Title: Confidentiality of Spatial Point Data
Version: 1.0.4
Date: 2023-07-12
Depends: R (≥ 3.3.2), methods, stats, sp (≥ 2.0-0), dplyr,
Description: Provides an automatic aggregation tool to manage point data privacy, intended to be helpful for the production of official spatial data and for researchers. The package pursues the data accuracy at the smallest possible areas preventing individual information disclosure. The methodology, based on hierarchical geographic data structures performs aggregation and local suppression of point data to ensure privacy as described in Lagonigro, R., Oller, R., Martori J.C. (2017) <doi:10.2436/20.8080.02.55>. The data structures are created following the guidelines for grid datasets from the European Forum for Geography and Statistics.
License: MIT + file LICENSE
Suggests: sf, knitr, devtools, rmarkdown
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2023-07-13 08:54:54 UTC; raymond
Author: Raymond Lagonigro ORCID iD [aut, cre], Ramon Oller ORCID iD [aut], Joan Carles Martori ORCID iD [aut]
Maintainer: Raymond Lagonigro <raymond.lagonigro@uvic.cat>
Repository: CRAN
Date/Publication: 2023-07-19 08:50:06 UTC

AQuadtree: A package to anonymise spatial points data.

Description

This package provides an S4 class for creating, manipulating and exporting spatial quadtree varying size grids, and for methods including print/show, plot, spplot, subset, [, [[, names, dim, summary, write.

Introduction

The quadtree functions and class provide the tools to build a varying size quadtree grid performing a bottom-up aggregation considering a minimum threshold for each the cell. The main goal of the package is the anonymization of a set of spatial point data by an aggregation process as in a k-anonymity model. The grid created follows the INSPIRE Specification on Geographical Grid Systems.

Author(s)

Maintainer: Raymond Lagonigro raymond.lagonigro@uvic.cat (ORCID)

Authors:

References

D2.8.I.2 INSPIRE Specification on Geographical Grid Systems – Guidelines https://inspire.ec.europa.eu/documents/Data_Specifications/INSPIRE_Specification_GGS_v3.0.1.pdf

EEA reference grid dataset https://data.europa.eu/euodp/data/dataset/data_eea-reference-grids-2

Class "AQuadtree".

Description

An S4 class representing a Quadtree hierarchical geographic Grid to anonymise spatial point data.

Objects can be created by calls to the function AQuadtree

Wrapper function AQuadtree.

Usage

AQuadtree(
  points,
  dim = 1000,
  layers = 5,
  colnames = NULL,
  threshold = 100,
  thresholdField = NULL,
  funs = NULL,
  ineq.threshold = 0.25,
  loss.threshold = 0.4
)

Arguments

points

object of class "SpatialPoints" or "SpatialPointsDataFrame".

dim

a single integer specifying the initial cell sizes in meters, defaults to 1000.

layers

a single integer specifying the number of divisions of the initial cells, defaults to 5.

colnames

character string or character string vector specifying the columns to summarise in the resulting quadtree.

threshold

number. The threshold minimum value each cell must have in the column thresholdField.

thresholdField

character string specifying the column at which the threshold value will apply.

funs

character string or character string vector specifying the summary functions for each of the colnames. If vector, the size must be the same as colnames.

ineq.threshold

inequality threshold value to be considered on the disaggregation process. Forces disaggregation under the given inequality threshold.

loss.threshold

loss threshold value to be considered on the disaggregation process. Forces aggregation when there's much loss (i.e loss rate > ineq.threshold ).

