geomerge: Geospatial Data Integration
In css-konstanz/geomerge: Geospatial Data Integration
geomerge R Documentation
Geospatial Data Integration
Description
This function conducts a series of spatial joins for Geographic Information Systems (GIS) data. It integrates three of R's most commonly used GIS data classes - polygons, points and rasters. With flexible options for assignment rules and including the calculation of spatial and temporal lags, geomerge returns a spatial (panel) dataset in the form of a SpatialPolygonsDataFrame that users may import into any predictive statistical analysis.
Usage
geomerge(...,target=NULL,time=NA,time.lag=TRUE,spat.lag=TRUE,
zonal.fun=sum, assignment="max(area)",population.data = NA,
point.agg = "cnt",t_unit="days",silent=FALSE)
Arguments
...
input datasets and, if provided, optional arguments. See Details.
target
SpatialPolygonsDataFrame representing desired units of analysis. See Details.
time
temporal window for dynamic temporal binning of point data. Required format is c(start_date, end_date, interval_length), each specified as String. Default = NA. See Details.
time.lag
Boolean indicating whether or not first and second order temporal lag values of all variables are returned. Only affects dynamic point data integration. Default = TRUE.
spat.lag
Boolean indicating whether or not first and second order spatial lag values of all variables are returned. Default = TRUE.
zonal.fun
object of class function applied to values of RasterLayer when generating zonal statistics for each target polygon. Default = sum. See Details.
assignment
identification of either population- or area-weighting assignment rules when handling SpatialPolygonsDataFrame joins to target. Default = "max(area)". See Details.
population.data
specifies data used for weighting if a population-based assignment rule is selected. See Details.
point.agg
specification of aggregation format for data of type SpatialPointsDataFrame. Default = "cnt". See Details.
t_unit
temporal unit used for dynamic point aggregation. Default = "days".
silent
Boolean switch to suppress any (non-critical) warnings and messages. Default = FALSE.
Details
geomerge accepts any number of data inputs of the most common spatial data classes in R - SpatialPolygonsDataFrame, SpatialPointsDataFrame, and RasterLayer. The target they are merged to may be of any shape but must be a SpatialPolygonsDataFrame. The extent of each data input should at least match the extent of the target; if not, the package returns a warning. In order to perform accurate area calculations at any scale, geomerge projects any data geometry into WGS84. Input data (including target) not in WGS84 are automatically re-projected.
geomerge assumes that all inputs of type SpatialPolygonsDataFrame and RasterLayer are static and contemporary. If polygons or raster are changing, we advise to simply rerun geomerge for each interval in which data are static and contemporary. The package allows for dynamic integration of all inputs that are a SpatialPointsDataFrame, i.e., one can, for example, automatically generate the counts of events that occur within a specific unit of target within a specific time period. Further details are given below.
If SpatialPolygonsDataFrame data are joined to target, they must contain only one column with the data of interest. The package also accepts the short-hand variable specification using the standard "$" notation to denote the selection of a specific variable from the SpatialPolygonsDataFrame. RasterLayer are by default single-valued. These data may be of class factor or numeric.
If SpatialPointsDataFrame are joined to target they must have one column coding the variable of interest and, if points carry timestamps, dates must be given in a second column timestamp and formatted as a UTC date string with format "YYYY-MM-DD" or "YYYY-MM-DD hh:mm:ss".
In practice, our input logic implies that if more than one variable of interest are to be merged to target, statically or dynamically, each has to be separately entered as argument. Note that variable names in target derive from the name of the input data and it is therefore advised to use meaningful labels for input data.
In merging SpatialPolygonsDataFrame values to units of analysis given by target, users have a choice among a number of different assignment rules based on area overlap and population size. Area-based assignment generally can take the values "max(area)" or "min(area)", i.e., the value assigned to a given unit in target comes from that polygon in the SpatialPolygonsDataFrame with maximal or minimal area overlap respectively. If the value of interest is of class numeric, the user may also choose "weighted(area)", i.e., the values is assigned as the area-weighted average of the values in all polygons intersecting a given unit in target.
