Calculate several measures of Area Relative Curvature

Description

A function that calculates the average slope over a tooth or some other 3D surface

Usage

ARC(plyFile, BoundaryDiscard = "Vertex", Range = c(0.01, 0.99))

Arguments

Details

The function requires an object created by reading in a ply file.

This function calculates Area Relative Curvature, as described by Guy et al. (2013)

Examples

arc_output <- ARC(Tooth)
summary(arc_output)

Plot Area Relative Curvature (ARC) on a surface (HTML widget; continuous bar legend)

Description

Creates a three-dimensional rendering of Area Relative Curvature (ARC) on a mesh and returns an HTML widget with a continuous, vertical color-bar legend. Curvature is split into four negative and four positive bands (quantiles on each side of zero) for per-face coloring. The legend uses a single blended bar assembled from the same eight colors used on the surface, with negative values at the bottom and positive values at the top.

Usage

ARC3d(
  ARC_object,
  main = "",
  cex = 1,
  colors = c("darkblue", "blue", "powderblue", "gray", "gray", "tan", "orange",
    "darkorange1"),
  fieldofview = 0,
  legend = TRUE,
  widget_size_px = 768,
  scene_zoom = 1.5,
  leftOffset = 0,
  title_font_size_px = 30,
  legend_magnify = 1,
  legendTextCol = "black",
  legendLineCol = "black",
  fileName = NA,
  binary = FALSE
)

Arguments

Details

Run ARC() first to compute per-face ARC values.

Binning scheme: The mean face curvature values are split by sign. For negative values, the empirical quartiles (Q1..Q3) define three internal boundaries, creating four bins below zero; the same is done for positive values above zero. The eight bins map to the eight provided colors. The legend bar is a continuous CSS gradient built from those same colors so that the bar visually matches the surface and blends smoothly from one band to the next. Tick labels are shown at LowQs, 0, and HighQs (top to bottom = high to low).

Value

An htmltools::browsable object containing the title, 3D widget, and legend.

Examples

# ARC_out <- ARC(Tooth)
if(interactive()){ARC3d(ARC_out, main = "Area Relative Curvature")}

Visual check of 2D footprint triangles (HTML widget; no Quartz)

Description

Plot the 2D footprint triangles and their vertices used in the RFI 2D area calculation, as a visual QA step to detect spurious triangles inside the footprint. The result is an HTML widget (no Quartz/X11 window) with an optional legend, suitable for RStudio Viewer, Quarto/HTML, and browsers.

Usage

Check2D(
  RFI_Output,
  FootColor = "red",
  TriPointsColor = "black",
  main = "",
  cex = 1,
  legend = TRUE,
  widget_size_px = 768,
  scene_zoom = 1.5,
  leftOffset = 0,
  fieldofview = 0,
  title_font_size_px = 30,
  legend_magnify = 1,
  point_size = 5,
  alpha = 0.35
)

Arguments

Details

This reproduces the same intent as the classic Check2D(): it draws the triangles from RFI_Output$Footprint_Triangles and the corresponding 2D coordinates in RFI_Output$Flattened_Pts. The triangles are plotted in the XY plane (z = 0). If you see points/triangles inside the footprint that shouldn’t be there, it typically indicates an alpha value that is too small in the RFI step, leading to an inflated 2D footprint.

The function uses a headless rgl device and returns an rglwidget embedded in an HTML layout (title atop, legend on the right)—matching the approach used in DNE3d().

Value

An htmltools-browsable object containing the title, 3D widget, and legend.

Examples

# RFI_out <- RFI(Tooth, alpha = 0.5)
# Check2D(RFI_out, FootColor = "tomato", TriPointsColor = "black",
# main = "RFI 2D Footprint QA")

Calculate Dirichlet normal energy of a surface

Description

A function that calculates Dirichlet normal energy following the method of Bunn et al. (2011) Comparing Dirichlet normal surface energy of tooth crowns, a new technique of molar shape quantification for dietary inference, with previous methods in isolation and in combination. Am J Phys Anthropol 145:247-261 doi: 10.1002 ajpa.21489

Usage

DNE(plyFile, outliers = 0.1, kappa = 0, BoundaryDiscard = "Vertex", oex = "c")

Arguments

Details

The function requires an object created by reading in a ply file.

Dirichlet normal energy is calculated on meshes that represent specimen surfaces and have already been simplified and pre-smoothed in a 3D data editing program.

