GMMImage                'GMM' clustering of image imported as a
                        RasterStack.
alignLan                Align images using landmarks
alignReg                Aligns images using 'niftyreg' utilities for
                        automated image registration..
colorChecker            Calibrate images using ColorChecker.
colorChecker_customGray
                        Calibrate images using ColorChecker.
colorChecker_half       Calibrate images using (right) half of
                        ColorChecker. Only works for X-Rite.
createPhenotype         Plot color pattern prediction for specified PCA
                        values
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'.
kImageHSV               '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.
patGMM                  Extract colors using GMM clustering (for
                        pre-aligned images).
patK                    Extract colors using k-means clustering (for
                        pre-aligned images).
patK_HSV                Extract colors using k-means clustering (for
                        pre-aligned images).
patLanHSV               Aligns images usings transformations obtained
                        from fixed landmarks and extracts colors using
                        a predefined RGB values and cutoff value.
patLanK                 Aligns images usings transformations obtained
                        from fixed landmarks and extracts colors using
                        k-means clustering.
patLanK_HSV             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.
patLanW                 Extracts color pattern from landmark
                        transformed image using watershed segmentation.
                        This function works interactively by allowing
                        to pick a starting pixel within each pattern
                        element from which the watershed will extract
                        the pattern. This function works best for
                        patterns with sharp boundaries.
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.
patRDA                  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 constrained
                        Redundancy Analysis (RDA) ('rda'). This
                        function also allows to plot the analysis
                        including a visualization of the shape changes
                        along the axis.
patRegHSV               Aligns images using 'niftyreg' utilities for
                        automated image registration and extracts
                        colors using a predefined HSV values and cutoff
                        value.
patRegK                 Aligns images using 'niftyreg' utilities for
                        automated image registration and extracts
                        colors using k-means clustering.
patRegK_HSV             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.
patRegW                 Aligns images using 'niftyreg' utilities for
                        automated image registration and extracts color
                        pattern using watershed segmentation. This
                        function works interactively by allowing to
                        pick a starting pixel within each pattern
                        element from which the watershed will extract
                        the pattern. This function works best for
                        patterns with sharp boundaries.
patternize              patternize - An R package for quantifying color
                        pattern variation.
plotHeat                Plots the color pattern heatmaps from
                        'sumRaster' output.
plotRasterstackAsImage
                        Plot rasterStack as image.
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.
sampleLandmarks         Sample landmarks in an image.
sampleRGB               Interactive function to sample RGB value from
                        pixel or square area in an image.
setMask                 Interactive function to to draw an outline for
                        masking.
sumRaster               This function sums the individual color pattern
                        RasterLayes as obtained by the main patternize
                        functions.
