Author: Hannah L. Owens
Date: 2025-07-18

# 3. Environmental Data Sampling

#### Hannah L. Owens

#### Carsten Rahbek

#### 2025-07-18

# Introduction

As stated in the introduction to this package, one of the key contributions of `voluModel` is the way it handles the extraction of environmental data for niche modeling. Specifically, environmental data at presences, absences, pseudoabsences, and/or background points can be extracted from environmental data multi-layer `SpatRaster` objects based on depth in addition to horizontal coordinates. Another useful tool provided with `voluModel` is `marineBackground()`, which helps the user generate training regions from which background or pseudoabsence data are drawn. This is where we will start, so let’s get into it.

Here are the packages you will need.

    library(voluModel) # Because of course
    library(ggplot2) # For fancy plotting
    library(rangeBuilder) # To compare marineBackground to getDynamicAlphaHull
    library(dplyr) # To filter data
    library(terra) # Now being transitioned in
    library(sf) # Now being transitioned in

# 3D Data Extraction

First, we will cover how to extract environmental data from a multi-layer `SpatRaster` object using 3D occurrence coordinates. The species occurrences I will use are Steindachneria argentea, Luminous Hake, data downloaded via R (R Core Team, 2020) from GBIF (Chamberlain et al., 2021; Chamberlain and Boettiger, 2017) and OBIS (Provoost and Bosch, 2019) via `occCite` (Owens et al., 2021).

    # Get points
    occs <- read.csv(system.file("extdata/Steindachneria_argentea.csv",
                                 package='voluModel'))
    occurrences <- occs %>%
      dplyr::select(decimalLongitude, decimalLatitude, depth) %>%
      dplyr::distinct() %>%
      dplyr::filter(depth %in% 1:2000)

The environmental dataset I will use as an example is temperature (Locarnini et al., 2018) from the World Ocean Atlas (WOA; Garcia et al., 2019). I have chosen to focus on temperature for simple illustrative purposes–we recommend you explore additional variables from the World Ocean Atlas and other sources. These data are supplied by the World Ocean Atlas as point shapefiles; the version supplied here has been cropped between -110 and -40 longitude and between -5 and 50 latitude to make it more memory-efficient.

This chunk of code loads the example data shapefile, which results in a `SpatVector`:

    # Temperature
    td <- tempdir()
    unzip(system.file("extdata/woa18_decav_t00mn01_cropped.zip",
                      package = "voluModel"),
          exdir = paste0(td, "/temperature"), junkpaths = T)
    temperature <- vect(paste0(td, "/temperature/woa18_decav_t00mn01_cropped.shp"))

    # Looking at the dataset
    as.data.frame(temperature[1:5,1:10])

    ##   SURFACE    d5M   d10M   d15M   d20M   d25M   d30M   d35M   d40M   d45M
    ## 1  23.575 23.392 22.919 22.318 21.766 21.117 20.531 19.860 19.266 18.673
    ## 2  23.204 22.979 22.559 22.057 21.401 20.651 19.978 19.433 18.835 18.247
    ## 3  23.451 23.125 22.726 22.134 21.520 20.828 20.128 19.472 18.875 18.353
    ## 4  23.261 22.968 22.559 22.052 21.528 20.945 20.337 19.759 19.198 18.669
    ## 5  22.977 22.790 22.463 22.036 21.611 21.079 20.521 20.000 19.423 18.835

As you can see, each point in the `SpatVector` is a line in the associated `data.frame`; each column is a depth layer at that point–“d5M” translates to “5 meters deep”. For more details on how to process environmental data, see the raster data tutorial. This next chunk converts the `SpatVector` to a multi-layer `SpatRaster`; the layers of the multi-layer `SpatRaster` are then named the same as the column names of the `SpatVector`. I strip the “d” and “M” from the column names so they are a little easier to use as depth coordinates.

