Alexander Ilich October 13, 2022
Please cite as
Ilich, Alexander R.; Misiuk, Benjamin; Lecours, Vincent; Murawski, Steven A.; 2021. “MultiscaleDTM”, https://doi.org/10.5281/zenodo.5548338. https://github.com/ailich/MultiscaleDTM.
This package calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models (DTM; i.e. elevation or bathymetry rasters) via a specified window size.
Figure adapted from Wilson et al. (2007)
The package can be installed from CRAN using
install.packages("MultiscaleDTM") or the development version can be
installed from github using the code
remotes::install_github("ailich/MultiscaleDTM"). If you are using
Windows, you may need to install Rtools using the instructions found
here). To install from
github you must already have the remotes package installed, which can be
installed using install.packages("remotes")
This package relies on the terra package for handling of spatial
raster data.
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SlpAspcalculates multi-scale slope and aspect according to Misiuk et al (2021) which is a modification of the traditional 3 x 3 slope and aspect algorithms (Fleming and Hoffer, 1979; Horn et al., 1981; Ritter, 1987). This algorithm only considers a subset of cells within the focal window, specifically the four cells on the edge of the focal window directly up, down, left, and right of the focal cell for the “rook” case and an additional four corner cells for the “queen” case.
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Qfitcalculates slope, aspect, curvature, and morphometric features by fitting a quadratic surface to the focal window using ordinary least squares using the equation shown below where a-f are regression parameters, Z is the elevation/depth, X is the east/west coordinates in the focal window relative to the focal cell, and Y is the north/south coordinates in the focal window relative to the focal cell (Evans, 1980; Wilson et al., 2007; Wood, 1996). The morphometric features algorithm has been modified to use more robust measures of curvature based on the suggestions of Minár et al. (2020).
Figure adapted from Walbridge et al., (2018)
VRM- Vector ruggedness measure (Sappington et al. 2007) quantifies terrain ruggedness by measuring the dispersion of vectors normal to the terrain surface. This is accomplished by calculating the local (3 x 3 cell) slope and aspect, and constructing unit vectors normal to each cell in the DTM. These unit vectors are then decomposed into their corresponding x, y, and z components (i.e. the x, y, and z coordinates of the head of the vector relative to its origin) and used in the following equation (note: n is the number of cells in the window). VRM ranges from zero to one, representing completely smooth to rugose surfaces, respectively. .
Figure adapted from Sappington et al. (2007)
Figure adapted from Habib (2021)
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SAPA- Calculates the Surface Area to Planar Area (Jenness, 2004). More rugose surfaces will have a greater surface area to planar area ratio, and perfectly smooth surfaces will have a value of 1. This is a 3D analog to the classical “chain-and-tape” method, which calculates rugosity as the ratio of the contoured distance (chain length) and linear distance (tape measure distance; Risk, 1972). Additionally, planar area can be corrected for slope by dividing the product of the x and y resolution by the cosine of slope (Du Preez 2015). Moreover, a proposed extension to multiple scales is provided by summing the surface areas within the focal window and adjusting the planar area of the focal window using multi-scale slope.SurfaceArea- Calculate the surface area of each grid cell (Jenness, 2004). This is accomplished by connecting a focal cell to its immediate neighbors to create 8 large triangles. These large triangles are then trimmed back to the extent of the focal cell using the principle of similar triangles, and then the area of those 8 smaller triangles are calculated and summed to estimate the surface area of the focal pixel. This is used withinSAPA.
Figure adapted from Friedman et al. (2012) and created with BioRender.com.
Figure adapted from Jenness (2004)
AdjSD- This new proposed rugosity metric modifies the standard deviation of elevation/bathymetry to account for slope. It does this by first fitting a plane to the data in the focal window using ordinary least squares, and then extracting the residuals, and then calculating the standard deviation of the residuals within the focal window.
RIE- Calculates the Roughness Index-Elevation which quantifies the standard deviation of residual topography (Cavalli et al., 2008). This measure is conceptually similar toAdjSDbut rather than fitting a plane and extracting residuals for the entire focal window, residual topography is calculated as the focal pixel minus the focal mean. Then the local standard deviation is calculated from this residual topography using a focal filter.
