Procrustes Analysis Software For Mac
Geometric Morphometric Analyses of 2D/3D Landmark Data
Read, manipulate, and digitize landmark data, generate shapevariables via Procrustes analysis for points, curves and surfaces, performshape analyses, and provide graphical depictions of shapes and patterns ofshape variation.
Readme
Geomorph is a software package for performing all stages of geometric morphometric shape analysis of 2- and 3-dimensional landmark points, as well as semilandmarks on curves and surfaces, in the R statistical computing environment. This repository is dedicated to providing beta versions between CRAN uploads.
Jul 24, 2017 When a shape is compared to another, or a set of shapes is compared to an arbitrarily selected reference shape, Procrustes analysis is sometimes further qualified as. Procrustes analysis takes as input two coordinate matrices with corresponding points (in QIIME, these are generated by running principalcoordinates.py on a distance matrix generated by betadiversity.py), and transforming the second coordinate set by rotating, scaling, and translating it to minimize the distances between corresponding points. SYN-TAX - a program (DOS and MAC, Windows under development) for PCA, PCoA, CA, NMDS, CCA, RDA, seriation, Procrustes analysis, testing ordination dissimilarities, hierarchical and nonhierarchical clustering, fuzzy clustering, minimum spanning trees, block clustering, comparison of dendrograms, partitions, consensus partitions, simulated. Mar 13, 2014 Last update: Thursday, 13-Mar-2014 12:56:32 EDT The following software is distributed 'as is', and it is free for anyone to use. Even though I have made every effort to ensure that computations are performed correctly, it is always a good idea to check for mathematical errors if you intend to publish results produced with this software.
To install the current geomorph R-package from CRAN:
Within R:
install.packages('geomorph')
For Mac users: please also install XQuartz from https://www.xquartz.org/. This allows the library(rgl) to function.
To install the current version of geomorph R-package from Github using devtools:
Within R:
install.packages('devtools')
devtools::install_github('geomorphR/geomorph', ref = 'Stable', build_vignettes = TRUE)
This installs a stable release of the current version of geomorph on CRAN, allowing us to quickly fix errors that slip thorough the cracks and are uploaded with the CRAN version.
To install the Development version (beta) of geomorph R-package from Github using devtools:
Within R:
Iphone webpage from app to mac. install.packages('devtools')
devtools::install_github('geomorphR/geomorph', ref = 'Develop', build_vignettes = TRUE)
NOTE FOR THE PRE-RELEASE (BETA) VERSION: We strongly discourage you from publishing results with this version, unless you check with the authors first.
Functions in geomorph
Software For Mac Free
| Name | Description | |
| buildtemplate | Build 3D surface template | |
| bilat.symmetry | Analysis of bilateral symmetry | |
| compare.multi.evol.rates | Comparing net rates of shape evolution among traits on phylogenies | |
| compare.evol.rates | Comparing net rates of shape evolution on phylogenies | |
| coords.subset | Subset landmark coordinates via a factor | |
| compare.pls | Comparisons of Effect Sizes from Partial Least Squares | |
| arrayspecs | Convert landmark data matrix into array (p x k x n) | |
| combine.subsets | Combine separate landmark configurations | |
| compare.CR | Comparisons of Effect Sizes from Modularity Analyses | |
| define.links | Define links between landmarks | |
| digit.fixed | Digitize 3D landmarks on mesh3d object | |
| digit.curves | Calculate semilandmarks along a curve | |
| digitize2d | Digitize 2D landmarks on .jpg files | |
| digitsurface | Digitize 3D fixed landmarks and surface semilandmarks | |
| geomorph-package | Geometric morphometric analyses for 2D/3D data | |
| globalIntegration | Quantify global integration relative to self-similarity | |
| fixed.angle | Rotate a subset of 2D landmarks to common articulation angle | |
| findMeanSpec | Identify specimen closest to the mean of a set of Procrustes shape variables | |
| gpagen | Generalized Procrustes analysis of points, curves, and surfaces | |
| estimate.missing | Estimate locations of missing landmarks | |
| interlmkdist | Calculate linear distances between landmarks | |
| gm.prcomp | Principal and phylogenetically-aligned components analysis of shape data | |
| editTemplate | Edit 3D template | |
| mshape | Estimate mean shape for a set of aligned specimens | |
| lizards | Dorsal head shape data of lizards | |
| modularity.test | Evaluate the degree of modular signal in shape data | |
| geomorph.data.frame | Create a data frame with shape data | |
| phylo.integration | Quantify phylogenetic morphological integration between two or more sets of variables under Brownian motion | |
| hummingbirds | Landmark data from hummingbird bills (includes sliding semilandmarks on curves) | |
| morphol.disparity | Morphological disparity for one or more groups of specimens | |
| plot.bilat.symmetry | Plot Function for geomorph | |
| plot.evolrate | Plot Function for geomorph | |
| gridPar | Set up parameters for grids, points, and links in plotRefToTarget | |
| phylo.modularity | Evaluate the degree of phylogenetic modular signal in Procrustes shape variables | |
| larvalMorph | Head and tail shapes of larval salamanders | |
| define.modules | Define modules (landmark partitions) | |
| integration.test | Quantify morphological integration between modules | |
