AnnotatedOutline        Class containing functions and data relating to
                        annotating outlines
CountSet                Subclass of 'FeatureSet' to represent counts
                        centred on points
E                       The deformation energy function
Ecart                   The deformation energy function
Fcart                   The deformation energy gradient function
FeatureSet              Superclass containing functions and data
                        relating to sets of features in flat 'Outline's
FeatureSetCommon        Class containing functionality common to
                        'FeatureSet's and 'ReconstructedFeatureSet's
Fragment                Construct an outline object. This sanitises the
                        input points 'P', as described below.
LandmarkSet             Subclass of 'FeatureSet' to represent points
Outline                 Class containing basic information about flat
                        outlines
OutlineCommon           Class containing functionality common to flat
                        and reconstructed outlines
PathOutline             Add point fullcuts to the outline
PointSet                Subclass of 'FeatureSet' to represent points
R6_to_list              Convert an R6 object into a list, ignoring
                        functions and environments
Rcart                   Restore points to spherical manifold
ReconstructedCountSet   Class containing functions and data to map
                        CountSets to ReconstructedOutlines
ReconstructedFeatureSet
                        Class containing functions and data to map
                        FeatureSets to ReconstructedOutlines
ReconstructedLandmarkSet
                        Class containing functions and data to map
                        LandmarkSets to ReconstructedOutlines
ReconstructedOutline    Class containing functions to reconstruct
                        StitchedOutlines and store the associated data
ReconstructedPointSet   Class containing functions and data to map
                        PointSets to ReconstructedOutlines
RetinalOutline          Class containing functions and data relating to
                        retinal outlines
RetinalReconstructedOutline
                        A version of ReconstructedOutline that is
                        specific to retinal datasets
StitchedOutline         Class containing functions and data relating to
                        Stitching outlines
TriangulatedFragment    Class to triangulate Fragments
TriangulatedOutline     Class containing functions and data relating to
                        Triangulation
azel.to.sphere.colatitude
                        Convert azimuth-elevation coordinates to
                        spherical coordinates
azimuthal.conformal     Azimuthal conformal or stereographic or Wulff
                        projection
azimuthal.equalarea     Lambert azimuthal equal area projection
azimuthal.equidistant   Azimuthal equidistant projection
bary.to.sphere.cart     Convert barycentric coordinates of points in
                        mesh on sphere to cartesian coordinates
central.angle           Central angle between two points on a sphere
checkDatadir            Check the whether directory contains valid data
circle                  Return points on the unit circle
compute.intersections.sphere
                        Find the intersection of a plane with edges of
                        triangles on a sphere
compute.kernel.estimate
                        Kernel estimate over grid
create.polar.cart.grid
                        Create grid on projection of hemisphere onto
                        plane
csv.read.dataset        Read a retinal dataset in CSV format
dE                      The deformation energy gradient function
depthplot3D             Draw the "flat" outline in 3D with depth
                        information
directories             File system directories used by shinyFiles
f                       Piecewise smooth function used in area penalty
fire                    The FIRE algorithm
flatplot                Plot "flat" (unreconstructed) representation of
                        outline
flatplot.AnnotatedOutline
                        Flat plot of AnnotatedOutline
flatplot.Outline        Flat plot of outline
flatplot.ReconstructedOutline
                        Flat plot of reconstructed outline
flatplot.StitchedOutline
                        Flat plot of AnnotatedOutline
flatplot.TriangulatedOutline
                        Plot flat 'TriangulatedOutline'.
flipped.triangles       Determine indices of triangles that are flipped
flipped.triangles.cart
                        Determine indices of triangles that are flipped
fp                      Piecewise smooth function used in area penalty
identity.transform      The identity transformation
idt.read.dataset        Read one of the Thompson lab's retinal datasets
ijroi.read.dataset      Read a retinal dataset in IJROI format
ijroimulti.read.dataset
                        Read a retinal dataset in IJROI format
interpolate.image       Interpolate values in image
invert.sphere           Invert sphere about its centre
invert.sphere.to.hemisphere
                        Invert sphere to hemisphere
karcher.mean.sphere     Karcher mean on the sphere
kde.L                   Estimate of the log likelihood of the points mu
                        given a particular value of the concentration
                        kappa
kde.compute.concentration
                        Find the optimal concentration for a set of
                        data
kde.fhat                Kernel density estimate on sphere using
                        Fisherian density with polar coordinates
kde.fhat.cart           Kernel density estimate on sphere using
                        Fisherian density with Cartesian coordinates
kr.compute.concentration
                        Find the optimal concentration for a set of
                        data
kr.sscv                 Cross validation estimate of the least squares
                        error of the points mu given a particular value
                        of the concentration kappa
kr.yhat                 Kernel regression on sphere using Fisherian
                        density with polar coordinates
kr.yhat.cart            Kernel regression on sphere using Fisherian
                        density with Cartesian coordinates
line.line.intersection
                        Determine intersection between two lines
list.datasets           List datasets underneath a directory
list_to_R6              Convert an list created by R6_to_list() into an
                        R6 object.