In the default settings, the function seeks to discard boundary faces. This can be changed by adjusting the BoundaryDiscard argument to 'None' which will not discard any faces on the boundary. Further, there are two ways of excluding boundary faces. Either if they have a leg on the boundary by setting BoundaryDiscard='Leg' or by excluding any face which has a vertex on the boundary with BoundaryDiscard='Vertex'. The function defaults to remove the top 0.1 percent of calculated energy densities as outliers. Mesh orientation does not affect this calculation.

Faces are labeled as concave or convex on the basis of the kappa value, which defaults to 0. Each face is assigned a kappa value, which describes the the localized degree of convergence or divergence among the three vertex normals on each face. Faces with positive kappa values have vertex normals that are divergent. Faces with negative kappa values possess vertex normals that are convergent. Users can adjust the kappa value to redefine areas of the tooth assigned to the convex or concave bin.

The mode of Outlier exclusion can be modified with the oex argument. The default, oex='c' considers the Dirichlet energy density values of all faces on the surface and removes those in the top percentile defined by outliers, regardless of the convexity or concavity bins. The alternative, oex='s', divides the surface into concave and convex portions, then removes the percentile defined by outliers from each of these subsets before calculating total surface DNE.

Examples

DNE_output <- DNE(Tooth)
summary(DNE_output)

Plot results of a DNE analysis of a surface

Description

A molaR surface plotting function.

Usage

DNE3d(
  DNE_File,
  setMax = 0,
  logColors = TRUE,
  signColor = TRUE,
  concaveMute = FALSE,
  cuttingFocus = FALSE,
  main = "",
  cex = 1,
  legend = TRUE,
  widget_size_px = 768,
  scene_zoom = 1.5,
  leftOffset = 0,
  fieldofview = 0,
  title_font_size_px = 30,
  legend_magnify = 1,
  fileName = NA,
  binary = FALSE
)

Arguments

Examples

## Not run: 
DNE_output <- DNE(Tooth)
DNE3d(DNE_output)

## End(Not run)

Plot discarded-face results of a DNE analysis (HTML widget; no Quartz)

Description

Produces a three-dimensional rendering that highlights the faces discarded from the DNE calculation—boundary faces and statistical outliers—along with optional concavity marking. The plot is returned as an HTML widget with a simple, readable legend panel to the right.

Usage

DNE3dDiscard(
  DNE_File,
  baseCol = "gray",
  boundCol = "red",
  outlierCol = "lawngreen",
  concaveCol = baseCol,
  main = "",
  cex = 1,
  legend = TRUE,
  widget_size_px = 768,
  scene_zoom = 1.5,
  leftOffset = 0,
  fieldofview = 0,
  title_font_size_px = 30,
  legend_magnify = 1,
  legendTextCol = "black",
  legendLineCol = "black",
  fileName = NA,
  binary = FALSE
)

Arguments

Details

Run DNE() first to compute per-face values and discard sets.

What this shows

• Boundary faces (e.g., with >=1 boundary vertex) and outlier faces (top extreme tail) that were excluded from DNE are colored distinctly; all other faces get baseCol. If concaveCol differs from baseCol, concave regions are tinted accordingly and labeled in the legend.

HTML widget

• Uses a headless rgl device and returns an rglwidget embedded beside a simple HTML legend (no Quartz window). Layout and centering mirror the updated DNE3d.

Saving a PLY

• If fileName is provided, a colorized PLY is written. For ascii PLY, a comment line noting the generator/version is inserted (as in the updated DNE3d).

Value

An htmltools-browsable object containing the title, 3D widget, and legend.

Examples

# DNE_out <- DNE(Tooth)
if(interactive()){DNE3dDiscard(DNE_out, main = "DNE -- Discarded Faces")}

Plot advanced results of a DNE surface analysis

Description

Plot advanced results of a DNE surface analysis

Usage

DNEDensities(
  DNE_File,
  main = "",
  type = "DNE",
  legendPos = "topright",
  convexCol = "hotpink",
  concaveCol = "deepskyblue"
)

Arguments

Details

This function creates a set of overlapping density plots of two potential types. The user can plot overlapping density plots that sort the surface into concave and convex portions for plotting. The function will default to plotting DNE density values, however density of face surface areas sorted into concave and convex portions of the surface can be plotted by calling type='area'. Colors can be customized by altering the convexCol and concaveCol arguments.