| plotGMPhyloMorphoSpace | Deprecated functions in geomorph | |
| plotOutliers | Find potential outliers | |
| physignal | Assessing phylogenetic signal in Procrustes shape variables | |
| plot.mshape | Plot Function for geomorph | |
| define.sliders | Select points to 'slide' along curves | |
| plot.gm.prcomp | Plot Function for geomorph | |
| picknplot.shape | Pick points in geomorph scatterplots to visualize shape variation | |
| procD.lm | Procrustes ANOVA/regression for Procrustes shape variables | |
| print.pls | Print/Summary Function for geomorph | |
| print.combined.set | Print/Summary Function for geomorph | |
| print.procD.lm | Print/Summary Function for geomorph | |
| print.physignal | Print/Summary Function for geomorph | |
| print.compare.pls | Print/Summary Function for geomorph | |
| plot.physignal | Plot Function for geomorph | |
| mosquito | Landmarks on mosquito wings | |
| plot.CR | Plot Function for geomorph | |
| plethodon | Landmark data from Plethodon salamander heads | |
| plethShapeFood | Head shape and food use data from Plethodon salamanders | |
| plot.CR.phylo | Plot Function for geomorph | |
| plotTangentSpace | Deprecated functions in geomorph | |
| plot.gpagen | Plot Function for geomorph | |
| plotRefToTarget | Plot shape differences between a reference and target specimen | |
| plotAllSpecimens | Plot landmark coordinates for all specimens | |
| scallopPLY | 3D scan of a scallop shell from a .ply file in mesh3d format | |
| plotAllometry | Plotting to assist visualization of shape-size covariation (allometry) | |
| scallops | Landmark data from scallop shells | |
| print.gpagen | Print/Summary Function for geomorph | |
| summary.geomorphShapes | Print/Summary Function for geomorph | |
| summary.evolrate1 | Print/Summary Function for geomorph | |
| summary.gpagen | Print/Summary Function for geomorph | |
| plotspec | Plot 3D specimen, fixed landmarks and surface semilandmarks | |
| print.evolrate1 | Print/Summary Function for geomorph | |
| summary.gm.prcomp | Print/Summary Function for geomorph | |
| print.CR | Print/Summary Function for geomorph | |
| print.evolrate | Print/Summary Function for geomorph | |
| plot.pls | Plot Function for geomorph | |
| plot.procD.lm | Plot Function for geomorph | |
| plethspecies | Average head shape and phylogenetic relationships for several Plethodon salamander species | |
| readland.nts | Read landmark data matrix from nts file | |
| warpRefOutline | Creates a 2D outline warped to the mean shape | |
| warpRefMesh | Creates a mesh3d object warped to the mean shape | |
| print.geomorphShapes | Print/Summary function for geomorph | |
| print.gm.prcomp | Print/Summary function for geomorph | |
| readland.shapes | Read landmark data from a shapes object (StereoMorph) | |
| readland.fcsv | Read landmark data matrix from fcsv file | |
| print.morphol.disparity | Print/Summary Function for geomorph | |
| print.CR.phylo | Print/Summary Function for geomorph | |
| read.ply | Read mesh data (vertices and faces) from ply files | |
| readland.tps | Read landmark data from tps file | |
| procD.pgls | Phylogenetic ANOVA/regression for Procrustes shape variables | |
| summary.compare.pls | Print/Summary Function for geomorph | |
| ratland | Landmark data from dataset rat | |
| summary.pls | Print/Summary Function for geomorph | |
| readmulti.nts | Read landmark data from multiple nts files | |
| writeland.tps | Write landmark data to tps file | |
| summary.evolrate | Print/Summary Function for geomorph | |
| print.bilat.symmetry | Print/Summary Function for geomorph | |
| summary.procD.lm | Print/Summary Function for geomorph | |
| pupfish | Landmarks on pupfish | |
| read.morphologika | Read landmark data from Morphologika file(s) | |
| shape.predictor | Shape prediction from numeric predictors | |
| shapeHulls | Update Plots with Convex Hulls for Groups | |
| readmulti.tps | Read and combine multiple tps files | |
| rotate.coords | Rotate or flip landmark or coordinate configurations | |
| summary.CR | Print/Summary Function for geomorph | |
| summary.CR.phylo | Print/Summary Function for geomorph | |
| two.b.pls | Two-block partial least squares analysis for Procrustes shape variables | |
| two.d.array | Convert (p x k x n) data array into 2D data matrix | |
| summary.bilat.symmetry | Print/Summary Function for geomorph | |
| summary.morphol.disparity | Print/Summary Function for geomorph | |
| summary.physignal | Print/Summary Function for geomorph | |
| summary.combined.set | Print/Summary Function for geomorph | |
| No Results! | ||
Vignettes of geomorph
| Name | ||
| figs/PCAplot2D.png | ||
| figs/example_spec2.png | ||
| figs/example_template.png | ||
| figs/fixed.3D.png | ||
| figs/tree.plot.png | ||
| geomorph.PCA.Rmd | ||
| geomorph.assistance.Rmd | ||
| geomorph.digitize3D.Rmd | ||
| geomorph.functions.Rmd | ||
| No Results! | ||
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Details
| License | GPL (>= 2) |
| URL | https://github.com/geomorphR/geomorph |
| Encoding | UTF-8 |
| LazyData | true |
| RoxygenNote | 7.1.0 |
| VignetteBuilder | knitr |
| NeedsCompilation | no |
| Packaged | 2020-06-12 19:54:19 UTC; dcadams |
| Repository | CRAN |
| Date/Publication | 2020-06-12 23:50:07 UTC |
| imports | ape , graphics , grDevices , jpeg , stats , utils |
| suggests | knitr , rmarkdown , testthat |
| depends | R (>= 3.5.0) , rgl , RRPP |
| Contributors | Michael Collyer, Antigoni Kaliontzopoulou |
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