Author: Alec L. Robitaille, Quinn Webber and Eric Vander Wal

# Geometry interface and spatial measures

#### Alec L. Robitaille, Quinn Webber and Eric Vander Wal

## 1 Introduction

{spatsoc} v 0.2.13 provides a geometry interface and internal functions that provide consistent spatial measures across all {spatsoc} functions.

The motivation for `get_geometry` is to allow users to supply a geometry column instead of providing coordinates and optionally crs through the “coords” and “crs” args. This interface is enabled by default on all functions that accept coordinates / geometry, by leaving the coords null and ensuring the geometry column has been set up using `get_geometry()`.

Details on spatial measures below under Spatial measures.

See the other vignettes for further information:

- Introduction to spatsoc
  - temporal grouping
  - spatiotemporal grouping with `group_pts`, `group_lines`, `group_polys`
  - distance based edge-list generation with `edge_dist`
- Frequently asked questions about spatsoc
  - install
  - function details for `group_times`, `group_pts`, `group_lines`, `group_polys`, `edge_dist`, `edge_nn`, and `randomizations`
  - package design including modify-by-reference, data.table column allocation
  - calculating summary information
- Using spatsoc in social network analysis
  - generating gambit-of-the-group data
  - generating observed networks
  - data stream randomization, randomized networks
  - network metrics
- Using distance based edge-lists generating functions, dyad_id, and fusion_id
  - generate distance based edge-lists with `edge_dist` and `edge_nn`
  - generate dyad identifiers for edge-lists with `dyad_id`
  - identify fusion events with `fusion_id`
- Geometry interface
  - using `get_geometry` to setup a geometry column and use the geometry interface
  - details of underlying distance, direction and centroid spatial measures
  - converting to and from related packages
- Interspecific interactions
  - combine two movement datasets
  - identify interspecific interactions

## 2 Setup

Load packages

    library(spatsoc)
    library(data.table)

Example data and variables

    # Read example data
    DT <- fread(system.file('extdata', 'DT.csv', package = 'spatsoc'))

    coords <- c('X', 'Y')
    crs <- 32736
    datetime <- 'datetime'
    id <- 'ID'

## 3 `get_geometry`

`get_geometry` can be used to setup a `DT` with a simple feature geometry list column. Optionally, the input coordinates can be transformed using the argument “output_crs”. The default output geometry column name can be changed using the argument “geometry_colname”.

### 3.1 Usage

    # Get geometry
    get_geometry(DT, coords = coords, crs = crs)

    print(DT)
    #>            ID        X       Y            datetime population
    #>        <char>    <num>   <num>              <POSc>      <int>
    #>     1:      A 715851.4 5505340 2016-11-01 00:00:54          1
    #>     2:      A 715822.8 5505289 2016-11-01 02:01:22          1
    #>     3:      A 715872.9 5505252 2016-11-01 04:01:24          1
    #>     4:      A 715820.5 5505231 2016-11-01 06:01:05          1
    #>     5:      A 715830.6 5505227 2016-11-01 08:01:11          1
    #>    ---
    #> 14293:      J 700616.5 5509069 2017-02-28 14:00:54          1
    #> 14294:      J 700622.6 5509065 2017-02-28 16:00:11          1
    #> 14295:      J 700657.5 5509277 2017-02-28 18:00:55          1
    #> 14296:      J 700610.3 5509269 2017-02-28 20:00:48          1
    #> 14297:      J 700744.0 5508782 2017-02-28 22:00:39          1
    #>                        geometry
    #>                     <sfc_POINT>
    #>     1: POINT (715851.4 5505340)
    #>     2: POINT (715822.8 5505289)
    #>     3: POINT (715872.9 5505252)
    #>     4: POINT (715820.5 5505231)
    #>     5: POINT (715830.6 5505227)
    #>    ---
    #> 14293: POINT (700616.5 5509069)
    #> 14294: POINT (700622.6 5509065)
    #> 14295: POINT (700657.5 5509277)
    #> 14296: POINT (700610.3 5509269)
    #> 14297:   POINT (700744 5508782)

## 4 Spatial measures

### 4.1 Distance

The underlying distance function used depends on the crs of the coordinates or geometry provided.