Examples

DNE_output <- DNE(Tooth)
DNEDensities(DNE_output)

Plot advanced results of a DNE surface analysis

Description

a molaR plotting function

Usage

DNEbar(
  DNE_File,
  main = "",
  convexCol = "hotpink",
  concaveCol = "deepskyblue",
  type = "both",
  legendPos = "topright",
  legendInset = 0,
  las = 1,
  names.arg = "",
  cex.names = 1
)

Arguments

Details

This function creates a stacked barplot of DNE values. It colors them according to curve orientation, which is defined by the kappa parameter in DNE() function. If multiple DNE objects are grouped together the barplot will return a set. When employed on a single DNE object this will return a single stacked bar.

The argument type accepts either 'Concave' or 'Convex' to plot only concave or convex DNE totals respectively. Default=NA and results in both totals being plotted in stacked barplot.

The argument legendPos is a string that determines the position of the legend. Default='topright' but will accept any of the following keywords: 'bottomright', 'bottom', 'bottomleft', 'left', 'topleft', 'top', 'topright', 'right', or 'center'.

Examples

DNEs <- list()
DNEs$Tooth <- DNE(Tooth)
DNEs$Hills <- DNE(Hills)
DNEbar(DNEs)

Plot advanced results of a DNE surface analysis

Description

Plot advanced results of a DNE surface analysis

Usage

DNEpie(
  DNE_File,
  main = "",
  type = "area",
  convexCol = "hotpink",
  concaveCol = "deepskyblue"
)

Arguments

Details

This function creates a pie chart of the total area or DNE of the surface originating from the concave or convex portions of the surface. The function defaults to plotting surface area, however, relative proportion of total DNE from the concave and convex portions of the surface can be plotted by calling type='DNE'. Colors can be customized by altering the convexCol and concaveCol arguments.

Examples

DNE_output <- DNE(Tooth)
DNEpie(DNE_output)

Hills surface mesh

Description

Sample mesh created with the formula: 'z=3cos(x/2)+3sin(y/2)

A triangular mesh representing a sine-cosine plane - called by data(Hills)

Usage

data(Hills)

Format

An object of class "mesh3d"

Hills: triangular mesh representing a sine-cosine plane.

Examples

data(Hills)
DNE_Output <- DNE(Hills)
DNE3d(DNE_Output)

Calculate orientation patch count of a surface

Description

A function that bins patches of a mesh surface that share general orientation and sums the number of unique patches given certain parameters Modified into 3D from the original 2.5D method described by Evans et al. (2007) High-level similarity of dentitions in carnivorans and rodents. Nature 445:78-81 doi: 10.1038/nature05433

Usage

OPC(plyFile, rotation = 0, minimum_faces = 3, minimum_area = 0)

Arguments

Details

The function requires a mesh object created by reading in a ply file utilizing either the, vcgPlyRead function.

Orientation patch count is calculated on meshes that represent specimen surfaces and have already been downsampled to 10,000 faces and pre-smoothed in a 3D data editing program. Alignment of the surface will have a large effect on patch orientation and must be performed in a 3D data editing program such as Avizo. The occlusal surface of the specimen must be made parallel to the X- and Y-axes and perpendicular to the Z-axis.

The default for minimum_faces is to ignore patches consisting of two or fewer faces on the mesh. Changing the minimum_area value will disable minimum_faces.

Examples

OPC_output <- OPC(Tooth)
summary(OPC_output)

Plot results of OPC analysis of a surface (3D HTML widget; numbered legend; distinct colors)

Description

Produces a three-dimensional rendering of face orientation on a surface and returns an HTML widget with a clean, numbered pie legend Wedges can be scaled by patch counts. Default colors emphasize clarity.

Usage

OPC3d(
  OPC_File,
  binColors = NULL,
  patchOutline = FALSE,
  outlineColor = "black",
  maskDiscard = FALSE,
  legend = TRUE,
  main = "",
  cex = 1,
  scaleLegend = FALSE,
  legendTextCol = "black",
  legendLineCol = "black",
  leftOffset = 0,
  fieldofview = 0,
  widget_size_px = 768,
  scene_zoom = 1.5,
  title_font_size_px = 30,
  title_font_family =
    "system-ui, -apple-system, Segoe UI, Roboto, Helvetica, Arial, sans-serif",
  legend_magnify = 1,
  fileName = NA,
  binary = FALSE
)

Arguments

Details

Run OPC() first to compute patches and directional bins.

