Morpho

Package ‘Morpho’
January 27, 2023

Type Package
Title Calculations and Visualisations Related to Geometric
Morphometrics
Version 2.11
Date 2023-01-26
Description A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Suggests car, lattice, shapes, testthat
Depends R (>= 3.2.0)
Imports Rvcg (>= 0.7), rgl (>= 0.100.18), foreach (>= 1.4.0), Matrix
(>= 1.0-1), MASS, parallel, doParallel (>= 1.0.6), colorRamps,
Rcpp, graphics, grDevices, methods, stats, utils, jsonlite, sf,
bezier
LinkingTo Rcpp, RcppArmadillo (>= 0.4)
Copyright see COPYRIGHTS file for details
License GPL-2
BugReports https://github.com/zarquon42b/Morpho/issues
LazyLoad yes
URL https://github.com/zarquon42b/Morpho
Encoding UTF-8
RoxygenNote 7.2.1
NeedsCompilation yes
Author Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb],
Dryden Ian [cph]
Maintainer Stefan Schlager <zarquon42@gmail.com>
Repository CRAN
Date/Publication 2023-01-27 11:00:02 UTC
1
2 R topics documented:
R topics documented:
Morpho-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
align2procSym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
angle.calc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
angleTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
anonymize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
applyTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
areaSphere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
areaSpherePart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
armaGinv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
array2list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
arrMean3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
asymPermute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
barycenter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
bindArr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
boneData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
CAC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
cExtract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
checkLM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
checkNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
classify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
closemeshKD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
computeArea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
computeTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
covDist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
covW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
createAtlas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
CreateL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
createMissingList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
crossProduct . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
cSize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
cutMeshPlane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
cutSpace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
CVA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
data2platonic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
deformGrid2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
deformGrid3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
equidistantCurve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
exVar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
fastKmeans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
file2mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
find.outliers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
fixLMmirror . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
fixLMtps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
getFaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
getMeaningfulPCs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
R topics documented: 3
getOuterViewpoints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
getPCscores . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
getPCtol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
getPLSCommonShape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
getPLSfromScores . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
getPLSscores . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
getPointAlongOutline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
getSides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
getTrafo4x4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
getTrafoRotaxis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
getVisibleVertices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
groupPCA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
histGroup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
icpmat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
invertFaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
kendalldist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
line2plane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
lineplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
list2array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
LPS2RAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
mcNNindex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
mergeMeshes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
mesh2grey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
mesh2obj . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
meshcube . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
meshDist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
meshPlaneIntersect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
meshres . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
mirror . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
mirror2plane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
name2factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
NNshapeReg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
nose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
pcAlign . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
pcaplot3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
PCdist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
permudist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
permuvec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
placePatch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
plot.slider3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
plotAtlas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
plotNormals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
pls2B . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
plsCoVar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
plsCoVarCommonShape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
points2plane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
prcompfast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
predict.bgPCA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
4 R topics documented:
predict.CVA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
predictPLSfromData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
predictPLSfromScores . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
predictRelWarps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
predictShape.lm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
proc.weight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
procAOVsym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
ProcGPA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
procSym . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
projRead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
qqmat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
quad2trimesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
r2morphoj . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
ray2mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
read.csv.folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
read.fcsv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
read.lmdta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
read.mpp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
read.pts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
read.slicerjson . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
readallTPS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
readLandmarks.csv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
regdist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
RegScore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
relaxLM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
relWarps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
render . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
resampleCurve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
restoreFromPCA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
restoreShapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
retroDeform3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
retroDeformMesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
rotaxis3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
rotaxisMat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
rotmesh.onto . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
rotonmat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
rotonto . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
scalemesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
slider2d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
slider3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
solutionSpace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
sortCurve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
symmetrize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
tps3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
typprob . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
unrefVertex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
updateIndices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
updateNormals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Morpho-package 5
vecx . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
virtualMeshScan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
warpmovie3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
write.fcsv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
write.pts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
write.slicerjson . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Index 181
Morpho-package A toolbox providing methods for data-acquisition, visualisation and

statistical methods related to Geometric Morphometrics and shape
analysis
Description
A toolbox for Morphometric calculations. Including sliding operations for Semilandmarks, import-
ing, exporting and manipulating of 3D-surface meshes and semi-automated placement of surface
landmarks.
Details
Package: Morpho
Type: Package
Version: 2.11
Date: 2023-01-26
License: GPL
LazyLoad: yes
Note
The pdf-version of Morpho-help can be obtained from CRAN on https://cran.r-project.org/

package=Morpho
For more advanced operations on triangular surface meshes, check out my package Rvcg: https:
//cran.r-project.org/package=Rvcg or the code repository on github https://github.com/
zarquon42b/Rvcg
Author(s)
Stefan Schlager <zarquon42@gmail.com>

