Spnaf: An R package for analyzing and mapping the hotspots of flow datasets

Abstract

This paper introduces {spnaf} (spatial network autocorrelation for flows), an R package designed for the hotspot analysis of flow (e.g., human mobility, transportation, and animal movement) datasets based on Berglund and Karlström’s G index. We demonstrate the utility of the {spnaf} package through two example analyses by data forms: 1) bike-sharing trip patterns in Columbus, Ohio, USA, using polygon data, and 2) U.S. airports’ passenger travel patterns, using point data. The {spnaf} is available for download from the Comprehensive R Archive Network (CRAN), which contains a vignette and sample data/code for immediate use. This package addresses limitations in existing spatial analysis packages and emphasizes its efficiency in detecting flow hotspots. It is highly applicable in various urban and geographic data science applications. {spnaf} is still in its early stages and we hope that interested readers can contribute to the development and enhancement of the package.

Introduction

This paper introduces an R package for identifying flow hotspots, applicable to human mobility, animal movement, and transportation flows. Despite the benefits of the hotspot analysis of flows as a part of Exploratory Spatial Data Analysis (ESDA), there is a lack of open-source codes or user-friendly programs for facilitating that process. For instance, despite a variety of ESDA tools in R such as {spdep} (Bivand et el., 2017), {geostan} (Donegan and Morris, 2022), and {rgeoda} (Anselin et al., 2021) for other kinds of spatial datasets (e.g., point, lattice), progress in developing open-source programs for reproducible flow data analysis and visualization has lagged. In response, we present {spnaf} (spatial network autocorrelation for flows) (https://cran.r-project.org/web/packages/spnaf/index.html). {spnaf} is an open-source R package that enables users to conduct hotspot analysis of flow by detecting statistically significant flow clusters based on Berglund and Karlström’s ${G_{ij}}^{*}$ index (1999). We acknowledge that {spnaf} is still in its early stages. We hope that this study encourages interested readers to contribute to the development and enhancement of the package.

Background

Berglund and Karlström’s G statistic

The ${G_{ij}}^{*}$ statistic used in {spnaf} to detect hotspots of flows stems from the work of Berglund and Karlström (1999) who developed ${G_{ij}}^{*}$ statistic as an extension of Getis and Ord’s G-statistic. It detects the spatial clustering of flows, enabling the identification of flow clusters at the local level within the context of neighboring flows based on network spatial weight matrices.

The ${{\hspace{0.17em}G}_{ij}}^{*}$ values are utilized to identify flow clusters based on statistical significance. The computation of ${G_{ij}}^{*}$ follows the formula presented in Equation (1) (Berglund and Karlström, 1999) $G_{ij}^{*}=\frac{{\sum }_{k,l}{w}_{ij,kl}{r}_{kl}-W_{ij}\overline{r}}{s{\left\{\left(t-1\right)S_1-W_{ij}^2/t-2\right\}}^{\frac{1}{2}}}$ (1) $\overline{r}=\frac{1}{t-1}\sum _{kl,\left(k,l\right)\ne \left(i,j\right)}{r}_{kl},$ $s^2=\frac{1}{t-2}\sum _{kl,\left(k,l\right)\ne \left(i,j\right)}{\left(r_{kl}-\overline{r}\right)}^2,$ $W_{ij}=\sum _{kl,\left(k,l\right)\ne \left(i,j\right)}{w}_{ij,kl},$ $S_1=\sum _{kl,\left(k,l\right)\ne \left(i,j\right)}{w}_{ij,kl}^2.$ $w_{ij}$ represents the spatial weight matrix, and t is the number of the origin-destination pairs, where i and j denote the origins and destinations, respectively, with k being the origin-constrained neighbors and l the destination-constrained neighbors. $r$ denotes the flow volumes between each pair of origin-destination census blocks. A network spatial weight matrix $W=\left[w_{ij,kl}\right]$ can be determined by the three options: 1) only neighbors of the origin are considered, 2) only neighbors of the destination are considered, and 3) neighbors of both the origin and the destination are considered.

