extract_raster_stack: Extracts data values from a raster stack or raster birck,...

In allisonglider/seabiRds: Prepares biologging data for analysis and upload to the lab database

Extracts data values from a raster stack or raster birck, where layers correpond to a time series

Description

Extracts data values from a raster stack or raster birck, where layers correpond to a time series

Usage

extract_raster_stack(raster_stack, locations, names_var)

Arguments

raster_stack	A stack or raster brick of environmental data, created using the 'raster' package
locations	A spatial points dataframe or simple features multipoints object.
names_var	A character string giving the name of the variable in locations that matches the layer names in raste_stack.

Details

This function extends the raster::extract() function to extract data from a RasterStack or RasterBrick. A stack or brick has a third dimension of raster layers, in addition to the x-y coordinates.

To use this function convert your spatial point location data to a spatial object class, either a SpatialPointsDataFrame (sp package) or a Simple Features object (sf package).

Add a new column to your spatial object that matches the layer names in your raster data. Usually, the raster stack/brick layer names are based on dates and you can create a matching column using base::strftime() to make a new vector with a specifid format.

The function will loop through layers in your raster file extracting environmental data for all locations that match that layer name.

Value

A vector of values extracted from the raster_stack, of the same length as the number of rows in locations.

Examples

# Create example raster stack
r <- expand.grid(
  lon = seq(-10, 10, 1),
  lat = seq(-10, 10, 1),
  X2020.01.01 = 1,
  X2020.01.02 = 2
)
r <- raster::rasterFromXYZ(xyz = r, crs = '+proj=longlat')
r

# Create random location data
locs <- data.frame(
  lon = runif(20, -9, 9),
  lat = runif(20, -9, 9),
  time = seq.POSIXt(as.POSIXct('2020-01-01 12:00:00'), as.POSIXct('2020-01-02 12:00:00'),
                    length.out = 20)
)

# Add column with of values with names that match layers in stack
names(r)
locs$rn <- strftime(locs$time, 'X%Y.%m.%d')
intersect(locs$rn, names(r))

# Extract values
locs <- SpatialPointsDataFrame(coords = locs[,c('lon','lat')],
                               data = locs, proj4string = CRS('+proj=longlat'))

extract_raster_stack(raster_stack = r, locations = locs, names_var = 'rn')

allisonglider/seabiRds documentation built on Feb. 14, 2025, 7:37 a.m.