Legend Wedges are numbered (1..N) and can be scaled to patch counts.

Saving a PLY When fileName is provided, a colorized PLY is written. Colors are assigned per face via a vertex-duplication strategy so external tools (e.g., MeshLab) show the same appearance. For ascii PLY, a comment line notes the generator/version.

Value

• Interactive: an htmltools-browsable object (title, 3D widget, legend).

• Non-interactive: (invisibly) a list with class "OPC3d_spec" containing: title, bin_colors, face_colors, bin_sizes, bin_labels, legend, scaled.

Examples

# OPC_out <- OPC(Tooth)
if (interactive()) {
  OPC3d(OPC_out, legend = TRUE, scaleLegend = TRUE,
        main = "OPC -- Numbered Bins")
}

Visualize surface area distribution into separate OPC orientation bins.

Description

This function will make either a bar plot or pie chart showing the surface area assigned to each OPC orientation bin.

Usage

OPCbinareas(
  OPC_File,
  main = "",
  binColors = hsv(h = (seq(10, 290, 40)/360), s = 0.9, v = 0.85),
  type = "bar"
)

Arguments

Details

This function will create either bar or pie chats visualising the distribution of surface area into each of the OPC orientation bins. Colors can be customized but are meant to match the default settings in the OPC3d() function.

Examples

OPC_Object <- OPC(Tooth)
OPCbinareas(OPC_Object) 

Calculate average orientation patch count after several rotations

Description

A function that calls OPC iteratively after rotating mesh a selected number of degrees around the Z-axis following Evans and Jernvall (2009) Patterns and constraints in carnivoran and rodent dental complexity and tooth size. J Vert Paleo 29:24A

Usage

OPCr(plyFile, steps = 8, stepSize = 5.625, minimum_faces = 3, minimum_area = 0)

Arguments

Details

The function requires a mesh object created by reading in a ply file utilizing either the, vcgPlyRead function.

Default number of steps is 8, with a stepSize of 5.625 degrees, following the original published definition of OPCR.

See the details for the OPC function for more information about preparing mesh surfaces and the effects of minimum_faces and minimum_area.

OPCr_Example1 - object created by OPCr function used as an example.

Description

This object is needed to pass the CRAN upload requirements and still keep the vignette.

Format

OPCr_Example1: molaR produced object.

OPCr_Example2 - object created by OPCr function used as an example.

Description

This object is needed to pass the CRAN upload requirements and still keep the vignette.

Format

OPCr_Example2: molaR produced object.

Calculate relief index for a surface

Description

A function that calculates relief index following Boyer (2008) Relief index of second mandibular molars is a correlate of diet among prosimian primates and other mammals. J Hum Evol 55:1118-1137 doi: 10.1016/j.jhevol.2008.08.002

Usage

RFI(plyFile, alpha = 0.075, findAlpha = FALSE)

Arguments

Details

The function requires an object created by reading in a ply file utilizing either the vcgPlyRead function.

Relief index is calculated by the ratio of three-dimensional surface area to two dimensional area on meshes that represent specimen surfaces and have already been pre-smoothed in a 3D data editing program. Surface alignment will have a large effect on 2D area calculation and must be performed prior to creating and reading in the ply file. The mesh must be oriented such that the occlusal plane is parallel to the X- and Y-axes and perpendicular to the Z-axis (i.e., tooth cusps pointing towards +Z).

The alpha parameter traces the outline of the 2D footprint. An alpha that is too low will result in a tracing error (returning an "Alpha adjustment required" message), while an alpha value that is too high may result in an overestimate of the 2D footprint area by failing to take into account infoldings. The user is encouraged to carefully review results using the RFI3d or Check2D functions.

Alternatively, the findAlpha argument can be used to compute an ideal alpha value for a particular PLY file for use in the RFI calculation. This is defined as the lowest value (to the nearest thousandth) returning no error or warning messages. This feature ensures accuracy, but may increase computing time significantly, depending on the number of alpha values tested. Unfortunately, there is no way to guess an appropriate alpha value a priori. After 100 unsuccessful attempts to find an appropriate alpha, the function will terminate.

The alpha value used in the calculation (whether chosen by the user or auto- computed with findAlpha) is returned in the analysis results.