    # Creating a SpatRaster vector
    template <- centerPointRasterTemplate(temperature)
    tempTerVal <- rasterize(x = temperature, y = template, field = names(temperature))

    # Get names of depths
    envtNames <- gsub("[d,M]", "", names(temperature))
    envtNames[[1]] <- "0"
    names(tempTerVal) <- envtNames
    temperature <- tempTerVal

    rm(tempTerVal)

At this point, you may have noticed a message popping up about which columns `voluModel` is interpreting as coordinates. `voluModel` is fairly flexible in how the coordinate columns are named, and it relies on names instead of column position to interpret x, y, and z (or latitude, longitude, and depth) coordinates. We do this to make `voluModel` as flexible as possible to a diversity of input formats, although English is the only supported language at the moment. Here are some examples of names that work.

    occsTest <- occurrences[19:24,]
    xyzSample(occs = occsTest, envBrick = temperature)

    ## Using decimalLongitude, decimalLatitude, and depth
    ##  as x, y, and z coordinates, respectively.

    ## [1] 25.770 15.091     NA  9.137     NA     NA

    colnames(occsTest) <- c("x", "y", "z")
    xyzSample(occs = occsTest, envBrick = temperature)

    ## Using x, y, and z
    ##  as x, y, and z coordinates, respectively.

    ## [1] 25.770 15.091     NA  9.137     NA     NA

    rm(occsTest)

One common step in a niche modeling workflow is to down-sample occurrence data to the same resolution as the environmental data. We do this to avoid over-fitting the model due to biased sampling. The next chunk of code downsamples occurrence points so that there is only one per voxel (i.e. 3D pixel) of environmental data. It does this by looping through each layer of the multi-layer `SpatRaster`, selecting the occurrence points with depths closest to the depths represented by the corresponding layer in the `SpatRaster` vector. I then downsample these points using `voluModel`’s `downsample()` function.

    # Gets the layer index for each occurrence by matching to depth
    layerNames <- as.numeric(names(temperature))
    occurrences$index <- unlist(lapply(occurrences$depth, FUN = function(x) which.min(abs(layerNames - x))))
    indices <- unique(occurrences$index)
    downsampledOccs <- data.frame()
    for(i in indices){
      tempPoints <- occurrences[occurrences$index==i,]
      tempPoints <- downsample(tempPoints, temperature[[1]])
      tempPoints$depth <- rep(layerNames[[i]], times = nrow(tempPoints))
      downsampledOccs <- rbind(downsampledOccs, tempPoints)
    }

    occurrences <- downsampledOccs
    head(occurrences)

    ##   decimalLongitude decimalLatitude depth
    ## 1            -54.5             7.5   450
    ## 2            -82.5            12.5   450
    ## 3            -93.5            19.5   450
    ## 4            -97.5            22.5   450
    ## 5            -82.5            23.5   450
    ## 6            -89.5            23.5   450

    print(paste0("Original number of points: ", nrow(occs), "; number of downsampled occs: ", nrow(occurrences)))

    ## [1] "Original number of points: 301; number of downsampled occs: 71"

The resampled points returned by `downsample()` are horizontally centered in each voxel. The red dots in the plot show occurrences from the original dataset; the orange dots show the downsampled dataset. Not all of the orange dots may be visible underneath the red dots.

    land <- rnaturalearth::ne_countries(scale = "small", returnclass = "sf")[1]

    pointCompMap(occs1 = occs, occs2 = occurrences,
                 occs1Name = "original", occs2Name = "cleaned",
                 spName = "Steindachneria argentea",
                 land = land, verbose = FALSE)

At this point, we can demonstrate one of the key contributions of `voluModel`– an improvement in how the environmental data are extracted at species’ occurrences. `voluModel` samples environmental conditions at the depth where each record was located, instead of extrapolating to surface or bottom conditions. Finally, we add a column called “response” and fill it by repeating “1”, to signify that these occurrences should be interpreted as presences for the purposes of modeling.

    # Extraction
    occurrences$temperature <- xyzSample(occs = occurrences, envBrick = temperature)

    ## Using decimalLongitude, decimalLatitude, and depth
    ##  as x, y, and z coordinates, respectively.

    # Add "response" column for modeling
    occurrences$response <- rep(1, times = nrow(occurrences))
    occurrences <- occurrences[complete.cases(occurrences),]

    head(occurrences)

    ##    decimalLongitude decimalLatitude depth temperature response
    ## 3             -93.5            19.5   450       9.137        1
    ## 5             -82.5            23.5   450      11.395        1
    ## 6             -89.5            23.5   450       9.285        1
    ## 7             -84.5            26.5   450       9.145        1
    ## 9             -91.5            27.5   450       9.091        1
    ## 15            -89.5            28.5    80      20.440        1

In a “real” modeling scenario, you would extract all your environmental variables using `xyzSample()`, then add the response column. Or add the response column first or in the middle. I’m not the boss of you.