The assignment rules "max(pop)", "min(pop)" and "weighted(pop)" (the latter again for numeric variables only) analogously use the population value given by population.data in overlapping areas as basis for assignment. If any of them is selected in the assignment argument, users must provide population.data as a RasterLayer. The geographical resolution of population.data should be the same or better than that of target. The zonal statistic used for population within overlapping polygons is sum.
When a SpatialPointsDataFrame is merged to target, one of two operations can be performed. For point.agg = "cnt" the function calculates the sum of the number of locations that fall within each unit of target. For numerical variables of interest, point.agg = "sum" returns the sum across for all values associated with points within each unit of target. If different aggregation formats are to be applied to different SpatialPointsDataFrame inputs, these have to be specified as a character vector, i.e., point.agg = c("sum", "cnt"), in the order of inputs.
Values for inputs of type SpatialPointsDataFrame are either calculated statically across the entire frame if time = NA or dynamically within a given time period that can be specified using time = c(start_date, end_date, interval_length). All three inputs must be Strings where interval_length is defined in multiples of t_unit. The default value is t_unit = "days", the package also accepts inputs of "secs", "mins", "hours", "months" or "years".
Zonal statistics are applied to objects of class RasterLayer that are joined to target. The specific operations are defined in the function call using the argument zonal.fun and each is added into the result. Any zonal statistics compatible with the extract function in raster is accepted. Note that geomerge does not accept raster stacks. If you have raster stacks they must be separated and the layers integrated separately into the function.
If spat.lag = TRUE spatial lags of all numeric variables from a SpatialPolygonsDataFrame or RasterLayer joined to target polygons are returned using first and also second order neighboring weights matrices. The package assigns target polygons the mean value of units within each neighborhood. When dynamic point aggregation is run and time.lag = TRUE, geomerge returns the values of every target polygon, as well as its first and second order neighboring unit averages, separately, at time t-1 and t-2 defined by interval in the argument time.
Value
Returns an object of class "geomerge".
The functions summary, print, plot overload the standard outputs for objects of type geomerge providing summary information and and visualizations specific to the output object. An object of class "geomerge" is a list containing the following three components:
data
SpatialPolygonsDataFrame that contains all information merged with the target layer. Column names are assigned the name of the input data object separated by "." from a short description of the calculation, as well as modifiers such as ".1st" and ".2nd" for first- and second-order neighborhoods of target. In the case of dynamic point data aggregation, ".t_1" and ".t_2" are used to label first- and second-order temporal lags. For example, if geomerge is told to use a SpatialPointsDataFrame called "vio" to count incidents of conflict contained within units of target, the default output would include columns named "vio.cnt", "vio.cnt.t_1", "vio.cnt.t_2", "vio.cnt.1st", "vio.cnt.1st.t_1", "vio.cnt.1st.t_2", "vio.cnt.2nd", "vio.cnt.2nd.t_1", "vio.cnt.2nd.t_2".
inputData
List containing the spatial objects used as input.
parameters
List containing information on all input parameters used during integration.
Note
geomerge exclusively merges data using the global WGS84 coordinate reference system (CRS) to ensure that areal statistics are accurate at all scales. If data are entered that are using a different and/or projected CRS, the tool automatically first transforms the data. This on-the-fly transformation, however, may be very slow and it is advised to always enter inputs in WGS84.
Author(s)
Karsten Donnay and Andrew M. Linke.
References
Andrew M. Linke, Karsten Donnay. (2017). "Scale Variability Misclassification: The Impact of Spatial Resolution on Effect Estimates in the Geographic Analysis of Foreign Aid and Conflict." Paper presented at the International Studies Association Annual Meeting, February 22-25 2017, Baltimore.
