. Hoffman, and Paul F. Hessburg. "Mapcurves: a quantitative method for comparing categorical maps." Journal of Geographical Systems 8.2 (2006): 187.

Examples

library(sf)
data("regions1")
data("regions2")

mc = mapcurves_calc(x = regions1, y = regions2, x_name = z, y_name = z)
mc

plot(mc$map1)
plot(mc$map2)

library(raster)
data("partitions1")
data("partitions2")
mc2 = mapcurves_calc(x = partitions1, y = partitions2)
mc2

plot(mc2$map1)
plot(mc2$map2)

Red regionalization (raster version)

Description

Raster data of the red regionalization used in Figure 1 of Stepinski and Nowosad (2018)

Usage

partitions1

Format

An object of class RasterLayer of dimension 8 x 10 x 1.

References

Nowosad, Jakub, and Tomasz F. Stepinski. "Spatial association between regionalizations using the information-theoretical V-measure." International Journal of Geographical Information Science (2018). https://doi.org/10.1080/13658816.2018.1511794

Blue regionalization (raster version)

Description

Raster data of the blue regionalization used in Figure 1 of Stepinski and Nowosad (2018)

Usage

partitions2

Format

An object of class RasterLayer of dimension 8 x 10 x 1.

References

Red regionalization

Description

Data of the red regionalization used in Figure 1 of Stepinski and Nowosad (2018)

Usage

regions1

Format

An object of class sf (inherits from data.frame) with 4 rows and 2 columns.

References

Blue regionalization

Description

Data of the blue regionalization used in Figure 1 of Stepinski and Nowosad (2018)

Usage

regions2

Format

An object of class sf (inherits from data.frame) with 3 rows and 2 columns.

References

V-measure

Description

A conditional entropy-based external cluster evaluation measure.

Usage

vmeasure(x, y, z = NULL, B = 1)

Arguments

x

A numeric vector, representing a categorical values.

y

A numeric vector, representing a categorical values.

z

A numeric matrix. A contingency table of the counts at each combination of categorical levels. By default this argument is set to NULL, and the value of z is calculated based on x and y.

B

A numeric value. If B > 1 then completeness is weighted more strongly than homogeneity, and if B < 1 then homogeneity is weighted more strongly than completeness. By default this value is 1.

Value

A list with three elements:

"v_measure"
"homogeneity"
"completeness"

References

Rosenberg, Andrew, and Julia Hirschberg. "V-measure: A conditional entropy-based external cluster evaluation measure." Proceedings of the 2007 joint conference on empirical methods in natural language processing and computational natural language learning (EMNLP-CoNLL). 2007.

Examples

x = c(1, 1, 1, 2, 2, 3, 3, 3, 1, 1, 2, 2, 2, 3, 3)
y = c(rep(1, 5), rep(2, 5), rep(3, 5))
vmeasure(x, y)

V-measure calculation

Description

It calculates a degree of spatial association between regionalizations using an information-theoretical measure called the V-measure

Usage

vmeasure_calc(x, y, x_name, y_name, B = 1, precision = NULL)

## S3 method for class 'sf'
vmeasure_calc(x, y, x_name, y_name, B = 1, precision = NULL)

## S3 method for class 'stars'
vmeasure_calc(x, y, x_name = NULL, y_name = NULL, B = 1, precision = NULL)

## S3 method for class 'SpatRaster'
vmeasure_calc(x, y, x_name = NULL, y_name = NULL, B = 1, precision = NULL)

## S3 method for class 'RasterLayer'
vmeasure_calc(x, y, x_name = NULL, y_name = NULL, B = 1, precision = NULL)

Arguments

x

An object of class sf with a POLYGON or MULTIPOLYGON geometry type or a spatial raster object of class RasterLayer, SpatRaster, or stars.

y

An object of class sf with a POLYGON or MULTIPOLYGON geometry type or a spatial raster object of class RasterLayer, SpatRaster, or stars.

x_name

A name of the column with regions/clusters names.

y_name

A name of the column with regions/clusters names.

B

A numeric value. If B > 1 then completeness is weighted more strongly than homogeneity, and if B < 1 then homogeneity is weighted more strongly than completeness. By default this value is 1.

precision

numeric, or object of class units with distance units (but see details); see st_as_binary for how to do this.

Value

A list with five elements:

"map1" - the sf object containing the first preprocessed map used for calculation of GOF with two attributes - map1 (name of the category) and rih (region inhomogeneity)
"map2" - the sf object containing the second preprocessed map used for calculation of GOF with two attributes - map1 (name of the category) and rih (region inhomogeneity)
"v_measure"
"homogeneity"
"completeness"

References

Examples

library(sf)
data("regions1")
data("regions2")
vm = vmeasure_calc(x = regions1, y = regions2, x_name = z, y_name = z)
vm

plot(vm$map1["rih"])
plot(vm$map2["rih"])

library(raster)
data("partitions1")
data("partitions2")
vm2 = vmeasure_calc(x = partitions1, y = partitions2)
vm2

plot(vm2$map1[["rih"]])
plot(vm2$map2[["rih"]])

sabre: Spatial Association Between Regionalizations

Description

Author(s)

See Also

Ecoregions of the United States

Description

Usage

Format

Source

Mapcurves

Description

Usage

Arguments

Value

References

Examples

Mapcurves calculation

Description

Usage

Arguments

Value

References

Examples

Red regionalization (raster version)

Description

Usage

Format

References

Blue regionalization (raster version)

Description

Usage

Format

References

Red regionalization

Description

Usage

Format

References

Blue regionalization

Description

Usage

Format

References

V-measure

Description

Usage

Arguments

Value

References

Examples

V-measure calculation

Description

Usage

Arguments

Value

References

Examples