scaleraster {movegroup}

Scales individual utilization distribution rasters and volume area estimates

Description

Scales individual-level utilization distribution (UD) rasters from 0 to 1 to facilitate interpretation as relative intensity of utilization (as opposed to absolute), making comparisons across individuals and interpretations at the group level more straightforward. Subsequently, scaled individual-level rasters are aggregated to create a single group-level UD raster. See www.GitHub.com/SimonDedman/movegroup for issues, feedback, and development suggestions. There is an option to account for bias in acoustic receiver array spatial representation (see Details).

Usage

scaleraster(
  path = NULL,
  pathsubsets = NULL,
  pattern = ".asc",
  weighting = 1,
  format = "ascii",
  datatype = "FLT4S",
  bylayer = TRUE,
  overwrite = TRUE,
  scalefolder = "Scaled",
  scaledweightedname = "All_Rasters_Scaled_Weighted",
  crsloc = NULL,
  returnObj = FALSE
)

Arguments

path

Path to directory where the individual-level UDs are saved. Likely the same as savedir from movegroup. Default NULL.

pathsubsets

Path to parent directory that contains all UDs across spatial groups or subsets, i.e. if you ran movegroup multiple times for different areas in a connected system, this would be the parent folder within which all the movegroup savedir's are located. Default NULL.

pattern

Extension pattern used to read in all UDs in directory and pathsubsets directory. Default ".asc".

weighting

Addresses unbalanced receiver array design after receivers have first been partitioned into regions, and group-level UDs estimated per region. Numeric. Weights area-specific scaled group-level UD raster by value. This then means that estimated scaled individual-level volume areas also become weighted. Default is 1 for no weighting.

format

Character. Output file type for raster::writeRaster param format. Default "ascii".

datatype

Character. Data type for writing values to disk for raster::writeRaster param Datatype. Default "FLT4S".

bylayer

For raster::writeRaster param bylayer. Default TRUE.

overwrite

For raster::writeRaster param overwrite. Default TRUE.

scalefolder

Folder to save outputs to. Default "Scaled".

scaledweightedname

Name of chunk for scaled and weighted output rasters. Default "All_Rasters_Scaled_Weighted".

crsloc

Location of saved CRS Rds file from movegroup.R. Should be same as path. Default NULL.

returnObj

Logical. Return the scaled object to the parent environment? Default FALSE.

Details

Step 1. Scale rasters. Individual-level UD rasters are scaled from 0 to 1 by dividing each raster by the maximum probability density value occurring within the raster set.

Step 2. Aggregate into a group-level raster. Scaled individual-level rasters are summed to create a single group-level UD raster.

Step 3. Re-scale to 0 to 1. The group-level raster is divided by its own maximum value.

Step 4. Weight raster (optional). The scaled group-level UD raster is divided by the specified weighting factor(s). Note that this is only useful if you want to account for an unbalanced listening station (e.g., acoustic receivers) array and have split up the study site and receivers in regions, and have run the movegroup() for each regional data set separately. See van Zinnicq Bergmann et al. 2022 (https://doi.org/10.1016/j.biocon.2022.109469) for example. If not applicable, choose a value of "1".

Step 5. Standardize raster. Standardize the potentially weighted and scaled group-level UD raster so that its values sum to 1.

Step 6. Export as latlon CRS. Change crs to latlon for plotting and calculation purposes, save file, continue.

Step 7. Estimate 50 and 95pct contour volume areas. For each scaled individual-level UD raster, estimate 50 and 95pct contour volume areas, as well as their mean and standard deviation. Additionally, the 50 and 95pct volume area is estimated for the group-level UD raster.

Step 8. Export the projected-CRS group-level raster.

Errors and their origins:

1. Error in (function (cond): error in evaluating the argument 'x' in selecting a method for function 'res': subscript out of bounds. Probably path can't find any files of type=pattern: check you used a terminal slash in savedir in movegroup, and that path has files of type=pattern.

2. Error in if (substr(x = pathsubsets, start = nchar(pathsubsets), stop = nchar(pathsubsets))==: argument is of length zero: pathsubsets is wrong. Try setting to same as path. NULL does this.

3. Error in gzfile(file, "rb"): cannot open compressed file 'CRS.Rds', probable reason 'No such file or directory': crsloc is wrong. Try setting to same as path. NULL does this.

4. In min/max: No non-missing arguments to min; returning Inf: likely not enough memory, increase rasterResolution value.

Value

Scaled and weighted individual-level and group-level utilization distributions saved as rasters. Scaled 50 and 95pct contour volume area estimates (in km2) for individuals and the group , saved in .csv format. Latlon raster.

Author(s)

Simon Dedman, [e-mail]

Maurits van Zinnicq Bergmann, [e-mail]

Examples

# Having run the movegroup function example:
scaleraster(path = tempdir())

# Weighted by number of positions per ID, fewer locations = lower Weighting value = higher final 
# UD values after dividing by Weighting. This scales all IDs up to match the group max.
Weighting <- TracksCleaned |>
 dplyr::group_by(Shark) |>
 dplyr::summarise(N = n()) |> 
 dplyr::filter(N > 23) |> 
 dplyr::mutate(N = N / max(N, na.rm = TRUE)) |> 
 dplyr::pull(N)
 
 scaleraster(path = tempdir(), weighting = Weighting)