dynamic_proj_covariates: Combine explanatory variable rasters into covariates for each...

In dynamicSDM: Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution

Combine explanatory variable rasters into covariates for each projection date.

Description

Explanatory variable rasters are imported, resampled to a given spatial resolution and extent, stacked and then exported as a covariate data frame or raster stack for each projection date.

Usage

dynamic_proj_covariates(
  dates,
  varnames,
  drive.folder,
  user.email,
  local.directory,
  spatial.ext,
  spatial.mask,
  spatial.res.degrees,
  resample.method,
  cov.file.type,
  prj = "+proj=longlat +datum=WGS84",
  cov.prj,
  save.directory,
  save.drive.folder,
  static.rasters,
  static.varnames,
  static.resample.method,
  static.moving.window.matrix,
  static.GEE.math.fun
)

Arguments

dates	a character string, vector of dates in format "YYYY-MM-DD".
varnames	a character string, the unique names for each explanatory variable.
drive.folder	optional; a character string or vector, Google Drive folder or folders to read projection covariate rasters from. Folder must be uniquely named within Google Drive. Do not provide path.
user.email	optional; a character string, user email for initialising Google Drive. Required if drive.folder or save.drive.folder used.
local.directory	optional; a character string or vector, path to local directory or directories to read projection covariate rasters from.
spatial.ext	optional; the spatial extent to crop explanatory variable rasters to. Object of class SpatExtent, SpatRaster, an sf polygon or numeric vector listing xmin, xmax, ymin and ymax in order.
spatial.mask	an object of class Raster, sf or Spatial, representing a mask in which NA cells in the mask layer are removed from the projection covariates.
spatial.res.degrees	optional; a numeric value, the spatial resolution in degrees for projection rasters to be resampled to. Required if spatial.ext given.
resample.method	a character string or vector length of varnames, specifying resampling method to use. One of near and bilinear. See details for more information.
cov.file.type	a character string, the type of file to export projection covariates as. One of: tif (SpatRaster with multiple layers) or csv(data frame).
prj	a character string, the coordinate reference system desired for projection covariates. Default is "+proj=longlat +datum=WGS84".
cov.prj	a character string, the coordinate reference system desired for output projection covariates. Default is assumed to be the same as prj.
save.directory	optional; a character string, path to local directory to save projection covariates to.
save.drive.folder	optional; a character string, Google Drive folder to save projection covariates to. Folder must be uniquely named within Google Drive. Do not provide path.
static.rasters	a RasterStack of one or more rasters to be added to covariates for each date.
static.varnames	a character string or vector, the unique names for each explanatory variable in order of rasters in static.raster stack.
static.resample.method	a character string or vector length of static.varnames, specifying resampling method to use on static rasters provided. One of near and bilinear. See details for more information..
static.moving.window.matrix	optional; a matrix of weights with an odd number of sides, representing the spatial neighbourhood of cells (“moving window”) to calculate GEE.math.fun across from record co-ordinate. See details for more information.
static.GEE.math.fun	optional; a character string, the mathematical function to compute across the specified spatial matrix for each cell in spatial.ext

Value

Exports combined covariates in "csv" or "tif" file for each projection date to the local directory or Google Drive folder.

Input variable rasters

For each projection date, the rasters for each explanatory variable are imported from a local directory or Google Drive folder.

Such rasters should be uniquely named "tif" files within the directory or drive folder and contain the variable name (as stated in varnames) and projection date in format "YYYY-MM-DD". If more than one “tif” file in the Google Drive folder or local directory matches the projection date and explanatory variable name, then the function will error.

Processing rasters

If required, rasters are cropped and resampled to the same spatial extent and resolution. If spatial.mask is given, then cells with NA in this mask layer are removed from the returned projection covariates. See terra::mask() in R package terra for details (Hijmans et al., 2022).

Rasters are then stacked and reprojected if cov.prj is different to prj.

Note: if explanatory variable rasters are not of the same spatial resolution and extent, then the function will error. Resample methods (resample.method) include:

• near: Each cell acquires the value of its nearest neighbour cell in the original raster. This is typically used for categorical variables.

• bilinear: the distance-weighted average of the four nearest cells are used to estimate a new cell value. This is typically used for continuous variables.

