R/disturbanceMetrics.R
disturbanceMetrics.RdCalculate the predictors described in Table 52 of Environment Canada (2011) Scientific Assessment to Inform the Identification of Critical Habitat for Woodland Caribou (Rangifer tarandus caribou), Boreal Population, in Canada:2011 Update. Ottawa, Ontario.The variables calculated by this function include:
Fire: % fire
Anthro: % non-overlapping anthropogenic disturbance.
Total_dist: Percent total non-overlapping fire and anthropogenic disturbance.
fire_excl_anthro: % fire not overlapping with anthropogenic disturbance.
disturbanceMetrics(
landCover = NULL,
linFeat = NULL,
projectPoly = NULL,
isPercent = TRUE,
...
)Environment Canada. 2011. Scientific Assessment to Inform the Identification of Critical Habitat for Woodland Caribou (Rangifer tarandus caribou), Boreal Population, in Canada:2011 Update. Ottawa, Ontario.
filename, SpatRaster or RasterLayer. 0 and NA values are assumed to be water and omitted from the tabulated area. Note landCover is also used to define the input grid, so must be provided even if all values are 1.
filename, SpatRaster, RasterLayer, sf object or a list of these that will be combined. Linear features.
filename or sf object. Polygons defining range boundaries.
logical. Should the results be returned as a percentage?
optional arguments:
natDist: filename, SpatRaster or RasterLayer. Presence or absence of natural disturbance, primarily by fire. Should include 40 years cumulative disturbance.
anthroDist: filename, SpatRaster or RasterLayer. Anthropogenic disturbance including harvest. This can have an effect on any type of landcover except water. Should include 40 years cumulative disturbance.
padProjPoly: logical. Should the area around the projectPoly be
used to avoid edge effects? If FALSE, the default, only data from inside the
projectPoly is used. If TRUE then projectPoly is buffered and
the other variables are clipped to the extent of the buffered area. Results
are always clipped to the original projectPoly. It is ideal to set
this to TRUE and provide a dataset that is larger than the
projectPoly to avoid edge effects.
padFocal: logical. This value is passed to the pad argument in
terra::focal, if it is FALSE then cells near the edge will return
NA, if it is TRUE a value will be returned for each cell that assumes cells
outside the input data are 0 for all resource types. This is not a good
assumption and should be used with caution.
bufferWidth: number. Width of buffer applied to anthropogenic disturbance in metres. Default is 500.
linBuffMethod: character. The method used to buffer linear features if they are supplied as sf lines. The default is "raster" in which case they are rasterized and then buffered using a moving window method. If "sf" then the lines are buffered with st_buffer and then rasterized. Either way points are included in the raster output.
saveOutput: character. The filename to save the raster of binary disturbances with buffered anthropogenic disturbance. Note this will overwrite existing files with the same name. The .grd format is recommended because it will preserve layer names when the file is reloaded.
preppedData: list. A list containing pre-prepared input data sets. If
not NULL then data checks will be skipped. Names must match argument names
except that landCover should be called refRast and
projectPoly should be called projectPolyOrig
See loadSpatialInputs().
A DisturbanceMetrics Object see DisturbanceMetrics-class()
Note assume natDist and anthroDist include 40 years of cumulative disturbance.
Note that locations where landCover is NA or 0 are omitted from the tabulated
area. Missing layers are omitted from the output, not interpreted as 0
disturbance. To update an existing DisturbanceMetrics object with new data see
updateDisturbance().
DisturbanceMetrics-class() for information on the object
returned and updateDisturbance() for updating an existing
DisturbanceMetrics object.
Functions for calculating disturbance:
DisturbanceMetrics-class,
reclassDist(),
results(),
updateDisturbance()
# create example rasters
lc <- terra::rast(nrows = 10, ncols = 10, xmin = 0, xmax = 10, ymin = 0,
ymax = 10, crs = "EPSG:5070")
nd <- lc
nd[1:3, 1:3] <- 1
ad <- lc
ad[3:5, 3:5] <- 1
lc[] <- 1
# create sf objects
lf <- sf::st_as_sf(sf::st_sfc(list(sf::st_linestring(matrix(c(0, 0, 10, 10),
ncol = 2, byrow = TRUE))),
crs = 5070))
projPol <- sf::st_sf(sf::st_as_sfc(sf::st_bbox(ad)))
# calculate disturbance
disturbanceMetrics(landCover = lc,
linFeat = lf,
natDist = nd,
anthroDist = ad,
projectPoly = projPol,
padFocal = TRUE,
bufferWidth = 1)
#> buffering anthropogenic disturbance
#> calculating disturbance metrics
#> An object of class "DisturbanceMetrics"
#> Slot "landCover":
#> class : SpatRaster
#> dimensions : 10, 10, 1 (nrow, ncol, nlyr)
#> resolution : 1, 1 (x, y)
#> extent : 0, 10, 0, 10 (xmin, xmax, ymin, ymax)
#> coord. ref. : NAD83 / Conus Albers (EPSG:5070)
#> source(s) : memory
#> name : lyr.1
#> min value : 1
#> max value : 1
#>
#> Slot "natDist":
#> class : SpatRaster
#> dimensions : 10, 10, 1 (nrow, ncol, nlyr)
#> resolution : 1, 1 (x, y)
#> extent : 0, 10, 0, 10 (xmin, xmax, ymin, ymax)
#> coord. ref. : NAD83 / Conus Albers (EPSG:5070)
#> source(s) : memory
#> name : lyr.1
#> min value : 1
#> max value : 1
#>
#> Slot "anthroDist":
#> class : SpatRaster
#> dimensions : 10, 10, 1 (nrow, ncol, nlyr)
#> resolution : 1, 1 (x, y)
#> extent : 0, 10, 0, 10 (xmin, xmax, ymin, ymax)
#> coord. ref. : NAD83 / Conus Albers (EPSG:5070)
#> source(s) : memory
#> name : lyr.1
#> min value : 1
#> max value : 1
#>
#> Slot "linFeat":
#> [[1]]
#> Simple feature collection with 1 feature and 0 fields
#> Geometry type: LINESTRING
#> Dimension: XY
#> Bounding box: xmin: 0 ymin: 0 xmax: 10 ymax: 10
#> Projected CRS: NAD83 / Conus Albers
#> x
#> 1 LINESTRING (0 0, 10 10)
#>
#>
#> Slot "projectPoly":
#> Simple feature collection with 1 feature and 0 fields
#> Geometry type: POLYGON
#> Dimension: XY
#> Bounding box: xmin: 0 ymin: 0 xmax: 10 ymax: 10
#> Projected CRS: NAD83 / Conus Albers
#> sf..st_as_sfc.sf..st_bbox.ad..
#> 1 POLYGON ((0 0, 10 0, 10 10,...
#>
#> Slot "processedData":
#> class : SpatRaster
#> dimensions : 10, 10, 4 (nrow, ncol, nlyr)
#> resolution : 1, 1 (x, y)
#> extent : 0, 10, 0, 10 (xmin, xmax, ymin, ymax)
#> coord. ref. : NAD83 / Conus Albers (EPSG:5070)
#> source(s) : memory
#> names : Anthro, Fire, Total_dist, fire_excl_anthro
#> min values : 0, 0, 0, 0
#> max values : 1, 1, 1, 1
#>
#> Slot "disturbanceMetrics":
#> zone Anthro Fire Total_dist fire_excl_anthro
#> 1 1 52 9 58 6
#>
#> Slot "attributes":
#> $bufferWidth
#> [1] 1
#>
#> $padProjPoly
#> [1] FALSE
#>
#> $padFocal
#> [1] TRUE
#>
#>