Details

Given a set of points, the AQuadtree class represents a varying size Quadtree grid created performing a bottom-up aggregation considering a minimum threshold for each cell. Cells with a value under the threshold for the thresholdField are aggregated to the upper level in a quadtree manner.
When no thresholdField is given, total number of points in the cell will be used, and so, given a threshold of k, none of the cells in the resulting grid have a value less than k individuals as in a k-anonymity model.
The Quadtree produced balances information loss and accuracy. For instance, for the set of cells in the left image, where numbers in the cells represent the values in the thresholdField, using a threshold value of 100, the resulting Quadtree will be the one on the right. As we can see, some cells will be discarded, and some aggregated to maintain as much information as possible, keeping at the same time as much disaggregation as possible
62.5m2 cells resulting Quadtree
The INSPIRE coding system for cell identifiers will be used to generate a CellCode and CellNum for each cell in the Quadtree. The objective of the coding system is to generate unique identifiers for each cell, for any of the resolutions.
The cellCode is a text string, composed of cell size and cell coordinates. Cell codes start with a cell size prefix. The cell size is denoted in meter (m) for cell sizes below 1000 m and kilometre (km) for cell sizes from 1000 m and above.
Example: a 100 meter cell has an identifier starting with “100m”, the identifier of a 10000 meter cell starts with “10km”.
The coordinate part of the cell code reflects the distance of the lower left grid cell corner from the false origin of the CRS. In order to reduce the length of the string, Easting (E) and Northing (N) values are divided by 10^n (n is the number of zeros in the cell size value). Example for a cell size of 10000 meters: The number of zeros in the cell size value is 4. The resulting divider for Easting and Northing values is 10^4 = 10000.
The CellNum is a sequence of concatenated integers identifying all the hierarchical partitions of the main cell in which the point resides. For instance, the CellNum of the top right cell would be 416 (fourth in first partition, sixteenth in second partition)
The input object must be projected and units should be in 'meters' because the system uses the INSPIRE coding system.

function to create an object of class AQuadtree

Value

AQuadtree object representing a varying size Quadtree aggregation for the given points.

Slots

dim

= "numeric"

layers

= "numeric",

colnames

= "character",

threshold

= "numeric",

thresholdField

= "character",

loss

= "numeric"

See Also

Examples

data("BarcelonaPop", "BarcelonaCensusTracts")
aquadtree.Barcelona<-AQuadtree(BarcelonaPop, layers = 3)
plot(aquadtree.Barcelona)

aQuadtree.Charleston<-AQuadtree(CharlestonPop, colnames="sex", threshold=17,
  thresholdField=c("sex.male", "sex.female"))

## Not run: 
## spatial object not projected
sp.not.projected<-spTransform(CharlestonPop,CRS("+proj=longlat +datum=NAD27"))
is.projected(sp.not.projected)
aqt<-AQuadtree(sp.not.projected)

## not an SpatialPoints object
aqt<-AQuadtree(CharlestonCensusTracts)

## too many subdivisions
aqt<-AQuadtree(CharlestonPop, layers=15)


## End(Not run)

Census tract borders of Barcelona city in Catalonia.

Description

A SpatiaPolygons object containing the Census tract borders of Barcelona city in Catalonia.

Usage

BarcelonaCensusTracts

Format

A SpatialPolygons object

Radomly created population points for Barcelona city in Catalonia.

Description

A dataset containing randomly created population for the Barcelona city in Catalonia for the year 2018. Population has been created randomly with the real distributions of census tracts from the dataset dividing the total population by 20 (https://ajuntament.barcelona.cat/estadistica/catala/Estadistiques_per_temes/Poblacio_i_demografia/Poblacio/Padro_municipal_habitants/a2018/edat/index.htm).

Usage

BarcelonaPop

Format

A SpatialPointsDataFrame with 81359 rows and 2 attributes:

age

age the individual

sex

sex of the individual as a factor with levels: "man", "woman"

Census tract borders of Charleston, SC MSA, USA.

Description

A SpatiaPolygons object containing the Census tract borders of Charleston, SC MSA, USA.

Usage

CharlestonCensusTracts

Format

A SpatialPolygons object with 117 polygons

Radomly created population points for Charleston, SC MSA, USA.

Description

A dataset containing randomly created population for Charleston, SC MSA, USA. Population has been created randomly with distributions of census tracts from the dataset Charleston1, 2000 Census Tract Data for Charleston, SC MSA and counties

Usage

CharlestonPop

Format

A SpatialPointsDataFrame with 54619 rows and 3 attributes:

age

group age the individual as a factor with levels: "under16", "16_65", "over65"

sex

sex of the individual as a factor with levels: "male", "female"

origin

origin of the individual as a factor with levels: "asian", "black", "hisp", "multi_ra", "white"

See Also

https://spatial.uchicago.edu/sample-data

[<- AQuadtree-method

Description

Method [<-

Usage

## S4 replacement method for signature 'AQuadtree'
x[i, j, ...] <- value

Arguments

x

an object of class AQuadtree.

i, j

elements to extract or replace.

