d = procrustes(X,Y)
determinesa linear transformation (translation, reflection, orthogonal rotation,and scaling) of the points in matrix Y
to bestconform them to the points in matrix X
. The goodness-of-fitcriterion is the sum of squared errors. procrustes
returnsthe minimized value of this dissimilarity measure in d
. d
isstandardized by a measure of the scale of X
, givenby:X
.However, if X
comprises repetitions of the samepoint, the sum of squared errors is not standardized.X
and Y
must have thesame number of points (rows), and procrustes
matches Y(i)
to X(i)
.Points in Y
can have smaller dimension (numberof columns) than those in X
. In this case, procrustes
addscolumns of zeros to Y
as necessary.[d,Z] = procrustes(X,Y)
alsoreturns the transformed Y
values.[d,Z,transform] = procrustes(X,Y)
alsoreturns the transformation that maps Y
to Z
. transform
isa structure array with fields: c
— Translation componentT
— Orthogonal rotationand reflection componentb
— Scale component[..] = procrustes(..,'scaling',flag
)
,when flag
is false
,allows you to compute the transformation without a scale component(that is, with b
equal to 1
).The default flag
is true
.[..] = procrustes(..,'reflection',flag
)
,when flag
is false
,allows you to compute the transformation without a reflection component(that is, with det(T)
equal to 1
).The default flag
is 'best'
,which computes the best-fitting transformation, whether or not itincludes a reflection component. A flag
of true
forcesthe transformation to be computed with a reflection component (thatis, with det(T)
equal to -1
) install.packages('geomorph')
install.packages('devtools')
devtools::install_github('geomorphR/geomorph', ref = 'Stable', build_vignettes = TRUE)
Top web design software mac. install.packages('devtools')
devtools::install_github('geomorphR/geomorph', ref = 'Develop', build_vignettes = TRUE)
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! |
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! |
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 |
[![Rdoc](http://www.rdocumentation.org/badges/version/geomorph)](http://www.rdocumentation.org/packages/geomorph)