- If the crs is longlat degrees (as determined by `sf::st_is_longlat()`), the distance function is `sf::st_distance()` which passes to `s2::s2_distance()` if `sf::sf_use_s2()` is TRUE and `lwgeom::st_geod_distance()` if `sf::sf_use_s2()` is FALSE. The distance returned has units set according to the crs.

- If the crs is not longlat degrees (eg. NULL, `NA_crs_`, or projected), the distance function used is `stats::dist()`, maintaining expected behaviour from previous versions. The distance returned does not have units set.

Note: in both cases, if the coordinates are NA then the result will be NA.

### 4.2 Direction

The underlying distance function used depends on the crs of the coordinates or geometry provided.

- If the crs is provided and longlat degrees (as determined by `sf::st_is_longlat()`), the distance function is `lwgeom::st_geod_azimuth()`.

- If the crs is provided and not longlat degrees (eg. a projected UTM), the coordinates or geometry are transformed to `sf::st_crs(4326)` before the distance is measured using `lwgeom::st_geod_azimuth()`.

- If the crs is NULL or `NA_crs_`, the distance function cannot be used and an error is returned.

The crs for direction functions (eg. `direction_step`, `direction_to_centroid`) should be either longlat or a crs that can be transformed to `sf::st_crs(4326)`. A user can check their crs by using the function `sf::st_can_transform(src = crs, dst = 4326)`.

If a user provides a crs that is not longlat and cannot be transformed to 4326, they will receive an internal error with the following structure:

`"In CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy, : GDAL Error 6: Cannot find coordinate operations from..."`

### 4.3 Centroid

The underlying centroid function used depends on the crs of the coordinates or geometry provided.

- If the crs is longlat degrees (as determined by `sf::st_is_longlat()`) and `sf::sf_use_s2()` is TRUE, the distance function is `sf::st_centroid()` which passes to `s2::s2_centroid()`.

- If the crs is longlat degrees but `sf::sf_use_s2()` is FALSE, the centroid calculated will be incorrect. See `sf::st_centroid()`.

- If the crs is not longlat degrees (eg. NULL, NA_crs_, or projected), the centroid function used is mean.

Note: if the input is length 1, the input is returned directly without any processing.

The `distance_to_centroid`, `direction_to_centroid` and `leader_direction_group` expect a centroid column named ‘centroid’ when the geometry interface is used. Ensure the `centroid_group` function has been used with the geometry interface before running these functions.

The following warning may be returned when centroid functions are used with longlat coordinates / geometry and the {s2} package is not available or `sf::sf_use_s2()` is `FALSE`. Please set `sf::sf_use_s2(TRUE)` and try again.

## 5 Converting from other packages

Instead of using `get_geometry()`, coming from other packages, we can convert the objects to data.tables for processing with {spatsoc}. Caution: {spatsoc}’s expectation is that the “geometry” column is `sfc_POINT` representing each relocation.

### 5.1 Converting from {sftrack}

    library(sftrack)
    data("raccoon")
    raccoon$timestamp <- as.POSIXct(raccoon$timestamp, "EST")
    burstz <- list(id = raccoon$animal_id, month = as.POSIXlt(raccoon$timestamp)$mon)
    my_track <- as_sftrack(raccoon,
      group = burstz, time = "timestamp",
      error = NA, coords = c("longitude", "latitude")
    )