Previous studies of flow clusters

The application of ESDA to flow datasets has demonstrated its utility in examining the various mobility/movement datasets, including human migration (Chun, 2008; Lee et al., 2021), bike-sharing trips (Kim and Kim, 2020), and commodity flows (Chun et al., 2012). For instance, Lee et al. (2021) employed the ${{\hspace{0.17em}G}_{ij}}^{\ast }$ to illustrate how the migration patterns of millennials in Seoul, Korea, diverged from those of other age groups. Chun et al. (2012) devised an interregional commodity flow model that accounted for spatial network autocorrelation effects after identifying statistical significance in ${G_{ij}}^{\ast }$ , thereby ensuring the model’s unbiased estimates. Kim and Kim (2020) applied ${G_{ij}}^{\ast }$ to identify flow clusters of bike-sharing trips in urban areas. Their findings offered policy insights, suggesting potential enhancements for bike-sharing route maintenance and service improvements rooted in the local urban structures. Moreover, Tao and Thill (2020) introduced BiFlowLiSA, a local indicator of spatial association of bivariate flow data, which adapts the local bivariate Moran’s I to the origin-destination paired network datasets, expanding flow-related ESDA methods.

Working with {spnaf}: An overview

The {spnaf} package (designed for R version 3.5 or newer) requires several supporting packages: {deldir}, {dplyr}, {magrittr}, {sf}, {spdep}, {tidyr}, and {rlang}. The{spnaf} package includes the main function—Gij.flow, and four internal sub-functions—Gstat, Boot, Resultlines, and SpatialWeights.

To utilize the {spnaf} package, users need to import two types of files. Users should first import their flow data in the “data frame” class format with three required columns: 1) oid (origin id); 2) did (destination id); and 3) n (the magnitude of flow between an origin-destination pair). They should also import the corresponding polygon or point shapefile of a study area (e.g., boundaries of census blocks when these census blocks are considered as origins and destinations of flows or points of interest when these points are considered as origins and destinations). The shapefile needs to be imported in the “sf” class format using the {sf} package. This shapefile must include an id column, which is used as the origin id (i.e., oid) or destination id (i.e., did) in the first dataset (i.e., flow data in the “data frame” format).

Figure 1 illustrates the workflow of the {spnaf} package. The main function (Gij.flow) first calls the SpatialWeights function to calculate spatial weights using various spatial weight matrix options. The first option involves creating contiguity-based neighbors using the “Queen” method within the Gij.flow function (Getis and Aldstadt, 2004). The second and third options involve computing the spatial matrix based on distance, represented by “KNN” (k-nearest neighbors) and “fixed-distance” methods, respectively. The “KNN” option calculates an adaptive distance weight matrix, while the “fixed_distance” option computes a fixed-distance weight matrix. For the KNN method and the fixed distance method, the value for the k (the number of the nearest neighbors considered) and the d (the distance considered) need to be determined. The SpatialWeights function supports not only binary weight but also allows users to adopt the inverse distance weight matrix with “idw = TRUE” command. Additionally, the function provides an option to standardize neighbors’ values using the row standardization method with “row_standardized = TRUE” command. By default, the Queen method with a binary weight and without row standardization is applied to create a spatial weight matrix.

Figure 1.

An overview of the {spnaf}'s workflow and functions.

Next, the Gstat function uses the results from Spatialweights and calculates Berglund and Karlström’s ${G_{ij}}^{*}$ based on the selected option of neighbor structure. This option determines how the origins and destinations of flows should be considered in terms of neighbor structure. The default value of the option is t (total). In this case, both origins’ and destinations’ adjacent polygons or points (specified by the SpatialWeights function) are considered as a default setting. The alternatives o and d consider “only the neighbors of the origin” and “only the neighbors of the destination,” respectively.

