Summarize total habitat scores

Calculate the sum of the predicted presence/absence or probability of presence from species distribution models corresponding to a set of landscape rasters.

Usage

sum_habitat(
  pathin,
  SDM = NULL,
  landscape_name = NULL,
  zones = NULL,
  subtype = NULL,
  rollup = TRUE,
  key = NULL,
  scale = NULL
)

Arguments

pathin

Character string defining the filepath to the highest-level directory containing the predicted presence/absence or probability of presence from species distribution models, such as those created from running fit_SDM() or transform_SDM()

SDM, landscape_name

Optional character strings defining the subdirectories within pathin for which habitat should be summarized; see Details; SDM must be one of "riparian", "waterbird_fall", or "waterbird_win".

zones

Optional SpatRaster or character string giving the filepath to a raster encoding zones within which pixel values should be summarized

subtype

Optional character string appended to the field METRIC_SUBTYPE, such as for distinguishing probability of presence from presence/absence

rollup

Logical; If TRUE (default), summarize total habitat across all species/groups by set of SDMs

key

Optional tibble, dataframe, or character string defining the filepath passed to readr::read_csv(), used to translate the individual species names as encoded in the file names in pathin to readable METRIC names in the output table; see Details

scale

Optional value by which to scale the results; see Details

Value

tibble

Details

By default, this function will calculate the sum of all pixel values in each raster found in pathin and any subdirectories, to efficiently process multiple rasters located in the pathin directory at once. The file structure within pathin is used to infer the name of the corresponding SDM and landscape_name. However, SDM or both SDM and landscape_name can be optionally specified to only process a subset of these.

If provided, key should refer to a tibble, dataframe, or filepath to a CSV containing the fields spp and label, used for converting the filenames of the rasters within pathin to a more readable label, which will be renamed METRIC in the final output.

If provided, the sum of all pixel values will be multiplied by scale. For example, to rescale the total in terms of the total area, enter the area of each pixel.

See also

fit_SDM(), transform_SDM()

Examples

# See vignette