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` |
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 |

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 |