See Also
geomerge-package, print.geomerge, plot.geomerge, summary.geomerge, generateGrid
Examples
require(rgdal)
data(geomerge)
# 1) Simple static integration of polygon data
output <- geomerge(geoEPR,target=states,silent=TRUE)
summary (output)
# 2) Static integration for point, polygon, raster data
output <- geomerge(ACLED$EVENT_TYPE,AidData$project_id,geoEPR,
gpw,na.rm=TRUE,target=states)
summary(output)
plot(output)
# 3) Dynamic point data integration for numeric variables
output <- geomerge(ACLED$FATALITIES,AidData$commitme_1,geoEPR,
target=states,time=c("2011-01-01", "2011-12-31","1"),
t_unit='months',point.agg='sum')
summary(output)
plot(output)
# 4) Population weighted assignment
output <- geomerge(geoEPR,target=states,assignment='max(pop)',
population.data = gpw)
summary(output)
plot(output)
css-konstanz/geomerge documentation built on Nov. 26, 2022, 12:24 p.m.
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| geomerge | R Documentation |
Geospatial Data Integration
Description
This function conducts a series of spatial joins for Geographic Information Systems (GIS) data. It integrates three of R's most commonly used GIS data classes - polygons, points and rasters. With flexible options for assignment rules and including the calculation of spatial and temporal lags, geomerge returns a spatial (panel) dataset in the form of a SpatialPolygonsDataFrame that users may import into any predictive statistical analysis.
Usage
geomerge(...,target=NULL,time=NA,time.lag=TRUE,spat.lag=TRUE,
zonal.fun=sum, assignment="max(area)",population.data = NA,
point.agg = "cnt",t_unit="days",silent=FALSE)
Arguments
... |
input datasets and, if provided, optional arguments. See Details. |
target |
|
time |
temporal window for dynamic temporal binning of point data. Required format is |
time.lag |
Boolean indicating whether or not first and second order temporal lag values of all variables are returned. Only affects dynamic point data integration. Default = TRUE. |
spat.lag |
Boolean indicating whether or not first and second order spatial lag values of all variables are returned. Default = TRUE. |
zonal.fun |
object of class function applied to values of |
assignment |
identification of either population- or area-weighting assignment rules when handling |
population.data |
specifies data used for weighting if a population-based |
point.agg |
specification of aggregation format for data of type |
t_unit |
temporal unit used for dynamic point aggregation. Default = "days". |
silent |
Boolean switch to suppress any (non-critical) warnings and messages. Default = FALSE. |
Details
geomerge accepts any number of data inputs of the most common spatial data classes in R - SpatialPolygonsDataFrame, SpatialPointsDataFrame, and RasterLayer. The target they are merged to may be of any shape but must be a SpatialPolygonsDataFrame. The extent of each data input should at least match the extent of the target; if not, the package returns a warning. In order to perform accurate area calculations at any scale, geomerge projects any data geometry into WGS84. Input data (including target) not in WGS84 are automatically re-projected.
geomerge assumes that all inputs of type SpatialPolygonsDataFrame and RasterLayer are static and contemporary. If polygons or raster are changing, we advise to simply rerun geomerge for each interval in which data are static and contemporary. The package allows for dynamic integration of all inputs that are a SpatialPointsDataFrame, i.e., one can, for example, automatically generate the counts of events that occur within a specific unit of target within a specific time period. Further details are given below.
If SpatialPolygonsDataFrame data are joined to target, they must contain only one column with the data of interest. The package also accepts the short-hand variable specification using the standard "$" notation to denote the selection of a specific variable from the SpatialPolygonsDataFrame. RasterLayer are by default single-valued. These data may be of class factor or numeric.
If SpatialPointsDataFrame are joined to target they must have one column coding the variable of interest and, if points carry timestamps, dates must be given in a second column timestamp and formatted as a UTC date string with format "YYYY-MM-DD" or "YYYY-MM-DD hh:mm:ss".
In practice, our input logic implies that if more than one variable of interest are to be merged to target, statically or dynamically, each has to be separately entered as argument. Note that variable names in target derive from the name of the input data and it is therefore advised to use meaningful labels for input data.
In merging SpatialPolygonsDataFrame values to units of analysis given by target, users have a choice among a number of different assignment rules based on area overlap and population size. Area-based assignment generally can take the values "max(area)" or "min(area)", i.e., the value assigned to a given unit in target comes from that polygon in the SpatialPolygonsDataFrame with maximal or minimal area overlap respectively. If the value of interest is of class numeric, the user may also choose "weighted(area)", i.e., the values is assigned as the area-weighted average of the values in all polygons intersecting a given unit in target.
