Spatial data for western fence lizards in Yosemite

Description

A dataset containing a RasterStack with two RasterLayer objects, a digital elevation model (DEM) for part of Yosemite National Park (USA) and a species distribution model (SDM) for the western fence lizard (Sceloporus occidentalis).

Usage

data(Yosemite)

Format

A RasterStack

Examples

data(Yosemite)

Topographic distances and paths

Description

Calculates shortest topographic distances and paths

Usage

topoDist(DEM, pts, directions = 8, paths = FALSE, zweight = 1)

Arguments

Details

If paths = FALSE, the function will return a matrix of pairwise topographic distances between the specified points. If paths = TRUE, the function will return a list with two items: (1) the matrix of pairwise topographic distances, and (2) a SpatialLines object containing the topographic paths.

Value

Matrix of topographic distances (if paths = FALSE), or a list containing a matrix of topographic distances and the topographic paths as an object of class SpatialLines (if paths = TRUE).

Examples

xy <- matrix(ncol = 2, byrow = TRUE,
   c(-119.5566, 37.72474,
   -119.4718, 37.76078))
topoDist(Yosemite$DEM, xy, paths = TRUE)

topoDistance: A package for calculating topographic paths and distances

Description

The topoDistance package provides functions for calculating topographic distances and identifying and plotting topographic paths. Topographic distances can be calculated along shortest topographic paths or topographic least cost paths. Functions can map topographic paths on colored or hillshade maps and plot topographic cross sections (elevation profiles) for the paths.

Details

Unlike the topographically-corrected distances calculated by some GIS software, which just adjust for elevational changes along a straight-line path between points, topoDistance calculates the distance along the shortest topographic path between points, which is more likely to realistically reflect biological movement on a topographically complex landscape.

Topographic distances are calculated as the hypotenuse of the horizontal and vertical distances between cells on an elevation raster. These distances are assignd to the weights of vertices between the nodes for each cell on a landscape graph, and functions from the gdistance and igraph packages are used to find the shortest path between nodes. For topographic least cost paths, resistance distance weights are multiplied by the topographic distance weights to get topographically corrected least cost path distances.

Topographic least cost paths and distances

Description

Calculates topographic least cost distances and paths

Usage

topoLCP(DEM, costSurface, pts, directions = 8, paths = FALSE, zweight = 1)

Arguments

Details

The values of the raster for costSurface should be conductance values rather than resistance values. These can be calculating by taking the inverse of resistance values.

Value

Matrix of topographic distances (if paths = FALSE), or a list containing a matrix of topographic distances and the topographic paths as an object of class SpatialLines (if paths = TRUE).

Examples

xy <- matrix(ncol = 2, byrow = TRUE,
   c(-119.5566, 37.72474,
   -119.4718, 37.76078))
topoLCP(Yosemite$DEM, Yosemite$SDM, xy, paths = TRUE)

Map of topographic paths

Description

Plots a map of topographic paths on a landscape layer

Usage

topoPathMap(
  DEM,
  pts,
  topoPaths,
  type = "hillshade",
  costSurface = NULL,
  costColors = NULL,
  pathWidth = 2,
  pathColor = "darkred",
  alpha = 0.65,
  angle = 45,
  direction = 0,
  cex = 2,
  bg = "gray",
  col = "black",
  pch = 21,
  ...
)

Arguments

Details

The objects supplied for the DEM and pts arguments (and, optionally, costSurface) are generally those used to calculate the topographic paths using topoDist or topoLCP.

For the type argument, choosing "hillshade" will plot a shaded relief map, "terrain" will plot a map with terrain colors, and "topo" will plot a map with topo colors.

Optional arguments can be supplied to control the size (cex), shape (pch), and color (bg and col) of the points.

Value

Plot of topographic paths

Examples

xy <- matrix(ncol = 2, byrow = TRUE,
   c(-119.5566, 37.72474,
   -119.4718, 37.76078))
YosPaths <- topoDist(Yosemite$DEM, xy, paths = TRUE)
topoPathMap(Yosemite$DEM, xy, topoPaths = YosPaths)

Identify shortest topographic paths

Description

Identify shortest topographic paths

Usage

topoPaths(t.dist, pts)

Arguments

Details

This function identifies shortest topographic paths from a topographic TransitionLayer. It does not need to be called separately from the topoDist and topoLCP functions.

Value

An object of class SpatialLines

Examples

xy <- matrix(ncol = 2, byrow = TRUE,
   c(-119.5566, 37.72474,
   -119.4718, 37.76078))
xy <- sp::SpatialPoints(xy)
topoTL <- topoSurface(Yosemite$DEM)
topoPaths(topoTL, xy)

Elevation profiles of topographic paths

Description

Plots topographic cross sections (elevation profiles) of topographic paths

Usage

topoProfile(
  DEM,
  topoPaths,
  pts = 100,
  type = "base",
  singlePlot = FALSE,
  rows = NULL,
  cols = NULL,
  limits = NULL,
  legendx = "bottomright"
)

Arguments

Details

For the type argument, choosing "base" will use base R plotting, and choosing "plotly" will draw an interactive plot with the plotly package.

If rows, cols, or limits are not specified, the most even arrangement will be detected and used.

Value

Plot of elevation profiles

Examples

xy <- matrix(ncol = 2, byrow = TRUE,
   c(-119.5566, 37.7247,
     -119.4718, 37.7608))
YosPaths <- topoDist(Yosemite$DEM, xy, paths = TRUE)
topoProfile(Yosemite$DEM, topoPaths = YosPaths)

Topographic distance surface

Description

Generates a TransitionLayer object for topographic distance from a RasterLayer

Usage

topoSurface(DEM, conductance = TRUE, directions = 8, zweight = 1)

Arguments

Details

This function generates a TransitionLayer from a DEM, which is used by the topoDist and topoLCP functions. It does not need to be called separately from the topoDist and topoLCP functions.

Value

TransitionLayer

Examples

YosTL <- topoSurface(Yosemite$DEM)

Weighted topographic distances and paths

Description

Calculates weighted topographic distances and paths

Usage

topoWeightedDist(
  DEM,
  pts,
  directions = 8,
  paths = FALSE,
  hFunction = NULL,
  vFunction = NULL
)

Arguments

Details

The hFunction argument can be set to "exponential" or "linear" to use standard functions for the cost of aspect angle changes. If providing a custom function instead, the equation should be a function of one variable, angle (in radians). The vFunction argument can be set to "exponential" or "quadratic" to use standard functions for the cost of movement along an incline. If providing a custom function instead, The equation should be a function of one variable, slope. If paths = FALSE, the function will return a matrix of pairwise topographic distances between the specified points. If paths = TRUE, the function will return a list with two items: (1) the matrix of pairwise topographic distances, and (2) a SpatialLines object containing the topographic paths.

Value

Matrix of transport costs (if paths = FALSE), or a list containing a matrix of transport costs and paths as an object of class SpatialLines (if paths = TRUE).

Examples

xy <- matrix(ncol = 2, byrow = TRUE,
             c(-119.5566, 37.7247,
               -119.4718, 37.7608))
topoWeightedDist(Yosemite$DEM, xy, vFunction = "exponential")