grec

[G]radient-based [REC]ognition of Spatial Patterns in Environmental Data

Provides algorithms for detection of spatial patterns from oceanographic data using image processing methods based on Gradient Recognition.

Installation

Get the development version from github:

# install.packages("devtools")
devtools::install_github("LuisLauM/grec")

Or install the CRAN version

install.packages("grec")

Examples

Next, we show an example of the use of getGradients function:

require(grec)

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)

Versions

1.6.0

• We are changing the name of the detectFronts function to getGradients. However, for backwards compatibility, detectFronts will still be available until v2.0.0.
• Adding new methods for getGradients: Agenbag-1 and Agenbag-2.
• Some minor improvements in documentation and code.

1.5.0

• Compatibility with imagine >= 2.0.0.
• New method for SpatRast objects (from terra package).
• Improvements on all methods.
• ConvolNormalization = FALSE by default now in detectFronts function.

1.3.5

• Corrections in Belkin and O'Reilly method (GX and GY kernel orientation).
• Adding methods for SpatRast (from terra package) objects.
• Support for Raster- objects will be retired since next versions of grec.
• Improving methods for array objects.
• ConvolNormalization argument is now set as FALSE by default in detectFronts function.
• Minor corrections and improvements in efficiency.

1.3.4

• Improvements on the way to work with matrix, arrays, list and RasterLayer objects.
• Correcting some bugs regarded with methods.
• Include ConvolNormalization argument and enable normalization of convolutions as default.
• Add documentation of methods.

1.2.2

• Improvements on the way to extract matrix data from RasterLayer object.
• Correcting a bug when RasterLayer has not in-memory loaded data (e.g. RasterLayer gotten from read a tif file).
• Add documentation for NW_USA_SST data.

1.2.1

• Some corrections in demos.
• Include a new example data set for SST: NW_USA_SST
• Testing normalization inside B&O method.

1.2.0

• Several changes and improvments on package structure.
• finalSmooth and control arguments detectFronts were deleted.
• extraParams function were deleted. Now, available advanced arguments will be showed in help.
• Help document for detectFronts were updated.
• Another little corrections and improvements.

1.1.2

• Now, detectFronts function has the method argument, using by default the Belkin & O'Reilly (2009) algorithm.
• Some little corrections.

1.1.1

• Modifications on the title of package.
• New set of exampling data (grecExData).
• Changes how the detectFronts algorithm works internally.

1.1.0

• Change function name: from fromDetection to detectFronts.
• Change several argument names on detectFronts function.
• thresholds argument has been replaced by qLimits. Check help of detectFronts function for details.
• On detectFronts function, the final smooth application is optional now, controling by finalSmooth argument.
• Now detectFronts is a method for classes: matrix, array and RasterLayer.
• Bugs and corrections.

1.0.0

• First Public Release