Geometric Morphometric Analyses of 2D and 3D Landmark Data
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Documentation for package ‘geomorph’ version 4.0.10
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A B C D E F G H I L M N P R S T W
| geomorph-package | Geometric morphometric analyses for 2D/3D data |
-- A --
| arrayspecs | Convert landmark data matrix into array (p x k x n) |
-- B --
| bilat.symmetry | Analysis of bilateral symmetry |
| buildtemplate | Build 3D surface template |
-- C --
| combine.subsets | Combine separate landmark configurations |
| compare.CR | Comparisons of Effect Sizes from Modularity Analyses |
| compare.evol.rates | Comparing net rates of shape evolution on phylogenies |
| compare.multi.evol.rates | Comparing net rates of evolution among traits on phylogenies |
| compare.physignal.z | Comparisons of Phylogenetic Signal Effect Sizes |
| compare.pls | Comparisons of Effect Sizes from Partial Least Squares |
| compare.ZVrel | Comparisons of Effect Sizes from Overall Integration Analyses |
| coords.subset | Subset landmark coordinates via a factor |
-- D --
| define.links | Define links between landmarks |
| define.modules | Define modules (landmark partitions) |
| define.sliders | Select points to "slide" along curves |
| digit.curves | Calculate semilandmarks along a curve |
| digit.fixed | Digitize 3D landmarks on mesh3d object |
| digitize2d | Digitize 2D landmarks on .jpg files |
| digitsurface | Digitize 3D fixed landmarks and surface semilandmarks |
-- E --
| editTemplate | Edit 3D template |
| estimate.missing | Estimate locations of missing landmarks |
| extended.pgls | Extended Phylogenetic ANOVA/regression for Procrustes shape variables |
-- F --
| findMeanSpec | Identify specimen closest to the mean of a set of Procrustes shape variables |
| fixed.angle | Rotate a subset of 2D landmarks to common articulation angle |
-- G --
| geomorph | Geometric morphometric analyses for 2D/3D data |
| geomorph.data.frame | Create a data frame with shape data |
| globalIntegration | Quantify global integration relative to self-similarity |
| gm.measurement.error | This function is a wrapper for the function measurement.error in RRPP |
| gm.prcomp | Principal and phylogenetically-aligned components analysis of shape data |
| gpagen | Generalized Procrustes analysis of points, curves, and surfaces |
| gridPar | Set up parameters for grids, points, and links in plotRefToTarget |
-- H --
| hummingbirds | Landmark data from hummingbird bills (includes sliding semilandmarks on curves) |
-- I --
| integration.test | Quantify morphological integration between modules |
| integration.Vrel | Quantify integration in a set of traits |
| interlmkdist | Calculate linear distances between landmarks |
-- L --
| larvalMorph | Head and tail shapes of larval salamanders |
| lizards | Dorsal head shape data of lizards |
-- M --
| make_ggplot | Convert geomorph plots to ggplot objects |
| modularity.test | Evaluate the degree of modular signal in shape data |
| morphol.disparity | Morphological disparity for one or more groups of specimens |
| mosquito | Landmarks on mosquito wings |
| mshape | Estimate mean shape for a set of aligned specimens |
-- N --
| na.omit.geomorph.data.frame | Handle missing values in rrpp.data.frame objects |
-- P --
| phylo.integration | Quantify phylogenetic morphological integration between two or more sets of variables under Brownian motion |
| phylo.modularity | Evaluate the degree of phylogenetic modular signal in Procrustes shape variables |
| physignal | Assessing phylogenetic signal in Procrustes shape variables |
| physignal.eigen | Assessing dimensions of phylogenetic signal in Procrustes shape variables |
| physignal.z | Assessing phylogenetic signal effect size in Procrustes shape variables |
| picknplot.shape | Pick points in geomorph scatterplots to visualize shape variation |
| plethodon | Landmark data from Plethodon salamander heads |
| plethShapeFood | Head shape and food use data from Plethodon salamanders |
| plethspecies | Head shape and phylogenetic relationships for several Plethodon salamander species |
| plot.bilat.symmetry | Plot Function for geomorph |
| plot.CR | Plot Function for geomorph |
| plot.CR.phylo | Plot Function for geomorph |
| plot.evolrate | Plot Function for geomorph |
| plot.gm.prcomp | Plot Function for geomorph |
| plot.gpagen | Plot Function for geomorph |