    DT_sftrack <- as.data.table(my_track)

    print(DT_sftrack)
    #> (id: TTP-058, month: 0)
    #> (id: TTP-058, month: 0)
    #> (id: TTP-058, month: 0)
    #> (id: TTP-058, month: 0)
    #> (id: TTP-058, month: 0)
    #> (id: TTP-041, month: 1)
    #> (id: TTP-041, month: 1)
    #> (id: TTP-041, month: 1)
    #> (id: TTP-041, month: 1)
    #> (id: TTP-041, month: 1)
    #>      animal_id latitude longitude           timestamp height  hdop  vdop    fix
    #>         <char>    <num>     <num>              <POSc>  <int> <num> <num> <fctr>
    #>   1:   TTP-058       NA        NA 2019-01-18 19:02:30     NA   0.0   0.0     NO
    #>   2:   TTP-058 26.06945 -80.27906 2019-01-18 20:02:30      7   6.2   3.2     2D
    #>   3:   TTP-058       NA        NA 2019-01-18 21:02:30     NA   0.0   0.0     NO
    #>   4:   TTP-058       NA        NA 2019-01-18 22:02:30     NA   0.0   0.0     NO
    #>   5:   TTP-058 26.06769 -80.27431 2019-01-18 23:02:30    858   5.1   3.2     2D
    #>  ---
    #> 441:   TTP-041 26.07068 -80.28009 2019-02-01 14:02:30     17   1.8   2.4     3D
    #> 442:   TTP-041 26.07069 -80.27996 2019-02-01 15:02:05     -6   2.4   2.2     3D
    #> 443:   TTP-041       NA        NA 2019-02-01 16:02:30     NA   0.0   0.0     NO
    #> 444:   TTP-041 26.07074 -80.28012 2019-02-01 17:02:09      7   1.6   3.0     3D
    #> 445:   TTP-041 26.07071 -80.28013 2019-02-01 18:02:07     13   1.6   2.7     3D
    #>         sft_group                   geometry
    #>      <c_grouping>                <sfc_POINT>
    #>   1: <s_group[2]>                POINT EMPTY
    #>   2: <s_group[2]> POINT (-80.27906 26.06945)
    #>   3: <s_group[2]>                POINT EMPTY
    #>   4: <s_group[2]>                POINT EMPTY
    #>   5: <s_group[2]> POINT (-80.27431 26.06769)
    #>  ---
    #> 441: <s_group[2]> POINT (-80.28009 26.07068)
    #> 442: <s_group[2]> POINT (-80.27996 26.07069)
    #> 443: <s_group[2]>                POINT EMPTY
    #> 444: <s_group[2]> POINT (-80.28012 26.07074)
    #> 445: <s_group[2]> POINT (-80.28013 26.07071)

### 5.2 Converting from {move2}

    library(move2)
    fishers <- mt_read(mt_example(file = "fishers.csv.gz"))
    DT_move2 <- as.data.table(fishers)