Then, the Boot function validates the ${G_{ij}}^{*}$ from Gstat through a bootstrapping technique. This method replicates samples n times to determine the statistical significance of the results. By default, samples are replicated 1,000 times. This bootstrapping procedure produces p-values for the ${G_{ij}}^{*}$ statistics.

Following this, the Resultlines function generates an output in the list class format which contains a data frame consisting of oid (origin id), did (destination id), n (the volume of flows), Gij ( ${G_{ij}}^{*}$ ), pval (p-value), along with an additional geometry column in the well-known text (WKT) form which includes line strings for visualizing the hotspot flows making it an sf class of the {sf} package.

Users have the flexibility to select their desired p-value. For example, a user might select a p-value of 0.05, with the default setting (1,000 times) of the bootstrapping procedure, to extract statistically significant flow hotspots. Through this, users can determine statistical significance of each ${G_{ij}}^{*}$ value, thereby identifying statistically significant hotspot flows (flows with high values, surrounded by other flows of similar volumes).

Examples

Polygon feature example: CoGo bike-sharing flows

The application of polygon features is demonstrated through the analysis of Columbus bike-sharing (CoGo) trips in the city of Columbus, Ohio, USA. The CoGo dataset (https://cogobikeshare.com/system-data) includes information about the origin and destination bike station of each trip from 2014 to 2023. We analyzed data from January through December 2019 before the COVID-19 pandemic, which encompasses 36,890 bike trips with 79 unique bike stations. We aggregated the individual trips at the census block level based on the locations of bike stations. This resulted in 1,416 origin-destination pairs, with a maximum bike-sharing trip volume of 1,453.

To test the effectiveness of this package in detecting flow hotspots for polygon features using CoGo bike-sharing data, we applied three different spatial weight matrices with inverse distance weights and the row standardization option: 1) the Queen method, 2) the KNN method with 10 nearest neighbors, and 3) the fixed distance with a 10 km radius. We considered both the origins and the destinations for the neighbors’ structure. The results were selected with a 99% statistical significance. The example codes for these analyses are represented in Table 1.

Table 1.

Example codes by the spatial weight matrix methods.

The spatial weight matrix method	Code
The Queen method	result<- Gij.flow (df, shape, idw = TRUE, row_ standardize = TRUE)
	result_pval<-result<-result [[2]][result [[2]]$pval < 0.01,]
The KNN method	result<- Gij.flow (df, shape, method = “KNN,” k = 10, idw = TRUE, row_ standardize = TRUE)
	result_pval<-result<-result [[2]][result [[2]]$pval < 0.01,]
The fixed distance method	result<- Gij.flow (df, shape, method = “fixed_distance,” d = 10, idw = TRUE, row_ standardize = TRUE)
	result_pval<-result<-result [[2]][result [[2]]$pval < 0.01,]

The results showed that among the 1,416 origin-destination pairs, the Queen method identified 13 origin-destination pairs as hotspots, the KNN method found 13 flow hotspots, and the fixed distance method detected 15 flow hotspots. On an Apple hexa-core M1 Pro CPU, operating at 3.6 GHz with 16 GB of RAM, the calculation of ${G_{ij}}^{*}$ for 1,416 OD pairs was completed in 180 s.

Based on these results, we exported the outputs as a shapefile, including the line strings of the flow hotspots, to identify the geographical distribution of these flows. We used QGIS version 3.26 to visualize the shapefile outputs (Figure 2). The bike-sharing flow hotspots are generally concentrated around the downtown area of Columbus for all three methods. However, the specific locations vary depending on each spatial weight matrix.

Figure 2.

Spatial distribution of bike-sharing flow hotspots between each census block by the spatial weight matrices: a) the Queen contiguity method b) the KNN method (k = 10), and c) the fixed distance method (d = 10).

Point feature example: US airport passengers travel patterns

The application of point features is demonstrated through the analysis of air passenger travel patterns across the mainland US. The air passengers travel data (Bureau of Transportation Statistics, 2024) includes information about passenger travel patterns between airports, represented as point features in the shapefile. We selected domestic flights within the mainland US for the period spanning to the first quarter of 2023, extracting only origin-destination pairs with over 1,000 passengers. This resulted in 396 origin-destination pairs, with the maximum travel volume being 19,955 passengers.