...

passed through.

value

value to set.

Details

An AQuadtree object cannot be assigned directly

Value

none

[ AQuadtree-method

Description

Method [

Usage

## S4 method for signature 'AQuadtree'
x[i, j, ..., drop = TRUE]

Arguments

x

an object of class AQuadtree.

i, j

elements to extract.

...

passed through.

drop

passed on to [ indexing operator.

Details

Extract a part of a AQuadtree object

Value

An AQuadtree object with the selected subset of rows or columns from the input object.

area.QT AQuadtree-method

Description

Method area.QT

Usage

area.QT(obj, residual = TRUE, ...)

## S4 method for signature 'AQuadtree'
area.QT(obj, residual = FALSE, ...)

Arguments

obj

an object of class AQuadtree.

residual

logical; if TRUE cells marked as residual cells are included

...

passed through.

Details

Get the areas of the Quadtree grid cells in square meters

Value

area of Quadtree grid cells in square meters

Create a Quadtree grid to anonymise spatial point data

Description

createAQuadtree returns a SpatialPointsDataFrame representing a Quadtree hierarchical geographic dataset. The resulting grid contains varying size cells depending on a given threshold and column. with identifiers A cellCode and cellNum is created for each cell as in INSPIRE Specification on Geographical Grid Systems.

Usage

createAQuadtree(
  points,
  dim = 1000,
  layers = 5,
  colnames = NULL,
  threshold = 100,
  thresholdField = NULL,
  funs = NULL,
  as = "Spatial",
  ineq.threshold = 0.25,
  loss.threshold = 0.4
)

Arguments

points

object of class "SpatialPoints" or "SpatialPointsDataFrame".

dim

a single integer specifying the initial cell sizes in meters, defaults to 1000.

layers

a single integer specifying the number of divisions of the initial cells, defaults to 5.

colnames

character or character vector specifying the columns to summarise in the resulting quadtree. For columns of class factor, a column for each factor level cill be created.

threshold

number. The threshold minimum value each cell must have in the column thresholdField.

thresholdField

character or character vector specifying the columns to which the threshold value will apply. If not specified, threshold value will be applied over the total cell points number. ThresholdField must be one of the colnames.

funs

character or character vector specifying the summary functions for each of the colnames. If vector, the size must be the same as colnames.

as

character indicating return type, if "AQuadtree" a quadtree class element will be returned, otherwise a SpatialPolygonsDataFrame will ber returned. Defaults to "Spatial".

ineq.threshold

inequality threshold value to be considered on the disaggregation process. Forces disaggregation under the given inequality threshold.

loss.threshold

loss threshold value to be considered on the disaggregation process. Stops disaggregation when there's much loss (i.e loss rate > ineq.threshold ).

Details

Given a set of points a varying size Quadtree grid is created performing a bottom-up aggregation considering a minimum threshold for each cell. Cells with a value under the threshold for the thresholdField are aggregated to the upper level in a quadtree manner.
When no thresholdField is given, total number of points in the cell will be used, and so, given a threshold of k, none of the cells in the resulting grid have a value less than k individuals as in a k-anonymity model.
The Quadtree produced balances information loss and accuracy. For instance, for the set of cells in the left image, where numbers in the cells represent the values in the thresholdField, using a threshold value of 100, the resulting Quadtree will be the one on the right. As we can see, some cells will be discarded, and some aggregated to maintain as much information as possible, keeping at the same time as much disaggregation as possible
62.5m2 cells resulting Quadtree
The INSPIRE coding system for cell identifiers will be used to generate a cellCode and cellNum for each cell in the Quadtree. The objective of the coding system is to generate unique identifiers for each cell, for any of the resolutions.
The cellCode is a text string, composed of cell size and cell coordinates. Cell codes start with a cell size prefix. The cell size is denoted in meter (m) for cell sizes below 1000 m and kilometre (km) for cell sizes from 1000 m and above.
Examples: a 100 meter cell has an identifier starting with “100m”, the identifier of a 10000 meter cell starts with “10km”.
The coordinate part of the cell code reflects the distance of the lower left grid cell corner from the false origin of the CRS. In order to reduce the length of the string, Easting (E) and Northing (N) values are divided by 10^n (n is the number of zeros in the cell size value). Example for a cell size of 10000 meters: The number of zeros in the cell size value is 4. The resulting divider for Easting and Northing values is 10^4 = 10000.
The cellNum is a sequence of concatenated integers identifying all the hierarchical partitions of the main cell in which the point resides. For instance, the cellNum of the top right cell would be 416 (fourth in first partition, sixteenth in second partition)
The input object must be projected and units should be in 'meters' because the system uses the INSPIRE coding system.

