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