    print(DT_move2)
    #>         event-id visible           timestamp behavioural-classification
    #>            <i64>  <lgcl>              <POSc>                     <fctr>
    #>     1: 170635808    TRUE 2011-02-11 17:30:00                       <NA>
    #>     2: 170635809    TRUE 2011-02-11 17:40:00                       <NA>
    #>     3: 170635810    TRUE 2011-02-11 17:50:00                       <NA>
    #>     4: 170635811    TRUE 2011-02-11 18:00:00                       <NA>
    #>     5: 170635812    TRUE 2011-02-11 18:06:13                       <NA>
    #>    ---
    #> 47343: 170705304    TRUE 2011-05-28 09:04:37                       <NA>
    #> 47344: 170705305    TRUE 2011-05-28 09:06:58                       <NA>
    #> 47345: 170705306    TRUE 2011-05-28 09:08:59                       <NA>
    #> 47346: 170705307    TRUE 2011-05-28 09:10:24                       <NA>
    #> 47347: 170705308    TRUE 2011-05-28 09:12:00                       <NA>
    #>        eobs:battery-voltage eobs:fix-battery-voltage
    #>                     <units>                  <units>
    #>     1:              NA [mV]                  NA [mV]
    #>     2:              NA [mV]                  NA [mV]
    #>     3:              NA [mV]                  NA [mV]
    #>     4:              NA [mV]                  NA [mV]
    #>     5:              NA [mV]                  NA [mV]
    #>    ---
    #> 47343:              NA [mV]                  NA [mV]
    #> 47344:              NA [mV]                  NA [mV]
    #> 47345:              NA [mV]                  NA [mV]
    #> 47346:              NA [mV]                  NA [mV]
    #> 47347:              NA [mV]                  NA [mV]
    #>        eobs:horizontal-accuracy-estimate eobs:key-bin-checksum
    #>                                  <units>                 <i64>
    #>     1:                            NA [m]                  <NA>
    #>     2:                            NA [m]                  <NA>
    #>     3:                            NA [m]                  <NA>
    #>     4:                            NA [m]                  <NA>
    #>     5:                            NA [m]                  <NA>
    #>    ---
    #> 47343:                            NA [m]                  <NA>
    #> 47344:                            NA [m]                  <NA>
    #> 47345:                            NA [m]                  <NA>
    #> 47346:                            NA [m]                  <NA>
    #> 47347:                            NA [m]                  <NA>
    #>        eobs:speed-accuracy-estimate eobs:start-timestamp eobs:status
    #>                             <units>               <POSc>       <ord>
    #>     1:                     NA [m/s]                 <NA>        <NA>
    #>     2:                     NA [m/s]                 <NA>        <NA>
    #>     3:                     NA [m/s]                 <NA>        <NA>
    #>     4:                     NA [m/s]                 <NA>        <NA>
    #>     5:                     NA [m/s]                 <NA>        <NA>
    #>    ---
    #> 47343:                     NA [m/s]                 <NA>        <NA>
    #> 47344:                     NA [m/s]                 <NA>        <NA>
    #> 47345:                     NA [m/s]                 <NA>        <NA>
    #> 47346:                     NA [m/s]                 <NA>        <NA>
    #> 47347:                     NA [m/s]                 <NA>        <NA>
    #>        eobs:temperature eobs:type-of-fix eobs:used-time-to-get-fix ground-speed
    #>                 <units>           <fctr>                   <units>      <units>
    #>     1:          NA [°C]             <NA>                   110 [s]     NA [m/s]
    #>     2:          NA [°C]             <NA>                   110 [s]     NA [m/s]
    #>     3:          NA [°C]             <NA>                   110 [s]     NA [m/s]
    #>     4:          NA [°C]             <NA>                   110 [s]     NA [m/s]
    #>     5:          NA [°C]             <NA>                    80 [s]     NA [m/s]
    #>    ---
    #> 47343:          NA [°C]             <NA>                    37 [s]     NA [m/s]
    #> 47344:          NA [°C]             <NA>                    58 [s]     NA [m/s]
    #> 47345:          NA [°C]             <NA>                    59 [s]     NA [m/s]
    #> 47346:          NA [°C]             <NA>                    24 [s]     NA [m/s]
    #> 47347:          NA [°C]             <NA>                   110 [s]     NA [m/s]
    #>        heading height-above-ellipsoid manually-marked-outlier sensor-type
    #>        <units>                <units>                  <lgcl>      <fctr>
    #>     1:  NA [°]                 NA [m]                      NA         gps
    #>     2:  NA [°]                 NA [m]                      NA         gps
    #>     3:  NA [°]                 NA [m]                      NA         gps
    #>     4:  NA [°]                 NA [m]                      NA         gps
    #>     5:  NA [°]                 NA [m]                      NA         gps
    #>    ---
    #> 47343:  NA [°]                 NA [m]                      NA         gps
    #> 47344:  NA [°]                 NA [m]                      NA         gps
    #> 47345:  NA [°]                 NA [m]                      NA         gps
    #> 47346:  NA [°]                 NA [m]                      NA         gps
    #> 47347:  NA [°]                 NA [m]                      NA         gps
    #>        individual-local-identifier                   geometry
    #>                             <fctr>                <sfc_POINT>
    #>     1:                          F1                POINT EMPTY
    #>     2:                          F1                POINT EMPTY
    #>     3:                          F1                POINT EMPTY
    #>     4:                          F1                POINT EMPTY
    #>     5:                          F1 POINT (-73.86015 42.79528)
    #>    ---
    #> 47343:                          M5  POINT (-73.4067 42.83955)
    #> 47344:                          M5 POINT (-73.40663 42.83997)
    #> 47345:                          M5 POINT (-73.40644 42.84002)
    #> 47346:                          M5  POINT (-73.4063 42.84024)
    #> 47347:                          M5                POINT EMPTY