Examples

RFI_output <- RFI(Tooth, alpha=0.5, findAlpha = FALSE)
summary(RFI_output)

Plot 3D and 2D areas of a mesh used to calculate relief index (HTML widget)

Description

Renders a three-dimensional model of the mesh surface and a footprint of the two-dimensional area side-by-side for visual comparison. The RFI() function must be performed prior to using RFI3d().

Usage

RFI3d(
  RFI_File,
  displacement = -1.9,
  SurfaceColor = "gray",
  FootColor = "red",
  FootPts = FALSE,
  FootPtsColor = "black",
  Opacity = 1,
  legend = TRUE,
  main = "",
  cex = 1,
  widget_size_px = 768,
  scene_zoom = 1.5,
  leftOffset = 0,
  fieldofview = 0,
  title_font_size_px = 30,
  title_font_family =
    "system-ui, -apple-system, Segoe UI, Roboto, Helvetica, Arial, sans-serif",
  legend_magnify = 1,
  fileName = NA,
  binary = FALSE
)

Arguments

Details

This function helps visualize the 3D surface area (numerator) and the 2D projected area (denominator) that comprise the relief index, by displaying both at once. Adjust Opacity to make the footprint more visible through the surface. The footprint plane can be moved along Z via displacement.

The plotting window is an HTML widget. The legend is rendered in HTML/CSS and aligned vertically at the right of the scene.

Examples

if(interactive()){
  rfi <- RFI(Tooth, alpha = 0.5)
  RFI3d(rfi)
}

Function to calculate the average slope of a surface

Description

A function that calculates the average slope over a tooth or some other 3D surface

Usage

Slope(plyFile, Guess = FALSE)

Arguments

Details

This function requires a ply file. It will calculate the slope on each face of the surface and will average the slope across the surface. This is functionally equivalent to the slope calculation used by Ungar and M'Kirera "A solution to the worn tooth conundrum in primate functional anatomy" PNAS (2003) 100(7):3874-3877

In the case of applying this function to teeth (its intended purpose), the function expects a surface with the occlusal plane normal to the Z-axis.

The Guess parameter is a logical asking whether or not you want the function to both guess as to the right side up of the surface, and to then discard all of the 'negative' slopes, i.e. surfaces which are over-hangs, as is frequently found on the sidewalls of teeth. If Guess is not engaged the mean slope will include the negative values of the overhang and will likely underestimate the average slope of the surface.

Regardless of if the Guess parameter is engaged, the function will also return a vector containing all of the face slope values ("Face_Slopes")

Examples

Slope_output <- Slope(Tooth)
summary(Slope_output)

Plot results of a Slope analysis of a surface (HTML widget)

Description

A function that produces a three-dimensional HTML-based rendering of surface slope. The Slope() function must be performed prior to using Slope3d().

Usage

Slope3d(
  Slope_File,
  colors = c("blue", "cornflowerblue", "green", "yellowgreen", "yellow", "orangered",
    "red"),
  maskNegatives = TRUE,
  legend = TRUE,
  main = "",
  cex = 1,
  widget_size_px = 768,
  scene_zoom = 1.5,
  leftOffset = 0,
  fieldofview = 0,
  title_font_size_px = 30,
  legend_magnify = 1,
  fileName = NA,
  binary = FALSE
)

Arguments

Details

Colors represent face slope magnitudes. With maskNegatives = TRUE, negative slopes are shown in black. With maskNegatives = FALSE, negative magnitudes are reflected into the positive range for coloring continuity (original behavior).

The plotting window is an HTML widget (no Quartz/rgl window). The legend is rendered in HTML/CSS and aligned vertically at the right of the scene.

Examples

s <- Slope(Tooth)
if(interactive()){Slope3d(s)}

Tooth a surface mesh of a tooth.

Description

Tooth scan of USNM_112176 lower M~1~ from Chlorocebus sp.

A triangular mesh representing a lower M1 Chlorocebus spp. tooth - called by data(Tooth)

Usage

data(Tooth)

Format

An object of class "mesh3d"

Tooth: triangular mesh representing a sine-cosine plane.

Examples

data(Tooth)
DNE_Output <- DNE(Tooth)
DNE3d(DNE_Output)

Split a mesh by a plane into two meshes

Description

Internal utility that clips an rgl mesh3d by a plane defined as Ax + By + C*z + D = 0, returning the two resulting meshes.