The assignment rules "max(pop)", "min(pop)" and "weighted(pop)" (the latter again for numeric variables only) analogously use the population value given by population.data in overlapping areas as basis for assignment. If any of them is selected in the assignment argument, users must provide population.data as a RasterLayer. The geographical resolution of population.data should be the same or better than that of target. The zonal statistic used for population within overlapping polygons is sum.
When a SpatialPointsDataFrame is merged to target, one of two operations can be performed. For point.agg = "cnt" the function calculates the sum of the number of locations that fall within each unit of target. For numerical variables of interest, point.agg = "sum" returns the sum across for all values associated with points within each unit of target. If different aggregation formats are to be applied to different SpatialPointsDataFrame inputs, these have to be specified as a character vector, i.e., point.agg = c("sum", "cnt"), in the order of inputs.
Values for inputs of type SpatialPointsDataFrame are either calculated statically across the entire frame if time = NA or dynamically within a given time period that can be specified using time = c(start_date, end_date, interval_length). All three inputs must be Strings where interval_length is defined in multiples of t_unit. The default value is t_unit = "days", the package also accepts inputs of "secs", "mins", "hours", "months" or "years".
Zonal statistics are applied to objects of class RasterLayer that are joined to target. The specific operations are defined in the function call using the argument zonal.fun and each is added into the result. Any zonal statistics compatible with the extract function in raster is accepted. Note that geomerge does not accept raster stacks. If you have raster stacks they must be separated and the layers integrated separately into the function.
If spat.lag = TRUE spatial lags of all numeric variables from a SpatialPolygonsDataFrame or RasterLayer joined to target polygons are returned using first and also second order neighboring weights matrices. The package assigns target polygons the mean value of units within each neighborhood. When dynamic point aggregation is run and time.lag = TRUE, geomerge returns the values of every target polygon, as well as its first and second order neighboring unit averages, separately, at time t-1 and t-2 defined by interval in the argument time.
Value
Returns an object of class "geomerge".
The functions summary, print, plot overload the standard outputs for objects of type geomerge providing summary information and and visualizations specific to the output object. An object of class "geomerge" is a list containing the following three components:
data |
|
inputData |
List containing the spatial objects used as input. |
parameters |
List containing information on all input parameters used during integration. |
Note
geomerge exclusively merges data using the global WGS84 coordinate reference system (CRS) to ensure that areal statistics are accurate at all scales. If data are entered that are using a different and/or projected CRS, the tool automatically first transforms the data. This on-the-fly transformation, however, may be very slow and it is advised to always enter inputs in WGS84.
Author(s)
Karsten Donnay and Andrew M. Linke.
References
Andrew M. Linke, Karsten Donnay. (2017). "Scale Variability Misclassification: The Impact of Spatial Resolution on Effect Estimates in the Geographic Analysis of Foreign Aid and Conflict." Paper presented at the International Studies Association Annual Meeting, February 22-25 2017, Baltimore.
See Also
geomerge-package, print.geomerge, plot.geomerge, summary.geomerge, generateGrid
Examples
require(rgdal)
data(geomerge)
# 1) Simple static integration of polygon data
output <- geomerge(geoEPR,target=states,silent=TRUE)
summary (output)
# 2) Static integration for point, polygon, raster data
output <- geomerge(ACLED$EVENT_TYPE,AidData$project_id,geoEPR,
gpw,na.rm=TRUE,target=states)
summary(output)
plot(output)
# 3) Dynamic point data integration for numeric variables
output <- geomerge(ACLED$FATALITIES,AidData$commitme_1,geoEPR,
target=states,time=c("2011-01-01", "2011-12-31","1"),
t_unit='months',point.agg='sum')
summary(output)
plot(output)
# 4) Population weighted assignment
output <- geomerge(geoEPR,target=states,assignment='max(pop)',
population.data = gpw)
summary(output)
plot(output)
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