Package 'grec'

Sea Surface Chlorophyll Data

Description

Surface chlorophyll maps downloaded from ERDDAP for running examples with grec functions.

Usage

chl

Format

A list with chlorophyll information from February to April of Aqua MODIS source.

References

ERDDAP website: https://coastwatch.pfeg.noaa.gov/erddap

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Default color palette most using on environmental representations.

Description

Vector with 2000 colors generated from tim.colors function.

Usage

colPalette

Format

A vector of 2000 colors in RGB format.

References

tim.colors from fields package

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Apply gradient-based methodologies to environmental data

Description

This function empowers users to analyze data from various sources, including numeric matrix, arrays, XYZ-lists, SpatRasters, or RasterLayers*, by applying gradient-seeking methodologies.

Usage

detectFronts(...)

Arguments

...	Same arguments than getGradients.

Details

Since version 1.6.0, this function has been entirely replaced by getGradients. As of version 2.0.0, detectFronts will no longer be available.

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Apply gradient-based methodologies to environmental data

Description

This function empowers users to analyze data from various sources, including numeric matrix, arrays, XYZ-lists, SpatRasters, or RasterLayers*, by applying gradient-seeking methodologies.

Usage

## S3 method for class 'RasterLayer'
getGradients(x, method = "BelkinOReilly2009", intermediate = FALSE, ...)

## S3 method for class 'SpatRaster'
getGradients(x, method = "BelkinOReilly2009", intermediate = FALSE, ...)

## S3 method for class 'array'
getGradients(x, method = "BelkinOReilly2009", intermediate = FALSE, ...)

## Default S3 method:
getGradients(
  x,
  method = "BelkinOReilly2009",
  intermediate = FALSE,
  ConvolNormalization = FALSE,
  ...
)

getGradients(
  x,
  method = c("BelkinOReilly2009", "median_filter", "Agenbag2003-1", "Agenbag2003-2"),
  intermediate = FALSE,
  ConvolNormalization = FALSE,
  ...
)

## S3 method for class 'list'
getGradients(x, method = "BelkinOReilly2009", intermediate = FALSE, ...)

## S3 method for class 'matrix'
getGradients(x, method = "BelkinOReilly2009", intermediate = FALSE, ...)

Arguments

x	An object of class matrix, array, XYZ list, SpatRaster or RasterLayer*. See 'Details.'
method	character string indicating the method that will be used. For the available methods, see 'Details'.
intermediate	logical indicating whether to get the intermediate matrices (TRUE) or just the final one (FALSE).
...	Extra arguments that will depend on the selected method. See Details.
ConvolNormalization	logical indicating if convolutions will perform a previous normalization (FALSE by default). See Details.

Details

The grec package collaborates with the imagine package to execute and apply image processing algorithms for identifying oceanic gradients. imagine furnishes the foundational algorithms, developed efficiently utilizing C++ tools. Conversely, grec oversees the utilization of these coding instruments in the context of oceanic gradient recognition and handles the development of input/output methods. In this context, the available methods offered by grec are contingent on the installed grec-imagine versions.

(*) Due to the deprecation of the raster package, grec will not be supporting the use of RasterLayer in future versions. Instead, grec will be incorporating support for SpatRaster-class, a more recent and actively developed method for working with raster data. This change will take effect as soon as raster is removed from CRAN.

Until the current version, grec performs four methods:

1. BelkinOReilly2009 (default): Based on Belkin & O'Reilly (2009) article, it uses a Contextual Median Filter (CMF) for smoothing the original data before the applying of Sobel filters.

2. median_filter: it uses a typical median filter (MF) for smoothing the original data. It also allows the user to change the window size for median filter (3 as default).

3. Agenbag2003-1: Performs method 1 described on Agenbag et al. (2003) paper, based on the equation:

   $SST_{grad}=\sqrt{(T_{i+1}-T_{i-1})^2 +(T_{j+1}-T_{j-1})^2}$

4. Agenbag2003-2: Performs method 2 described on Agenbag et al. (2003) paper, calculating the the standard deviation of the 3x3 neighbor area for each pixel.

The input data x can be represented in various formats to accommodate different data sources. It can be provided as a single numeric matrix extracted from an environmental map. Alternatively, it can be represented as a three-dimensional XYZ list, where X contains a vector of longitudes, Y contains a vector of latitudes, and Z is a matrix of dimensions length(x$X) x length(x$Y). Additionally, it can be specified as an array, SpatRaster, or RasterLayer* object. If x is an array, it must have three dimensions: longitude (lon), latitude (lat), and time. It is not mandatory to define the dimnames. The output will maintain all the attributes of the input data.

... allows the (advanced) users to modify some aspects of filter application. Depending on the selected methodology, some parameters can be modified:

times

numeric. How many times do you want to apply the filtering method?

kernelValues

A numeric vector that will be used for convolution to detect vertical and horizontal gradients.

radius

numeric. If median-filter method was selected, it allows to change the window size of the filter.

Normalization is a standard practice in convolution to maintain the range of output values consistent with the input data. This is achieved by dividing the convolution output by the absolute value of the kernel. While normalization is recommended to ensure consistent interpretation of results, it is disabled by default and can be enabled by setting the ConvolNormalization parameter to TRUE.

Finally, Belkin & O'Reilly's work suggests applying a logarithmic transformation to the gradient output. This step is not enabled by default, as it is primarily intended for chlorophyll data. Users are free to apply the transformation manually if it suits their specific needs.

Value

The output will preserve the input class.

References

Belkin, I. M., & O'Reilly, J. E. (2009). An algorithm for oceanic front detection in chlorophyll and SST satellite imagery. Journal of Marine Systems, 78(3), 319-326 (doi:10.1016/j.jmarsys.2008.11.018).

Agenbag, J.J., A.J. Richardson, H. Demarcq, P. Freon, S. Weeks, and F.A. Shillington. "Estimating Environmental Preferences of South African Pelagic Fish Species Using Catch Size- and Remote Sensing Data". Progress in Oceanography 59, No 2-3 (October 2003): 275-300. (doi:10.1016/j.pocean.2003.07.004).

Examples

data(sst)
exampleSSTData <- list(x = sst$longitude,
                       y = sst$latitude,
                       z = sst$sst[,,1])

data(chl)
exampleChlData <- list(x = chl$longitude,
                       y = chl$latitude,
                       z = chl$chlorophyll[,,1])

# Simple application (over a XYZ list)
out_sst <- getGradients(x = exampleSSTData)
out_chl <- getGradients(x = exampleChlData)

# External transformation for chl data
out_chl$z <- log10(out_chl$z)

par(mfrow = c(2, 2), mar = rep(0, 4), oma = rep(0, 4))

image(exampleSSTData, col = colPalette, axes = FALSE)
mtext(text = "Original SST", side = 3, line = -2, adj = 0.99, cex = 1.2)

image(out_sst, col = colPalette, axes = FALSE)
mtext(text = "SST gradient", side = 3, line = -2, adj = 0.99, cex = 1.2)

image(exampleChlData, col = colPalette, axes = FALSE)
mtext(text = "Original Chlorophyll", side = 3, line = -2, adj = 0.99, cex = 1.2)

image(out_chl, col = colPalette, axes = FALSE)
mtext(text = "Chlorophyll gradient\n(log scale)", side = 3, line = -4, adj = 0.99,
      cex = 1.2)

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Sea Surface Temperature Data

Description

SST maps downloaded from ERDDAP for running examples with grec functions.

Usage

sst

Format

A list with SST information from February to April of Aqua MODIS source.

References

ERDDAP website: https://coastwatch.pfeg.noaa.gov/erddap

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