A synopsis of geomorph functions
In geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

knitr::opts_chunk$set(echo = TRUE)

The tables below provide a summary index of geomorph functions and their main purpose, to assist users to find available tools. They are organized into: 1) Analytical, 2) Utility, and 3) Plotting functions. At the end, a separate table provides an overview of the example datasets available.

NOTE: Deprecated (or soon to be) functions are not included.

Analytical functions

These are the core analytical functions of geomorph. Many of them produce S3 objects which can then be further explored using summary() and plot().

Function name | Brief description | summary() | plot() :-------- | :--------------------------------------------| :----: | :----: | bilat.symmetry | Symmetry analysis and calculation of symmetric and asymmetric shape components | X | X compare.evol.rates | Calculate and compare rates of shape evolution among groups on a phylogeny | X | X compare.multi.evol.rates | Calculate and compare evolutionary rates for two or more shape traits on a phylogeny | X | X compare.pls | Compare effect sizes of two or more PLS fits | X | estimate.missing | Estimate the position of missing landmarks using regression or the TPS fixed.angle | Standardize the angle of articulated structures | | globalIntegration | Calculate global integration as the slope of the log-variance of partial warps vs. their bending energy | | gm.prcomp | Principal components analysis of Procrustes shape coordinates | X | X gpagen | Generalized Procrustes Analysis | X | X integration.test | Test for morphological integration using PLS | X | X modularity.test | Test for morphological modularity using the Covariance Ratio | X | X morphol.disparity | Estimate and compare across groups morphological disparity | X | mshape | Calculate the mean shape of a landmark configuration | | X phylo.integration | Test for morphological integration across species while accounting for phylogeny using PLS | X | X phylo.modularity | Test for morphological modularity across species using the Covariance Ratio, while accounting for phylogeny | X | X physignal | Calculate phylogenetic signal for shape data | X | X procD.lm | Linear model and Procrustes ANOVA with permutation procedures | X | X procD.pgls | Linear model and Procrustes ANOVA in a phylogenetic framework with permutation procedures | X | X shape.predictor | Estimate shape configurations based on linear predictors | | two.b.pls | Two-block partial least squares analysis | X | X

Utility functions

These include functions for reading and writing data, digitizing, data-formatting operations

Function name | Brief description :-------- | :---------------------------------------------------------------------- arrayspecs | Transform a matrix of landmark coordinates into an array buildtemplate | Build template of 3D surface semilandmarks combine.subsets | Combine subsets of landmarks into a single configuration by specimen coords.subset | Subset landmark coordinates by grouping factor define.links | Interactively make link definition matrix define.modules | Interactively make module definition matrix define.sliders | Interactively make sliding semilandmark definition matrix digit.curves | Digitize 3D curve semilandmarks in a 3D surface object digit.fixed | Digitize fixed 3D landmarks in a 3D surface object digitize2d | Digitize 2D landmarks in jpg files digitsurface | Digitize 3D fixed landmarks and surface semilandmarks in a 3D surface object using an already created template editTemplate | Manually remove surface semilandmarks from a 3D template findMeanSpec | Identify specimen closest to the mean geomorph.data.frame | Combine data for analyses into a geomorph data frame interlmkdist | Calculate linear distances between landmarks read.morphologika | Read morphologika file read.ply | Read ply file readland.nts | Read nts file readland.shapes | Read StereoMorph shapes object readland.tps | Read tps file readmulti.nts | Read multiple nts files simultaneously rotate.coords | Rotate or flip landmark coordinates two.d.array | Transform an array of landmark coordinates into a matrix writeland.tps | Save landmarks in tps file

Plotting functions

Stand-alone geomorph plotting functions. For S3 plot functions of geomorph objects see the section of analytical functions.

Function name | Brief description :-------- | :---------------------------------------------------------------------- picknplot.shape | Interactively pick a point in a scatterplot (output from another geomorph function) and visualize the corresponding shape plotAllometry | Different options for visualizing allometric plots from an lm fit plotAllSpecimens | Plot all the specimens in a sample plotGMPhyloMorphoSpace | Phylomorphospace plot, with the possibility of visualizing time as the z axis plotOutliers | Visualization of outliers through inspection of the distribution of Procrustes distances of individual shapes from the consensus configuration plotRefToTarget | Obtain deformation grids between a reference and plot specimen using the TPS plotspec | Single 3D specimen plotting shapeHulls | Update procD.lm or gm.prcomp plots to add convex hulls for groups warpRefMesh | Warp a 3D mesh into the mean shape warpRefOutline | Warp a 2D outline into the mean shape

Example datasets

Example datasets included in geomorph are:

Dataset | landmarks + semilandmarks (p) | Landmark dimensions (k) | Sample size (n) | Content :------: | :------: | :------: | :-: |:---------------------------------------: | hummingbirds | 10 + 15 | 2 | 44 | Hummingbird bill shape data, and slider definition matrix | larvalMorph | 1 + 25 / 6 + 58 | 2 | 114 | Salamander larvae head and tail landmark coordinates, and corresponding slider definition matrices and treatment and family indices | mosquito | 18 | 2 | 40 | Mosquito wings with individual, side and replicate indices for symmetry analysis | plethodon | 12 | 2 | 40 | Salamander skulls with links, outline, and species and site indices | plethShapeFood | 13 | 2 | 69 | Salamander skulls and corresponding food items matrix | plethspecies | 11 | 2 | 9 | Skull shape data for 11 salamander species and corresponding phylogeny | pupfish | 56 | 2 | 54 | Pupfish shape data (superimposed) and corresponding centroid size, sex and population indices | ratland | 8 | 2 | 164 | Rat skull landmark data | scallopPLY | 166 | 3 | 1 | Scallop 3D scan in ply format, and corresponding matrix with digitized surface sliding semilandmarks | scallops | 46 + 11 + 30 | 3 | 5 | Fixed landmarks, curve and surface semilandmarks for scallop specimens, and corresponding matrix of symmetric landmark pairs |