load_covariates: Load covariates

Description

Load covariates

Usage

load_covariates(
  directory,
  covariates_table,
  id_raster,
  year = NULL,
  file_format = "tif",
  add_intercept = FALSE,
  check_previous_years = 10
)

Value

A named list of formatted covariates. Each list item is a terra::SpatRaster

with one layer and the same dimensions as the id_raster

Arguments

directory

Directory containing all covariate sub-directories

covariates_table

data.frame containing at least the following fields:

'covariate': (character): Name of the covariate
'annual': (logical) Does the covariate vary by year? If so, look for the year in the name of the file.
'transform': (character) Name of a function to use to transform the covariate. Common options include 'identity' (no transformation), 'sqrt', 'abs', and 'log1p'
'normalize': (logical) Should the covariate be rescaled to have mean 0 and standard deviation 1 across all pixels in the study area? Generally should be set to TRUE for predictive covariates.

id_raster

terra::SpatRaster with non-NA pixels delineating the extent of the study area

year

(numeric, default NULL) Year of data to for time-varying covariates. If NULL, the default, uses the current year.

file_format

(character, default 'tif') File format for the raster covariate data. Used to search for the input file within the proper containing folder.

add_intercept

(logical, default FALSE) Should a covariate called "intercept", a raster object with 1s in all required cells, be placed at the start of the returned covariates list?

check_previous_years

(integer > 0, default 10) If annual data is not found in this year, how many previous years should be checked? If 0, will not check any previous years.

Details

Load a list of covariates from a specified directory structure