## 6 Converting to other packages

After processing with {spatsoc}, optionally convert output to work with other packages. Caution: {spatsoc}’s expectation is that users take their input data.table through any required functions in {spatsoc} before converting to other packages or using eg. {dplyr}. Intermixing packages between {spatsoc} functions can lead to issues with {data.table} class or column allocation. See more details under Package Design in FAQ.

An example of a potential issue with intermixing packages between spatsoc functions is that attributes such as the sf column’s bbox aren’t automatically updated when subsetting with data.table. This impacts the bbox returned, and also the bbox used for plotting. The recommendation is to run all required {spatsoc} functions then convert to standard spatial formats as described below for further processing and visualization.

    library(sf)
    #> Linking to GEOS 3.14.1, GDAL 3.12.3, PROJ 9.8.0; sf_use_s2() is TRUE
    DT[, st_bbox(geometry)]
    #>      xmin      ymin      xmax      ymax
    #>  693394.8 5490131.4  716205.1 5514805.9
    DT[1:10, st_bbox(geometry)]
    #>      xmin      ymin      xmax      ymax
    #>  693394.8 5490131.4  716205.1 5514805.9

    DT[, plot(geometry)]

    #> NULL
    DT[1:10, plot(geometry)]

    #> NULL

    # Note the bbox can also be manually recomputed
    DT[1:10, st_bbox(st_sfc(geometry, recompute_bbox = TRUE))]
    #>      xmin      ymin      xmax      ymax
    #>  714823.4 5505227.2  715872.9 5505837.2
    DT[1:10, plot(st_sfc(geometry, recompute_bbox = TRUE))]

    #> NULL

### 6.1 Converting to {sf}

    DT_sf <- st_as_sf(DT, sf_column_name = 'geometry')
    print(DT_sf)
    #> Simple feature collection with 14297 features and 5 fields
    #> Geometry type: POINT
    #> Dimension:     XY
    #> Bounding box:  xmin: 693394.8 ymin: 5490131 xmax: 716205.1 ymax: 5514806
    #> Projected CRS: WGS 84 / UTM zone 36S
    #> First 10 features:
    #>    ID        X       Y            datetime population                 geometry
    #> 1   A 715851.4 5505340 2016-11-01 00:00:54          1 POINT (715851.4 5505340)
    #> 2   A 715822.8 5505289 2016-11-01 02:01:22          1 POINT (715822.8 5505289)
    #> 3   A 715872.9 5505252 2016-11-01 04:01:24          1 POINT (715872.9 5505252)
    #> 4   A 715820.5 5505231 2016-11-01 06:01:05          1 POINT (715820.5 5505231)
    #> 5   A 715830.6 5505227 2016-11-01 08:01:11          1 POINT (715830.6 5505227)
    #> 6   A 715829.4 5505332 2016-11-01 10:01:18          1 POINT (715829.4 5505332)
    #> 7   A 715306.6 5505837 2016-11-01 12:00:49          1 POINT (715306.6 5505837)
    #> 8   A 715349.7 5505644 2016-11-01 14:01:23          1 POINT (715349.7 5505644)
    #> 9   A 715224.1 5505661 2016-11-01 16:00:51          1 POINT (715224.1 5505661)
    #> 10  A 714823.4 5505659 2016-11-01 18:01:16          1 POINT (714823.4 5505659)
    plot(DT_sf)

