createTarget            Create a target image (RasterStack) from a
                        polygon.
extdata                 External patternize data
imageList               imageList
kImage                  'kmeans' clustering of image imported as a
                        RasterStack. This function is used by 'patLanK'
                        and 'patRegK'.
lanArray                Build landmark array for 'Morpho'.
landmarkArray           landmarkArray
landmarkList            landmarkList
makeList                Build list of landmarks or RasterStacks from
                        images using filepath and file extension.
maskOutline             Intersects a RasterStack with an outline.
                        Everything outside of the outline will be
                        removed from the raster.
patArea                 This fucntion calculates the area in which the
                        color pattern is expressed in each sample as
                        the relative proportion using the provided
                        outline of the considered trait or structure.
patLanK                 Aligns images usings transformations obtained
                        from fixed landmarks and extracts colors using
                        k-means clustering.
patLanRGB               Aligns images usings transformations obtained
                        from fixed landmarks and extracts colors using
                        a predefined RGB values and cutoff value.
patPCA                  This function transforms the individual color
                        pattern rasters as obtained by the main
                        patternize functions to a dataframe of 0 and 1
                        values that can be used for Principal Component
                        Analysis ('prcomp'). This function also allows
                        to plot the analysis including a visualization
                        of the shape changes along the axis. Pixel
                        values are predicted by multiplying the
                        rotation matrix (eigenvectors) with a vector
                        that has the same length as the number of rows
                        in the rotation matrix and in which all values
                        are set to zero except for the PC value for
                        which we want to predict the pixel values.
patRegK                 Aligns images using 'niftyreg' utilities for
                        automated image registration and extracts
                        colors using k-means clustering.
patRegRGB               Aligns images using 'niftyreg' utilities for
                        automated image registration and extracts
                        colors using a predefined RGB values and cutoff
                        value.
patternize              patternize - An R package for quantifying color
                        pattern variation.
plotHeat                Plots the color pattern heatmaps from
                        'sumRaster' output.
rasterList_lanK         rasterList_lanK
rasterList_lanRGB       rasterList_lanRGB
rasterList_regK         rasterList_regK
rasterList_regRGB       rasterList_regRGB
redRes                  Reduce the resolution of an image imported as a
                        RasterStack by downsampling.
sumRaster               This function sums the individual color pattern
                        RasterLayes as obtained by the main patternize
                        functions.