We applied similar processes to test the ability of the package to identify flow hotspots for point features as we did with polygon features. We used three different spatial weight matrices options with inverse distance weight and row standardization option: 1) the Queen contiguity method, 2) the KNN method with 10 nearest neighbors (k = 10), and 3) the fixed distance with a 200 km radius (d = 200). The results showed that among the 396 origin-destination pairs, the Queen method found only 3 flow hotspots, the KNN method found 5 flow hotspots, and the fixed distance method detected 4 flow hotspots (Table 2). On an Apple hexa-core M1 Pro CPU, operating at 3.6 GHz with 16 GB of RAM, the calculation of ${G_{ij}}^{*}$ for 396 OD pairs was completed in 25 s.

Table 2.

The results of Gij* by the spatial weight matrices.

Spatial weight matrix	Origin airport ID	Destination airport ID	Travel volume	Gij*	p-value
The Queen contiguity method	ATL	BOS	9,749	17.39	0.001
	BWI	MCO	14,440	14.17	0.004
	CHS	LGA	2,909	14.11	0.001
The KNN method (k = 10)	ATL	BOS	9,749	19.71	0.001
	BNA	FLL	5,839	15.59	0.008
	BNA	LGA	7,203	17.13	0.004
	BNA	MCO	9,137	16.05	0.007
	CHS	LGA	2,909	14.11	0.006
The fixed distance method (d = 200)	ATL	AUS	4,830	26.55	0.005
	ATL	BNA	2,160	28.93	0.003
	ATL	BOS	9,749	29.43	0.001
	BOS	ATL	9,689	25.19	0.008

The geographical distribution of flow hotspots was predominantly concentrated along the East Coast, regardless of the spatial weight matrices employed (Figure 3). The Queen contiguity and the KNN spatial weight matrices exhibited similar patterns in the flow hotspots (Figures 3(b) and (c)). In contrast, the fixed distance-based method uniquely identified flow hotspots. For example, it detected flow hotspots from Hartsfield–Jackson Atlanta International Airport to Nashville International airport and Austin–Bergstrom International Airport, which did not appear in the KNN and Queen contiguity methods. (Figure 3(d)).

Figure 3.

Spatial distribution of air passengers’ flow hotspots between the US airports by the spatial weight matrices: (a) the locations of airports in the mainland US, (b) the Queen contiguity method (c) the KNN method (k = 10), and (d) the fixed distance method (d = 200).

Conclusion

The {spnaf} package (https://cran.r-project.org/web/packages/spnaf/index.html) enables the spatial analysis of flow data on human mobility (and animal movement), ranging from micro-scale (e.g., bike-sharing trips within a city) to macro-scale (e.g., air passenger travel patterns across the U.S.) movements, utilizing various spatial weight matrices regardless of the spatial data types. Over the past decade, we have witnessed a proliferation of data on human mobility (Miller et al., 2019). However, a deeper understanding of human mobility flows has been constrained by the lack of open-source tools capable of conducting cluster analysis of flows, while accommodating the size and complexity of datasets.

As the first R package specifically designed for hotspot analysis of flow datasets, {spnaf} overcomes these challenges. We demonstrated its effectiveness through an example analysis of bike-sharing trips in a mid-sized city in the US and an analysis of air passengers’ travel volume across the US. These example analyses demonstrated that users can employ various spatial weight matrices based on the purpose of their analysis. The different options for spatial weight matrices enable user to conduct sensitivity analysis and consider the contextual relevance for their specific analysis, thereby enhancing interpretations. We also demonstrated that the {spnaf} is capable of handling large sizes of flow datasets on standard PCs and laptops. We hope that this package can empower researchers to address a wide array of research questions related to the flows of moving objects such as humans, animals, and vehicles in the realm of integrated movement science.