If only one resample.method is given, but these are more than one explanatory variables, the same resample.method is used for all.

Output covariates

The raster stacks are then converted into data frames or remain as raster stacks depending on cov.file.type. Column names or raster layer names will be the unique explanatory variable names (varnames). These are exported to the local directory or Google Drive folder with file names containing the relevant projection date in "YYYY-MM-DD" format.

Google Drive compatibility

If drive.folder or save.drive.folder given, please ensure the folder name is unique within your Google Drive. Do not provide the path if the folder is nested within others.

If one of drive.folder or save.drive.folder are used then user.email is required to access the appropriate Google Drive user account. This requires users to have installed R package googledrive and initialised Google Drive with valid log-in credentials. Please follow instructions on https://googledrive.tidyverse.org/.

Static rasters

If static datasets are to be added into the dynamic projection covariates, then five arguments are available to specify their inclusion.

Please provide the static rasters in RasterStack format, specifying any spatial buffering needed (using static.moving.window.matrix and static.GEE.math.fun as described below).

The resample method or methods for rasters within the static raster stack need to be specified too using static.resample.method. Please also provide static.varnames to name the static variables in the covariate data exported.

#' # Spatial buffering of static rasters (optional)

Using the focal function from terra R package (Hijmans et al., 2022), GEE.math.fun is calculated across the spatial buffer area from the record co-ordinate. The spatial buffer area used is specified by the argument moving.window.matrix, which dictates the neighbourhood of cells surrounding the cell containing the occurrence record to include in this calculation.

See function get_moving_window() to generate appropriate moving.window.matrix.

Mathematical function

GEE.math.fun specifies the mathematical function to be calculated over the spatial buffered area and temporal period. Options are limited to Google Earth Engine ImageCollection Reducer functions (https://developers.google.com/earth-engine/apidocs/) for which an analogous R function is available. This includes: "allNonZero","anyNonZero", "count", "first","firstNonNull", "last", "lastNonNull", "max","mean", "median","min", "mode","product", "sampleStdDev", "sampleVariance", "stdDev", "sum" and "variance".

References

Hijmans, R.J., Bivand, R., Forner, K., Ooms, J., Pebesma, E. and Sumner, M.D., 2022. Package 'terra'. Maintainer: Vienna, Austria.

Examples

data("sample_extent_data")

# Set extraction variables
projectiondates <- dynamic_proj_dates("2018-01-01", "2018-12-01", interval = 3,interval.level =
"month")
variablenames <- c("eight_sum_prec", "year_sum_prec")
spatial.res.metres <- 500
cov_resolution <- 0.05

# Get Google Drive email
user.email<-as.character(gargle::gargle_oauth_sitrep()$email)

extract_dynamic_raster(dates=projectiondates,
                      datasetname = "UCSB-CHG/CHIRPS/DAILY",
                      bandname="precipitation",
                      user.email = user.email,
                      spatial.res.metres = spatial.res.metres,
                      GEE.math.fun = "sum",
                      temporal.direction = "prior",
                      temporal.res = 56,
                      spatial.ext = sample_extent_data,
                      varname = variablenames[1],
                      save.directory = tempdir())


extract_dynamic_raster(dates=projectiondates,
                     datasetname = "UCSB-CHG/CHIRPS/DAILY",
                     bandname="precipitation",
                     user.email = user.email,
                     spatial.res.metres = spatial.res.metres,
                     GEE.math.fun = "sum",
                     temporal.direction = "prior",
                     temporal.res = 364,
                     spatial.ext = sample_extent_data,
                     varname = variablenames[2],
                     save.directory = tempdir())

dynamic_proj_covariates(dates = projectiondates,
                       varnames = variablenames,
                       local.directory = tempdir(),
                       spatial.ext = sample_extent_data,
                       spatial.mask = sample_extent_data,
                       spatial.res.degrees = cov_resolution,
                       resample.method = c("bilinear","bilinear"),
                       cov.file.type = "csv",
                       prj="+proj=longlat +datum=WGS84",
                       save.directory = tempdir())

dynamicSDM documentation built on June 28, 2024, 5:08 p.m.