Figure adapted from Cavalli et al. (2008)
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TPI- Topographic Position Index (Weiss, 2001) is the difference between the value of a focal cell and the mean of the surrounding cells. -
RDMV- Relative Difference from Mean Value (Lecours et al., 2017) is the difference between the value of a focal cell and the mean of the cells in the focal window divided by the range or standard deviation of the values in the focal window. -
BPI- Bathymetric Position Index (Lundblad et al., 2006) is the difference between the value of a focal cell and the mean of the surrounding cells contained within an annulus shaped window. It is a modification of TPI that uses an annulus shaped focal window and therefore requires an inner and outer radius. For example, an annulus window with an inner radius of 4 cells and an outer radius of 6 cells would be
Figure adapted from Lundblad et al., (2006)
In this tutorial we will calculate various terrain attributes using a 5
x 5 cell rectangular window. Any rectangular odd numbered window size
however could be used (see figure directly below). Window sizes are
specified with a vector of length 2 of c(n_rows, n_cols). If a single
number is provided it will be used for both the number of rows and
columns. The only metric that does not follow this syntax is BPI which
uses an annulus shaped focal window which we will calculate using an
inner radius of 4 and an outer radius of 6 cells.
Load packages
library(MultiscaleDTM) #Load MultiscaleDTM packageSee package help page
help(package="MultiscaleDTM")Read in Data
r<- rast(volcano, extent= ext(2667400, 2667400 + ncol(volcano)*10, 6478700, 6478700 + nrow(volcano)*10), crs = "EPSG:27200")
slp_asp<- SlpAsp(r = r, w = c(5,5), unit = "degrees", method = "queen", metrics = c("slope", "aspect", "eastness", "northness"))
qmetrics<- Qfit(r, w = c(5,5), unit = "degrees", metrics = c("elev", "qslope", "qaspect", "qeastness", "qnorthness", "profc", "planc", "twistc", "meanc", "maxc", "minc", "features"), na.rm = TRUE)
To explore these measures in an interactive environment use
explore_terrain() or go to this
website
vrm<- VRM(r, w=c(5,5), na.rm = TRUE)
Note: multi-scale SAPA is experimental. The established metric by De
Preez (2015) would use w=1.
sapa<- SAPA(r, w=c(5,5), slope_correction = TRUE)
adj_SD<- AdjSD(r, w=c(5,5), na.rm = TRUE)
rie<- RIE(r, w=c(5,5), na.rm = TRUE)
tpi<- TPI(r, w=c(5,5), na.rm = TRUE)
rdmv<- RDMV(r, w=c(5,5), na.rm = TRUE, method="range")
bpi<- BPI(r, radius = c(4,6), unit = "cell", na.rm = TRUE)
The annulus window for BPI can be specified in either cell units (number
of raster cells) or in map units (e.g. meters) which can be useful if
your x and y resolutions are not equal. Additionally, the function
annulus_window can be used to verify that you are specifying your
window correctly (NA’s are excluded cells and 1’s are included cells)
and can be directly supplied to the w argument in the BPI funtion
instead of using radius and unit arguments.
annulus_window(radius = c(4,6), unit = "cell")## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
## [1,] NA NA NA NA NA NA 1 NA NA NA NA NA NA
## [2,] NA NA NA 1 1 1 1 1 1 1 NA NA NA
## [3,] NA NA 1 1 1 1 1 1 1 1 1 NA NA
## [4,] NA 1 1 1 NA NA NA NA NA 1 1 1 NA
## [5,] NA 1 1 NA NA NA NA NA NA NA 1 1 NA
## [6,] NA 1 1 NA NA NA NA NA NA NA 1 1 NA
## [7,] 1 1 1 NA NA NA NA NA NA NA 1 1 1
## [8,] NA 1 1 NA NA NA NA NA NA NA 1 1 NA
## [9,] NA 1 1 NA NA NA NA NA NA NA 1 1 NA
## [10,] NA 1 1 1 NA NA NA NA NA 1 1 1 NA
## [11,] NA NA 1 1 1 1 1 1 1 1 1 NA NA
## [12,] NA NA NA 1 1 1 1 1 1 1 NA NA NA
## [13,] NA NA NA NA NA NA 1 NA NA NA NA NA NA
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