Value

SpatialPolygonsDataFrame representing a varying size Quadtree aggregation for the given points.

See Also

Examples

data("CharlestonPop")
aQuadtree.Charleston<-createAQuadtree(CharlestonPop, threshold=10,
  colnames="sex", thresholdField=c("sex.male", "sex.female"))

Create a Grid grid covering a given geographic zone.

Description

createGrid returns a SpatialPolygons object representing a grid covering a given geographic zone following the INSPIRE Specification on Geographical Grid Systems. Each polygon will be identified with it's CellCode code.

Usage

createGrid(zone, dim = 1000, intersect = TRUE, outline = FALSE)

Arguments

zone

object of class "SpatialPoints", "SpatialPointsDataFrame", "SpatialPolygons" or "SpatialPolygonsDataFrame" specifying the zone to be covered by the grid.

dim

a single integer specifying the initial cell sizes in meters, defaults to 1000.

intersect

logical, if TRUE the resulting grid will be intersected with the given zone. If zone is of class SpatialPoints, only cells containing points will be kept on the resulting grid. If zone is of class SpatialPolygons, only cells inside or partially inside polygons in zone will be kept on the resulting grid. Defaults to TRUE

outline

logical, if TRUE the resulting grid will be clipped with the outlines of the given zone. Only applicable if zone is of class SpatialPolygons. Defaults to FALSE

Details

INSPIRE Specification on Geographical Grid Systems
The objective of the coding system is to generate unique identifiers for each point, for any of the recommended resolutions.
The cellCode is a text string, composed of cell size and cell coordinates. Cell codes start with the cell's size prefix. The cell size is denoted in meter (m) for cell sizes below 1000m and kilometre (km) for cell sizes from 1000m and above.
Examples: a 100 meter cell has an identifier starting with “100m”, the identifier of a 10000 meter cell starts with “10km”.
The coordinate part of the cell code reflects the distance of the lower left grid cell corner from the false origin of the CRS. In order to reduce the length of the string, Easting (E) and Northing (N) values are divided by 10^n (n is the number of zeros in the cell size value). Example for a cell size of 10000 meters: The number of zeros in the cell size value is 4. The resulting divider for Easting and Northing values is 10^4 = 10000.

Value

SpatialPolygons dataset representing a grid with squared cells of the given size.

See Also

Examples


data("BarcelonaPop")
BarcelonaPop.INSPIRE_GRID<-createGrid(BarcelonaPop)
plot(BarcelonaPop.INSPIRE_GRID)

## Not run: 
BarcelonaPop.INSPIRE_GRID.10km<-createGrid(BarcelonaPop, 10000, intersect=FALSE)
plot(BarcelonaPop.INSPIRE_GRID.10km)

data("BarcelonaCensusTracts")
Barcelona.INSPIRE_GRID<-createGrid(BarcelonaCensusTracts, outline=TRUE)
plot(Barcelona.INSPIRE_GRID)

## End(Not run)

Join two AQuadtree objects from the same area, to compare their data

Description

Given two objects of class AQuadtree for the same area, wich, for instance, may contain data from two different periods, joinAQuadtrees returns a new object of class AQuadtree with the common zones at the lowest shared level, summarising the data from both AQuadtrees.

Usage

joinAQuadtrees(qt1, qt2, withResiduals = FALSE, mean.1 = NULL, mean.2 = NULL)

Arguments

qt1

object of class "AQuadtree" containing the first object to join.

qt2

object of class "AQuadtree" containing the second object to join.

withResiduals

logical indicating if residual cells should be maintained (TRUE) or not (FALSE, default).

mean.1

character or character vector specifying the columns in the first AQuadtreeto which a weighted mean should be computed. By default the aggregation function used is sum.

mean.2

character or character vector specifying the columns in the first AQuadtreeto which a weighted mean should be computed. By default the aggregation function used is sum.