lvsLplot                Plot the fractional change in length of mesh
                        edges
morph.dataset.to.parabola
                        Morph a flat dataset to a parabola for testing
                        purposes
name.list               Return a new version of the list in which any
                        unnamed elements have been given standardised
                        names
normalise.angle         Bring angle into range
orthographic            Orthographic projection
panlabel                Ancillary function to place labels
parabola.arclength      Arc length of a parabola y=x^2/4f
parabola.invarclength   Inverse arc length of a parabola y=x^2/4f
parse.dependencies      Parse dependencies
polar.cart.to.sphere.spherical
                        Convert polar projection in Cartesian
                        coordinates to spherical coordinates on sphere
polartext               Put text on the polar plot
projection              Plot projection of a reconstructed outline
projection.ReconstructedOutline
                        Projection of a reconstructed outline
projection.RetinalReconstructedOutline
                        Plot projection of reconstructed dataset
read.datacounts         Read data counts in CSV format
read.datapoints         Read data points in CSV format
remove.identical.consecutive.rows
                        Remove identical consecutive rows from a matrix
remove.intersections    Remove intersections between adjacent segments
                        in a closed path
report                  Reporting utility function
retistruct              Start the Retistruct GUI
retistruct.batch        Batch operation using the parallel package
retistruct.batch.export.matlab
                        Export data from reconstruction data files to
                        MATLAB
retistruct.batch.figures
                        Plot figures for a batch of reconstructions
retistruct.batch.get.titrations
                        Get titrations from a directory of
                        reconstructions
retistruct.batch.plot.titrations
                        Plot titrations
retistruct.batch.summary
                        Extract summary data for a batch of
                        reconstructions
retistruct.check.markup
                        Retistruct check markup
retistruct.cli          Process a dataset with a time limit
retistruct.cli.figure   Print a figure to file
retistruct.cli.process
                        Process a dataset, saving results to disk
retistruct.export.matlab
                        Save reconstruction data in MATLAB format
retistruct.read.dataset
                        Read a retinal dataset
retistruct.read.markup
                        Read the markup data
retistruct.read.recdata
                        Read the reconstruction data from file
retistruct.reconstruct
                        Reconstruct a retina
retistruct.save.markup
                        Save markup
retistruct.save.recdata
                        Save reconstruction data
rotate.axis             Rotate axis of sphere
server                  Retistruct Shiny Server
simplifyFragment        Simplify an outline object by removing short
                        edges
simplifyOutline         Simplify an outline object by removing short
                        edges
sinusoidal              Sinusoidal projection
sphere.cart.to.sphere.dualwedge
                        Convert from Cartesian to 'dual-wedge'
                        coordinates
sphere.cart.to.sphere.spherical
                        Convert from Cartesian to spherical coordinates
sphere.cart.to.sphere.wedge
                        Convert from Cartesian to 'wedge' coordinates
sphere.spherical.to.polar.cart
                        Convert spherical coordinates on sphere to
                        polar projection in Cartesian coordinates
sphere.spherical.to.sphere.cart
                        Convert from spherical to Cartesian coordinates
sphere.tri.area         Area of triangles on a sphere
sphere.wedge.to.sphere.cart
                        Convert from 'wedge' to Cartesian coordinates
spherical.to.polar.area
                        Convert latitude on sphere to radial variable
                        in area-preserving projection
sphericalplot           Spherical plot of reconstructed outline
sphericalplot.ReconstructedOutline
                        Spherical plot of reconstructed outline
strain.colours          Generate colours for strain plots
stretchMesh             Stretch mesh
tri.area                Area of triangles on a plane
tri.area.signed         "Signed area" of triangles on a plane
ui                      Retistruct UI
vecnorm                 Vector norm