### 6.2 Converting to {sftrack}

    library(sftrack)

    # First convert to sf as above
    DT_sf <- st_as_sf(DT, sf_column_name = 'geometry')
    # Then convert to sftrack
    DT_sftrack <- as_sftrack(DT_sf, group = c(id = id), time = datetime)

    head(DT_sftrack)
    #> Sftrack with 6 features and 7 fields (0 empty geometries)
    #> Geometry : "geometry" (XY, crs: WGS 84 / UTM zone 36S)
    #> Timestamp : "datetime" (POSIXct in UTC)
    #> Groupings : "sft_group" (*id*)
    #> -------------------------------
    #>   ID        X       Y            datetime population sft_group
    #> 1  A 715851.4 5505340 2016-11-01 00:00:54          1   (id: A)
    #> 2  A 715822.8 5505289 2016-11-01 02:01:22          1   (id: A)
    #> 3  A 715872.9 5505252 2016-11-01 04:01:24          1   (id: A)
    #> 4  A 715820.5 5505231 2016-11-01 06:01:05          1   (id: A)
    #> 5  A 715830.6 5505227 2016-11-01 08:01:11          1   (id: A)
    #> 6  A 715829.4 5505332 2016-11-01 10:01:18          1   (id: A)
    #>                   geometry
    #> 1 POINT (715851.4 5505340)
    #> 2 POINT (715822.8 5505289)
    #> 3 POINT (715872.9 5505252)
    #> 4 POINT (715820.5 5505231)
    #> 5 POINT (715830.6 5505227)
    #> 6 POINT (715829.4 5505332)
    plot(DT_sftrack)

### 6.3 Converting to {move2}

    library(move2)

    # Convert to a {move2} object using mt_as_move2
    DT_move2 <- mt_as_move2(DT,
      time_column = datetime,
      track_id_column = id,
      sf_column_name = 'geometry'
    )

    print(DT_move2)
    #> A <move2> with `track_id_column` "ID" and `time_column` "datetime"
    #> Containing 10 tracks lasting on average 120 days in a
    #> Simple feature collection with 14297 features and 5 fields
    #> Geometry type: POINT
    #> Dimension:     XY
    #> Bounding box:  xmin: 693394.8 ymin: 5490131 xmax: 716205.1 ymax: 5514806
    #> Projected CRS: WGS 84 / UTM zone 36S
    #> First 10 features:
    #>    ID        X       Y            datetime population                 geometry
    #> 1   A 715851.4 5505340 2016-11-01 00:00:54          1 POINT (715851.4 5505340)
    #> 2   A 715822.8 5505289 2016-11-01 02:01:22          1 POINT (715822.8 5505289)
    #> 3   A 715872.9 5505252 2016-11-01 04:01:24          1 POINT (715872.9 5505252)
    #> 4   A 715820.5 5505231 2016-11-01 06:01:05          1 POINT (715820.5 5505231)
    #> 5   A 715830.6 5505227 2016-11-01 08:01:11          1 POINT (715830.6 5505227)
    #> 6   A 715829.4 5505332 2016-11-01 10:01:18          1 POINT (715829.4 5505332)
    #> 7   A 715306.6 5505837 2016-11-01 12:00:49          1 POINT (715306.6 5505837)
    #> 8   A 715349.7 5505644 2016-11-01 14:01:23          1 POINT (715349.7 5505644)
    #> 9   A 715224.1 5505661 2016-11-01 16:00:51          1 POINT (715224.1 5505661)
    #> 10  A 714823.4 5505659 2016-11-01 18:01:16          1 POINT (714823.4 5505659)
    #> Track features:
    #>    ID
    #> 1   A
    #> 2   B
    #> 3   C
    #> 4   D
    #> 5   E
    #> 6   F
    #> 7   G
    #> 8   H
    #> 9   I
    #> 10  J
    plot(DT_move2)