Details

The function joinAQuadtrees creates a new AQuadtree object from two given AQuadtree objects with data from the same area. The data of the two given objects is summarised at the smallest possible cells shared by both given objects. All the input data is maintained on the new created object. This function can be used to join the different attributes from the same area or information from different periods.

Value

AQuadtree with the information of the two given objects summarised at the lowest level shared by both objects.

Examples

data("CharlestonPop")
CharlestonPop.AQT_1<-AQuadtree(CharlestonPop, layers = 2)
CharlestonPop.AQT_2<-AQuadtree(CharlestonPop, colnames="sex",
       thresholdField=c("sex.male", "sex.female"), layers = 2)
CharlestonPop.AQT_1_2<-joinAQuadtrees(CharlestonPop.AQT_1, CharlestonPop.AQT_2)

## Not run: 
## non AQuadtree objects
joinAQuadtrees(CharlestonPop, CharlestonCensusTracts)

## End(Not run)

Merge an AQuadtree object with a data.frame

Description

Method merge.

Usage

## S4 method for signature 'AQuadtree,data.frame'
merge(x, y)

Arguments

x

an object of class AQuadtree.

y

an object of class data.frame

Details

Merges the AQuadtree object data with the data.frame on the columns "cellCode" and cellNum"

Value

An AQuadtree object where the data is extended with the input data.frame

plot AQuadtree-method

Description

Method plot

Usage

## S4 method for signature 'AQuadtree,missing'
plot(x, ..., residual = TRUE, add = FALSE, col)

Arguments

x

an object of class AQuadtree.

...

passed through.

residual

logical; if TRUE cells marked as residual cells are included

add

logical. TRUE to add plot to the current existing plot

col

default plotting color

Details

Plot an object of class AQuadtree.

Value

none

Add SpatialPoints to an AQuadtree obtject.

Description

Given an object of class AQuadtree and an object of class SpatialPoints or SpatialPointsDataFrame for the same area, pointsToAQuadtree returns a new object of class AQuadtree aggregating the data from the points to the cells where each point fall.

Usage

pointsToAQuadtree(qt, points)

Arguments

qt

object of class "AQuadtree".

points

object of class "SpatialPoints" or "SpatialPointsDataFrame".

Details

The function pointsToAQuadtree returns a new AQuadtree object with the input set of points aggregated to the input AQuadtree object. The function creates a “p.total” attribute to compute the total number of points aggregated to each cell of the input AQuadtree. If points is an object of class SpatialPointsDataFrame, the function summarises numeric attributes in the dataframe using the mean function, and deploys factor attributes creating a new attribute for each label of the factor to calculate the count. The attributes added to the resulting AQuadtree object are prefixed with “p.”.

Value

AQuadtree with the information of the given set of points aggregated at each corresponding cell of the given AQuadtree.

Examples

data("BarcelonaPop")
Barcelona.QT<-AQuadtree(BarcelonaPop)
BcnWomen75yPop<-BarcelonaPop[BarcelonaPop$sex=='woman' & BarcelonaPop$age>=75, 'age']
Barcelona.extended.QT<-pointsToAQuadtree(Barcelona.QT, BcnWomen75yPop)

## Not run: 
## not an AQuadtree object
pointsToAQuadtree(CharlestonCensusTracts, CharlestonPop)

## spatial object not projected
sp.not.projected<-spTransform(CharlestonPop,CRS("+proj=longlat +datum=NAD27"))
is.projected(sp.not.projected)
pointsToAQuadtree(AQuadtree(CharlestonPop), sp.not.projected)


## End(Not run)

print AQuadtree-method

Description

Method print.

Usage

## S4 method for signature 'AQuadtree'
print(x, ...)

Arguments

x

an object of class AQuadtree.

...

passed through.

Details

Prints the AQuadtree object

Value

none

show AQuadtree-method

Description

Method show.

Usage

## S4 method for signature 'AQuadtree'
show(object)

Arguments

object

an object of class AQuadtree.

Details

Display the AQuadtree object

Value

A data.frame showing the information attributes contained in the AQuadtree object.

Add cell identifiers to SpatialPoints as in INSPIRE Specification

Description

spatialPointsCellCodes returns a SpatialPointsDataFrame with identifiers (CellCode and CellNum) for each point as in INSPIRE Specification on Geographical Grid Systems.