# Generating Repeatable Training Regions

To generate a sample of pseudoabsences and/or background points, it is important to consider the environments the species of interest can access (Barve et al., 2011). There is ample discussion in the literature on how to best delimit a niche model training region (also variously called M or the background region), and we will not review the issue here. In the absence of specific information on species’ dispersal capabilities, algorithmically generating a repeatable sampling background from a clear set of rules may be suitable approximation, or a jumping-off point for hand-curating training regions in a GIS software of choice.

We designed `marineBackground()` as a wrapper around , a function provided by the `rangeBuilder` package (Davis-Rabosky et al., 2016) which generates background sampling regions by fitting an alpha hull polygon around an occurrence point dataset. Let’s look at how `marineBackground()` (and by extension `getDynamicAlphaHull()`) fits alpha hull polygons, based on the cleaned species occurrence data from above.

`getDynamicAlphaHull()`, which is run within `marineBackground()` generates a polygon (or polygons) that can be used as a training region by fitting an alpha hull (or hulls) around an occurrence dataset. Alpha is a parameter that controls the complexity of the polygon(s) that is being fit around the occurrences. `getDynamicAlphaHull()` adjusts the alpha parameter iteratively, until it meets criteria the user can set via the arguments `fraction`, which is the minimum fraction of occurrences that must be contained within the polygon(s), `partCount`, which is the maximum number of polygons generated to fit the data, and `buff`, which is the permissible distance from a point to the edge of a polyon in meters. `marineBackground()` takes these and many of the same other arguments as `getDynamicAlphaHull()`. Here’s how it works.

    trainingRegion <- marineBackground(occurrences,
                                       fraction = 1,
                                       partCount = 1,
                                       buff = 1000000,
                                       clipToOcean = F)
    plot(trainingRegion, border = F, col = "gray",
         main = "100% Points,\nMax 1 Polygon Permitted, 100 km Buffer",
         axes = T)
    plot(land, col = "black", add = T)
    points(occurrences[,c("decimalLongitude", "decimalLatitude")],
           pch = 20, col = "red", cex = 1.5)

What parameters you choose to fit the alpha hull will depend on the biology of the organism you are trying to model (e.g. you may choose a much smaller buffer for a sessile organism than you would for a highly vagile migratory species), your data, and the particulars of your study system and the geography of your study area. You may need to experiment to find something that looks sensible. If you do not provide a pre-defined buffer, `marineBackground()` will calculate a buffer that is the mean of the top and bottom 10% of distances between points in the dataset.

You may have noticed that the training regions in the above examples include some areas of the Pacific where the species has not been observed, and cannot access. This could cause problems if it is used to train your model. You could delete this area by hand in your favorite GIS software, OR you could change `clipToOcean` to `TRUE` in `marineBackground()`, and any polygon fragments that do not contain an occurrence will be deleted automatically. This is a key difference from `getDynamicAlphaHull()`.

    trainingRegion <- marineBackground(occurrences,
                                       buff = 1000000,
                                       clipToOcean = T)
    plot(trainingRegion, border = F, col = "gray",
         main = "100 km Buffer,\nClipped to Occupied Polygon",
         axes = T)
    plot(land, col = "black", add = T)
    points(occurrences[,c("decimalLongitude", "decimalLatitude")],
           pch = 20, col = "red", cex = 1.5)

The last major difference between `marineBackground()` and `getDynamicAlphaHull()` is how the functions handle training regions that are adjacent to the antimeridian (i.e. 180° E or W). `getDynamicAlphaHull()` truncates polygons at this line, which can lead to some strange-looking training areas or fatal errors. `marineBackground()`, on the other hand, wraps polygons across the meridian and merges them if they overlap. For this example, I am going to manipulate the longitudinal coordinates of our Luminous Hake dataset to generate a quick fictional example.

    # Fictional example occurrences
    pacificOccs <- occurrences
    pacificOccs$decimalLongitude <- pacificOccs$decimalLongitude - 100
    for (i in 1:length(pacificOccs$decimalLongitude)){
      if (pacificOccs$decimalLongitude[[i]] < -180){
        pacificOccs$decimalLongitude[[i]] <- pacificOccs$decimalLongitude[[i]] + 360
      }
    }

    # marine Background
    pacificTrainingRegion <- marineBackground(pacificOccs,
                                              fraction = 0.95, partCount = 3,
                                              buff = 1000000,
                                              clipToOcean = T)
    plot(pacificTrainingRegion, border = F, col = "gray",
         main = "marineBackground\nAntimeridian Wrap",
         axes = T)
    plot(land, col = "black", add = T)
    points(pacificOccs[,c("decimalLongitude", "decimalLatitude")],
           pch = 20, col = "red", cex = 1.5)