| plot.mshape | Plot Function for geomorph |
| plot.physignal | Plot Function for geomorph |
| plot.physignal.eigen | Plot Function for geomorph |
| plot.physignal.z | Plot Function for geomorph |
| plot.pls | Plot Function for geomorph |
| plot.procD.lm | Plot Function for geomorph |
| plotAllometry | Plotting to assist visualization of shape-size covariation (allometry) |
| plotAllSpecimens | Plot landmark coordinates for all specimens |
| plotOutliers | Find potential outliers |
| plotRefToTarget | Plot shape differences between a reference and target specimen |
| plotspec | Plot 3D specimen, fixed landmarks and surface semilandmarks |
| print.bilat.symmetry | Print/Summary Function for geomorph |
| print.combined.set | Print/Summary Function for geomorph |
| print.compare.CR | Print/Summary Function for geomorph |
| print.compare.physignal.z | Print/Summary Function for geomorph |
| print.compare.pls | Print/Summary Function for geomorph |
| print.compare.ZVrel | Print/Summary function for geomorph |
| print.CR | Print/Summary Function for geomorph |
| print.CR.phylo | Print/Summary Function for geomorph |
| print.evolrate | Print/Summary Function for geomorph |
| print.evolrate1 | Print/Summary Function for geomorph |
| print.geomorphShapes | Print/Summary function for geomorph |
| print.gm.prcomp | Print/Summary function for geomorph |
| print.gpagen | Print/Summary Function for geomorph |
| print.morphol.disparity | Print/Summary Function for geomorph |
| print.physignal | Print/Summary Function for geomorph |
| print.physignal.eigen | Print/Summary Function for geomorph |
| print.physignal.z | Print/Summary Function for geomorph |
| print.pls | Print/Summary Function for geomorph |
| print.procD.lm | Print/Summary Function for geomorph |
| procD.lm | Procrustes ANOVA/regression for Procrustes shape variables |
| procD.pgls | Phylogenetic ANOVA/regression for Procrustes shape variables |
| pupfish | Landmarks on pupfish |
| pupfish.ws | Landmarks on pupfish |
-- R --
| ratland | Landmark data from dataset rat |
| read.morphologika | Read landmark data from Morphologika file(s) |
| read.ply | Read mesh data (vertices and faces) from ply files |
| readland.fcsv | Read landmark data matrix from fcsv file |
| readland.nts | Read landmark data matrix from nts file |
| readland.shapes | Read landmark data from a shapes object (StereoMorph) |
| readland.tps | Read landmark data from tps file |
| readmulti.nts | Read and combine multiple nts files |
| readmulti.tps | Read and combine multiple tps files |
| rotate.coords | Rotate or flip landmark or coordinate configurations |
-- S --
| scallopPLY | 3D scan of a scallop shell from a .ply file in mesh3d format |
| scallops | Landmark data from scallop shells |
| shape.predictor | Shape prediction from numeric predictors |
| shapeHulls | Update Plots with Convex Hulls for Groups |
| summary.bilat.symmetry | Print/Summary Function for geomorph |
| summary.combined.set | Print/Summary Function for geomorph |
| summary.compare.CR | Print/Summary Function for geomorph |
| summary.compare.physignal.z | Print/Summary Function for geomorph |
| summary.compare.pls | Print/Summary Function for geomorph |
| summary.compare.ZVrel | Print/Summary Function for geomorph |
| summary.CR | Print/Summary Function for geomorph |
| summary.CR.phylo | Print/Summary Function for geomorph |
| summary.evolrate | Print/Summary Function for geomorph |
| summary.evolrate1 | Print/Summary Function for geomorph |
| summary.geomorphShapes | Print/Summary Function for geomorph |
| summary.gm.prcomp | Print/Summary Function for geomorph |
| summary.gpagen | Print/Summary Function for geomorph |
| summary.morphol.disparity | Print/Summary Function for geomorph |
| summary.physignal | Print/Summary Function for geomorph |
| summary.physignal.eigen | Print/Summary Function for geomorph |
| summary.physignal.z | Print/Summary Function for geomorph |
| summary.pls | Print/Summary Function for geomorph |
| summary.procD.lm | Print/Summary Function for geomorph |
-- T --
| two.b.pls | Two-block partial least squares analysis for Procrustes shape variables |
| two.d.array | Convert (p x k x n) data array into 2D data matrix |
-- W --
| warpRefMesh | Creates a mesh3d object warped to the mean shape |
| warpRefOutline | Creates a 2D outline warped to the mean shape |
| writeland.tps | Write landmark data to tps file |