Usage

meshClip(plyFile, A, B, C, D)

Arguments

Value

A list with two elements:

meshA

The submesh on the side where A*x + B*y + C*z + D >= 0.

meshB

The complementary submesh (may be NULL if empty).

Run molaR analyses on a batch of specimens

Description

A function that automates molaR analyses on multiple specimens. Several different analyses can be performed on each surface, with specifications for analysis parameters.

Usage

molaR_Batch(
  pathName = getwd(),
  fileName = "molaR_Batch.csv",
  DNE = TRUE,
  RFI = TRUE,
  OPCr = TRUE,
  OPC = FALSE,
  Slope = TRUE,
  details = TRUE,
  parameters = TRUE,
  ...
)

Arguments

Details

This function allows a user to set the analyses from molaR they want to run on a batch of ply files. Output is saved to a csv file. By default, the batch function will perform specified analyses on all ply files in the working directory. A different folder can be specified with pathName. Output saves as .csv to the folder that contains the analyzed ply files.

Any of the default arguments of the various topographic analysis functions can be modified for the batch by specifying them when calling molaR_Batch, e.g., the DNE kappa value can be changed to 'X' by specifying kappa = X. Users are strongly encouraged to review the documentation for DNE(), RFI(), OPCr(), OPC(), and Slope() and to understand the effects of alterations before making changes. A recommended practice for analyzing RFI in a batch of specimens is to enable findAlpha = TRUE given that the ideal alpha value is likely to vary among different specimens. However, this will increase calculation time (see documentation for RFI).

By default, the batch output will retain some additional details of the analysis. These include, in the case of DNE: convex and concave DNE values, convex and concave surface areas; in the case of RFI: 3D and 2D surface areas and analysis alpha values; in the case of OPCr: the surface OPC value calculated at each rotation; and in the case of OPC: the patch count for each bin. These results will be discarded and only the final result of each topographic analysis will be retained if details = FALSE.

The function will save a list of all parameters used in all batch analyses to the output .csv file, below the results. This can be suppressed with parameters = FALSE, but is recommended as a check on how analyses were performed when returning to results in the future. If the function is assigned to an object in R, the parameters are not included in the resultant data.frame, but will still be included in the .csv file by default.

Note that batch processing updates will not display by default if using RGui for Windows. Disable Misc -> Buffered output (Ctrl+W) if you wish to view batch processing progress in RGui for Windows.

Clean up problem ply files

Description

Function will remove floating verticies, and faces with zero area. These can cause issues when using molaR's primary functions of DNE, RFI, and OPC

Usage

molaR_Clean(plyFile, cleanType = "Both", verbose = TRUE)

Arguments

Details

This function cleans up problematic ply files. Some smoothed files will have faces of zero area, or floating vertices. DNE and OPC cannot be calculated on these files. Running the plys through this function will allow those calculations to be made.

Examples

Tooth <- molaR_Clean(Tooth)

Cut a PLY Mesh Along a Specified Plane (HTML widget; no Quartz)

Description

Cuts a mesh by a plane and returns either one side or both sides of the cut. The result is also previewed as an HTML widget (no Quartz/X11) with the kept side in solid color, the other side semi-transparent, and the cutting plane shown.

Usage

plyPlaneCut(
  plyFile,
  axis = "Z",
  vertIndex = NA,
  cut_value = NA,
  keepBoth = FALSE,
  plane = NA,
  flipAxis = FALSE,
  display = TRUE,
  kept_col = "#3C8DFF",
  other_col = "gray70",
  plane_col = "firebrick",
  plane_alpha = 0.35,
  main = "",
  widget_size_px = 768,
  scene_zoom = 1.5,
  leftOffset = 0,
  fieldofview = 0,
  title_font_size_px = 30,
  title_font_family =
    "system-ui, -apple-system, Segoe UI, Roboto, Helvetica, Arial, sans-serif"
)

Arguments

Details

This HTML-widget version avoids opening a native rgl window and mirrors the device-and-layout pattern you used in your updated DNE3d. Interactive vertex picking (select3d) isn’t supported in widget mode; supply the cut as plane, vertIndex + axis, or cut_value + axis. The kept side selection is controlled by the normal direction and flipAxis.

Value

If keepBoth = FALSE, a 'mesh3d' for the retained side. If keepBoth = TRUE, a list with elements 'meshA' and 'meshB'. The returned object also carries an attribute 'widget' with the htmltools::browsable preview when display = TRUE.