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.*

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

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`

| Idsentify 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

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 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 |

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