A synopsis of geomorph functions

Antigoni Kaliontzopoulou

2019-05-20

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 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

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