# Background Data Extraction

As discussed above, some modeling methods require the generation of a sampling region from which training/pseudoabsence/background points are drawn. The training region should approximately answer the question “What environments are most likely to have been experienced by Lumious Hakes?” Our answer to this question for the purposes of this tutorial is represented in `trainingRegion`, which we generated above using `marineBackground()`. Next, we generate 3D training points within this region using the `mSampling3D()` function. The function takes an occurrence `data.frame`, a multi-layer `SpatRaster` that will serve as a template for the resolution of the training points, a `SpatialPolygons` object representing the training region, and, optionally, information on the range of depths from which the function should sample. If you have reason to believe the species you are modeling can access depths higher or lower than those represented by occurrences, you can specify a maximum and minimum training depth from which to draw occurrence points. `mSampling3D()` by default draws training points from the full depth extent of the supplied multi-layer `SpatRaster`.

For this example, I am sampling training points from 50 to 1500 m.

    # Background
    backgroundVals <- mSampling3D(occs = occurrences,
                                  envBrick = temperature,
                                  mShp = trainingRegion,
                                  depthLimit = c(50, 1500))

    ## Using decimalLongitude, decimalLatitude, and depth
    ##  as x, y, and z coordinates, respectively.

    backgroundVals$temperature <- xyzSample(occs = backgroundVals, temperature)

    ## Using decimalLongitude, decimalLatitude, and depth
    ##  as x, y, and z coordinates, respectively.

    #Remove incomplete cases
    backgroundVals <- backgroundVals[complete.cases(backgroundVals),]

Once the points are sampled, we add a column called “response” and fill it by repeating “0”, to signify that these occurrences should be interpreted as absences for the purposes of modeling.

    # Add "response" column for modeling
    backgroundVals$response <- rep(0, times = nrow(backgroundVals))

    head(backgroundVals)

    ##    decimalLongitude decimalLatitude depth temperature response
    ## 72            -68.5            43.5    50       6.473        0
    ## 73            -67.5            43.5    50       6.669        0
    ## 74            -66.5            43.5    50       6.779        0
    ## 76            -64.5            43.5    50       3.679        0
    ## 77            -63.5            43.5    50       4.003        0
    ## 78            -62.5            43.5    50       5.038        0

It is important to note that this background data represents EVERY voxel within the training region that is not occupied by observances. Depending on your study design and the modeling algorithm you are using, these data will need to be subsampled. You could choose a random sample, select points based on geography, or any number of other strategies. Below is just one example–weighting the background points by their environmental dissimilarity to the Luminous Hake occurrence points. This manner of downsampling may be appropriate for modeling methods that interpret training points as pseudoabsences, such as generalized linear modeling, but will lead to overfit models when using algorithms like Maxent.

    # Sample background points weighted by distance from mean of occurrence temperatures
    meanTemp <- mean(occurrences[,c("temperature")])
    backgroundVals$distance <- abs(backgroundVals[,"temperature"] - meanTemp)
    backgroundVals$sampleWeight <- (backgroundVals$distance -
                                      min(backgroundVals$distance))/(max(backgroundVals$distance) -
                                                                      min(backgroundVals$distance))
    sampleForAbsence <- sample(x = rownames(backgroundVals),
                               size = nrow(occurrences) * 100,
                               prob = backgroundVals$backgroundVals)
    backgroundVals <- backgroundVals[match(sampleForAbsence,
                                           rownames(backgroundVals)),]

    backgroundVals$response <- as.factor(backgroundVals$response)

    # Unite datasets and see how things look
    dataForModeling <- rbind(occurrences, backgroundVals[,colnames(occurrences)])
    ggplot(dataForModeling, aes(x = temperature, fill = response, color = response)) +
      geom_density(alpha = .6) +
      scale_color_manual(values=c("#999999", "#E69F00"),
                         labels = c("Pseudoabsence", "Presence")) +
      scale_fill_manual(values=c("#999999", "#E69F00"),
                        labels = c("Pseudoabsence", "Presence")) +
      labs(title="Temperature Sampling Density,\nOccurrences vs. Pseudoabsences",
           x="Temperature (C)", y = "Density")+
      theme_classic()

For a more complex, multivariate example of environmental dissimilarity weighting, refer to the GLM workflow.

# Tidying up

Last, we need to close the temporary directory we opened when we opened the data.

    unlink(td, recursive = T)

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