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**geomorph**: Geometric Morphometric Analyses of 2D/3D Landmark Data**pupfish**: Landmarks on pupfish

# Landmarks on pupfish

### Description

Landmark data from Cyprindon pecosensis body shapes, with indication of Sex and Population from which fish were sampled (Marsh or Sinkhole).

### Details

These data were previously aligned with GPA. Centroid size (CS) is also provided.

### Author(s)

Michael Collyer

### References

Collyer, M.L., D.J. Sekora, and D.C. Adams. 2015. A method for analysis of phenotypic change for phenotypes described by high-dimensional data. Heredity. 113: doi:10.1038/hdy.2014.75.

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- advanced.procD.lm: Procrustes ANOVA and pairwise tests for shape data, using...
- arrayspecs: Convert landmark data matrix into array (p x k x n)
- bilat.symmetry: Analysis of bilateral symmetry
- buildtemplate: Build 3D surface template
- compare.evol.rates: Comparing rates of shape evolution on phylogenies
- compare.modular.partitions: Deprecated functions in geomorph
- compare.multi.evol.rates: Comparing rates of shape evolution among traits on...
- compare.pls: Comparisons of Effect Sizes from Partial Least Squares
- coords.subset: Subset landmark coordinates via a factor
- 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
- editTemplate: Edit 3D template
- estimate.missing: Estimate locations of missing landmarks
- findMeanSpec: Identify specimen closest to the mean of a set of aligned...
- fixed.angle: Rotate a subset of 2D landmarks to common articulation angle
- geomorph.data.frame: Create a data frame with shape data
- geomorph-package: Geometric morphometric analyses for 2D/3D data
- globalIntegration: Quantify global integration relative to self-similarity
- gpagen: Generalized Procrustes analysis of points, curves, and...
- gridPar: Set up parameters for grids, points, and links in...
- hummingbirds: Landmark data from hummingbird bills (includes sliding...
- integration.test: Quantify morphological integration between modules
- larvalTails: Tail-shapes of larval salamanders
- modularity.test: Evaluate the degree of modular signal in morphometric...
- morphol.disparity: Morphological disparity for one or more groups of specimens
- morphol.integr: Deprecated functions in geomorph
- mosquito: Landmarks on mosquito wings
- motionpaths: Simulated motion paths
- mshape: Estimate mean shape for a set of aligned specimens
- nested.update: Update procD.lm objects with nested effects
- phylo.integration: Quantify phylogenetic morphological integration between two...
- phylo.modularity: Evaluate the degree of phylogenetic modular signal in...
- phylo.pls: Deprecated functions in geomorph
- physignal: Assessing phylogenetic signal in morphometric data
- plethodon: Landmark data from Plethodon salamander heads
- plethShapeFood: Head shape and food use data from Plethodon salamanders
- plethspecies: Average head shape and phylogenetic relationships for several...
- plot.advanced.procD.lm: Plot Function for geomorph
- plotAllometry: Deprecated functions in geomorph
- plotAllSpecimens: Plot landmark coordinates for all specimens
- 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
- plotGMPhyloMorphoSpace: Plot phylogenetic tree and specimens in tangent space
- plot.gpagen: Plot Function for geomorph
- plotOutliers: Find potential outliers
- plot.physignal: Plot Function for geomorph
- plot.pls: Plot Function for geomorph
- plot.procD.allometry: Plot Function for geomorph
- plot.procD.lm: Plot Function for geomorph
- plotRefToTarget: Plot shape differences between a reference and target...
- plotspec: Plot 3D specimen, fixed landmarks and surface semilandmarks
- plotTangentSpace: Plot specimens in tangent space
- plot.trajectory.analysis: Plot Function for geomorph
- print.advanced.procD.lm: Print/Summary Function for geomorph
- print.bilat.symmetry: Print/Summary Function for geomorph
- print.compare.pls: 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.gpagen: Print/Summary Function for geomorph
- print.morphol.disparity: Print/Summary Function for geomorph
- print.physignal: Print/Summary Function for geomorph
- print.plotTangentSpace: Print/Summary Function for geomorph
- print.pls: Print/Summary Function for geomorph
- print.procD.allometry: Print/Summary Function for geomorph
- print.procD.lm: Print/Summary Function for geomorph
- print.trajectory.analysis: Print/Summary Function for geomorph
- procD.allometry: Procrustes ANOVA/regression, specifically for shape-size...
- procD.lm: Procrustes ANOVA/regression for shape data
- procD.pgls: Phylogenetic ANOVA/regression for shape data
- pupfish: Landmarks on pupfish
- ratland: Landmark data from dataset rat
- readland.nts: Read landmark data matrix from nts file
- readland.tps: Read landmark data from tps file
- read.morphologika: Read landmark data from Morphologika file
- readmulti.nts: Read landmark data from multiple nts files
- read.ply: Read mesh data (vertices and faces) from ply files
- 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
- summary.advanced.procD.lm: Print/Summary Function for geomorph
- summary.bilat.symmetry: Print/Summary Function for geomorph
- summary.compare.pls: 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.gpagen: Print/Summary Function for geomorph
- summary.morphol.disparity: Print/Summary Function for geomorph
- summary.physignal: Print/Summary Function for geomorph
- summary.plotTangentSpace: Print/Summary Function for geomorph
- summary.pls: Print/Summary Function for geomorph
- summary.procD.allometry: Print/Summary Function for geomorph
- summary.procD.lm: Print/Summary Function for geomorph
- summary.trajectory.analysis: Print/Summary Function for geomorph
- trajectory.analysis: Quantify and compare shape change trajectories
- two.b.pls: Two-block partial least squares analysis for shape data
- two.d.array: Convert (p x k x n) data array into 2D data matrix
- 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