Usage

spatialPointsCellCodes(points, dim = 1000, layers = 1)

Arguments

points

object of class "SpatialPoints" or "SpatialPointsDataFrame".

dim

a single integer specifying the initial cell sizes, defaults to 1km.

layers

a single integer specifying the number of divisions of the initial cells, defaults to 1.

Details

INSPIRE coding system for point identifiers
The objective of the coding system is to generate unique identifiers for each point, for any of the recommended resolutions.
The cellCode is a text string, composed of cell size and cell coordinates. Cell codes start with a cell size prefix. The cell size is denoted in meter (m) for cell sizes below 1000 m and kilometre (km) for cell sizes from 1000 m and above.
Examples: a 100 meter cell has an identifier starting with “100m”, the identifier of a 10000 meter cell starts with “10km”.
The coordinate part of the cell code reflects the distance of the lower left grid cell corner from the false origin of the CRS. In order to reduce the length of the string, Easting (E) and Northing (N) values are divided by 10n (n is the number of zeros in the cell size value). Example for a cell size of 10000 meters: The number of zeros in the cell size value is 4. The resulting divider for Easting and Northing values is 104 = 10000.
The cellNum is a sequence of concatenated integers identifying all the hierarchical partitions of the main cell in which the point resides. For instance, the cellNum of the top right cell would be 416 (fourth in first partition, sixteenth in second partition)
Hyerarchical CellNums The input object must be projected and units should be in 'meters' because the system uses the INSPIRE coding system.

Value

A "SpatialPointsDataFrame" containing all the points given. For each point a cellCode and cellNum identify the cell to which the point belongs.
CellCode is a text string, composed of cell size and cell coordinates. Cell codes start with a cell size prefix. The cell size is denoted in meter (m) for cell sizes below 1000 m and kilometer (km) for cell sizes from 1000 m and above.
The cellNum is a sequence identifying the different partitions of the main cell in which the point resides.

See Also

Examples

data("BarcelonaPop")
BarcelonaPop.IDs<-spatialPointsCellCodes(BarcelonaPop)
BarcelonaPop.IDs.10km<-spatialPointsCellCodes(BarcelonaPop, 10000, 3)

## Not run: 
## spatial object not projected
sp.not.projected<-spTransform(CharlestonPop,CRS("+proj=longlat +datum=NAD27"))
is.projected(sp.not.projected)
spatialPointsCellCodes(sp.not.projected)

## End(Not run)

Split CellNum sequence into a vector

Description

createQuadtree returns a vector decomposing the given CellNum into the sequence of the different cell numbers for each level.

Usage

splitCellNum(x)

Arguments

x

a character or character vector containing a sequence of cell numbers or an R object with a field named 'cellNum'

Details

CellNum is an integer with the concatenated sequence of hierarchical cell positions inside a main cell. splitCellNum splits that sequence into a vector. For instance, the CellNum of the top right cell would be 416 (fourth in first partition, sixteenth in second partition)
Hyerarchical CellNums

Value

integer vector or list of integer vectors with the sequence CellNums splitted

See Also

Examples

data("CharlestonPop")
CharlestonPop.IDs<-spatialPointsCellCodes(CharlestonPop, layers=2)
splitCellNum(CharlestonPop.IDs)

spplot AQuadtree-method

Description

Method spplot

Usage

## S4 method for signature 'AQuadtree'
spplot(obj, zcol = NULL, by.density = TRUE, residual = TRUE, ...)

Arguments

obj

an object of class AQuadtree.

zcol

character; attribute name(s) or column number(s) in attribute table

by.density

logical; if TRUE cell values specified in zcol are divided by cell areas

residual

logical; if TRUE cells marked as residual cells are included

...

passed through.

Details

Plots a AQuadtree object as a spatial object with its data

Value

Creates a lattice plot of class "trellis" created with the spplot method in the sp package

summary AQuadtree-method

Description

Method summary.

Usage

## S4 method for signature 'AQuadtree'
summary(object, ...)

Arguments

object

an object of class AQuadtree.

...

passed through.

Details

summarize information of an object of class AQuadtree

Value

An object of class "table" with summarising information in the AQuadtree input object

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