pa_compute_vi: Compute vegetation indices from a zipped Sentinel 2 file

In pacu: Precision Agriculture Computational Utilities

Compute vegetation indices from a zipped Sentinel 2 file

Description

Compute vegetation indices from a zipped Sentinel 2 file.

Usage

pa_compute_vi(
  satellite.images,
  vi = c("ndvi", "ndre", "gcvi", "reci", "evi", "bsi", "other"),
  aoi = NULL,
  formula = NULL,
  check.clouds = FALSE,
  buffer.clouds = 100,
  downscale.to = NULL,
  pixel.res = c("default", "10m", "20m", "60m"),
  img.formats = c("jp2", "tif"),
  fun = function(x) mean(x, na.rm = TRUE),
  verbose = TRUE
)

Arguments

satellite.images	list of file paths to the Sentinel 2 zip files
vi	the vegetation index to be computed
aoi	NULL or an sf object used to crop the vegetation index raster to an area of interest
formula	an optional two-sided formula with the vegetation index name on the left side and the relationship between the bands on the right side. See example.
check.clouds	whether to check for clouds over the area of interest. If clouds are found, the function will skip cloudy images.
buffer.clouds	distance in meters around the area of interest within a cloud would be considered to interfere with the index calculation. This is useful to eliminate the effect of cloud shading from the analysis.
downscale.to	the resolution in meters to downscale the resolution of the vegetation index raster layer
pixel.res	pixel resolution used to compute the vegetation index. Can be one of 10m, 20m, 30m
img.formats	image formats to search for in the zipped file
fun	function to be applied to consolidate duplicated images
verbose	whether to display information on the progress of operations

Details

This is script that unzips the Sentinel 2 zipped file into a temporary folder, searches for the index-relevant bands, and then computes the index. If no ‘aoi’ is provided, the script will compute the vegetation index for the area covered by the image. The pre-specified vegetation indices are computed as follows:

BSI = \frac{(SWIR + RED) - (NIR + BLUE)}{(SWIR + RED) + (NIR + BLUE)}

EVI = \frac{2.5 \times (NIR - RED)}{(NIR + (6 \times RED) - (7.5 \times BLUE) - 1) }

GCVI = \frac{(NIR)}{(GREEN)} - 1

NDRE = \frac{(NIR - RED edge)}{(NIR + RED edge)}

NDVI = \frac{(NIR - RED)}{(NIR + RED)}

RECI = \frac{(NIR)}{(RED edge)} - 1

The user can also specify custom vegetation indices using the formula argument. The formula should be two-sided, with the left side naming the vegetation index and the right side defining the mathematical operations used to calculate the vegetation index. The bands should be specified as B01, B02, ..., B12.

An important detail of this function is that, if there are duplicated dates, the function will consolidate the data into a single raster layer. The default behavior is to average the layers that belong to the same date. This can be changed with the 'fun' argument.

Value

an object of class veg.index and stars

Author(s)

Caio dos Santos and Fernando Miguez

Examples

extd.dir <- system.file("extdata", package = "pacu")
## List of zipped Sentinel files in a directory
s2a.files <- list.files(extd.dir, '\\.zip', full.names = TRUE)
area.of.interest <- sf::st_read(file.path(extd.dir, 'cobs_a_aoi.shp'))

## computing ndvi
ndvi <- pa_compute_vi(satellite.images = s2a.files,
                            vi = 'ndvi',
                            aoi = area.of.interest,
                            check.clouds = TRUE)

## computing ndre
ndre <- pa_compute_vi(satellite.images = s2a.files,
                            vi = 'ndre',
                            aoi = area.of.interest,
                            check.clouds = TRUE)

## specifying a differente vegetation index, in this case, the 
## excess green index
egi <- pa_compute_vi(satellite.images = s2a.files,
                            vi = 'other',
                            formula = EGI ~ (2 * B03) - B02 - B04,
                            aoi = area.of.interest,
                            check.clouds = TRUE)

pacu documentation built on June 8, 2025, 10:44 a.m.