Maintainer: Stefan Schlager <zarquon42@gmail.com>
6 align2procSym
References
Schlager S. 2013. Soft-tissue reconstruction of the human nose: population differences and sexual
dimorphism. PhD thesis, Universitätsbibliothek Freiburg. URL: http://www.freidok.uni-freiburg.
de/volltexte/9181/.
align2procSym align new data to an existing Procrustes registration
Description
align new data to an existing Procrustes registration
Usage
align2procSym(x, newdata, orp = TRUE)
Arguments
x result of a procSym call
newdata matrix or array of with landmarks corresponding to the data aligned in x
orp logical: allows to skip orthogonal projection, even if it was used in the procSym
call.
Value
an array with data aligned to the mean shape in x (and projected into tangent space)
Note
this will never yield the same result as a pooled Procrustes analysis because the sample mean is
iteratively updated and new data would change the mean.
Examples
require(Morpho)
data(boneData)
# run procSym on entire data set
proc <- procSym(boneLM)
# this is the training data
array1 <- boneLM[,,1:60]
newdata <- boneLM[,,61:80]
proc1 <- procSym(array1)
newalign <- align2procSym(proc1,newdata)
## compare alignment for one specimen to Proc. registration using all data
## Not run:
deformGrid3d(newalign[,,1],proc$orpdata[,,61])
## End(Not run)
angle.calc 7
angle.calc calculate angle between two vectors
Description
calculates unsigned angle between two vectors
Usage
angle.calc(x, y)
Arguments
x numeric vector (or matrix to be interpreted as vector)
y numeric vector (or matrix to be interpreted as vector) of same length as x
Value
angle between x and y in radians.
Examples
#calculate angle between two centered and

# superimposed landmark configuration
data(boneData)
opa <- rotonto(boneLM[,,1],boneLM[,,2])
angle.calc(opa$X, opa$Y)
angleTest Test whether the direction of two vectors is similar
Description
Test whether the direction of two vectors is similar
Usage
angleTest(x, y)
Arguments
x vector
y vector
8 anonymize
Details
Under the assumption of all (normalized) n-vectors being represented by an n-dimensional hyper-
sphere, the probability of the angle between two vectors is <= the measured values can be estimated
as the area of a cap defined by that angle and divided by the hypersphere’s complete surface area.
Value
a list with
angle angle between vectors

p.value p-value for the probability that the angle between two random vectors is smaller
or equal to the one calculatted from x and y
References
S. Li , 2011. Concise Formulas for the Area and Volume of a Hyperspherical Cap. Asian Journal of
Mathematics & Statistics, 4: 66-70.
Examples
x <- c(1,0); y <- c(1,1) # for a circle this should give us p = 0.25 as the angle between vectors
## is pi/4 and for any vector the segment +-pi/4 covers a quarter of the circle
angleTest(x,y)
anonymize Replace ID-strings of data and associated files.
Description
Replace ID-strings with for digits - e.g. for blind observer error testing.
Usage
anonymize(
data,
remove,
path = NULL,
dest.path = NULL,
ext = ".ply",
split = "_",
levels = TRUE,
prefix = NULL,
suffix = NULL,
sample = TRUE
)
applyTransform 9
Arguments
data Named array, matrix or vector containing data.
remove integer: which entry (separated by split) of the name is to be removed
path Path of associated files to be copied to renamed versions.
dest.path where to put renamed files.
ext file extension of files to be renamed.
split character: by which to split specimen-ID
levels logical: if a removed entry is to be treated as a factor. E.g. if one specimen has
a double entry, the anonymized versions will be named accordingly.
prefix character: prefix before the alias string.
suffix character: suffix after the alias ID-string.
sample logical: whether to randomize alias ID-string.
Value
data data with names replaced
anonymkey map of original name and replaced name
Examples
anonymize(iris,remove=1)
applyTransform apply affine transformation to data
Description
apply affine transformation to data
Usage
applyTransform(x, trafo, ...)
## S3 method for class 'matrix'

applyTransform(x, trafo, inverse = FALSE, threads = 1, ...)
## S3 method for class 'mesh3d'

## Default S3 method:
10 areaSphere
Arguments
x matrix or mesh3d
trafo 4x4 transformation matrix or an object of class "tpsCoeff"
... additional arguments, currently not used.
inverse logical: if TRUE, the inverse of the transformation is applied (for TPS coeffi-
cients have to be recomputed)
threads threads to be used for parallel execution in tps deformation.
Value
the transformed object
See Also
rotonto, link{rotmesh.onto}, tps3d, computeTransform
Examples
data(boneData)
rot <- rotonto(boneLM[,,1],boneLM[,,2])
trafo <- getTrafo4x4(rot)
boneLM2trafo <- applyTransform(boneLM[,,2],trafo)
areaSphere compute the area of an n-dimensional hypersphere
Description
compute the area of an n-dimensional hypersphere
Usage
areaSphere(n, r = 1)
Arguments
n dimensionality of space the hypersphere is embedded in (e.g.3 for a 3D-sphere)
r radius of the sphere
Value
returns the area
Examples
areaSphere(2) #gives us the circumference of a circle of radius 1
areaSpherePart 11
areaSpherePart compute the area of an n-dimensional hypersphere cap
Description
compute the area of an n-dimensional hypersphere cap
Usage
areaSpherePart(n, phi, r = 1)
Arguments
n dimensionality of space the hypersphere is embedded in (e.g.3 for a 3D-sphere)
phi angle between vectors defining the cone
r radius of the sphere
Value
returns the area of the hypersphere cap
Examples
areaSpherePart(2,pi/2) # covers half the area of a circle
armaGinv calculate Pseudo-inverse of a Matrix using RcppArmadillo
Description
a simple wrapper to call Armadillo’s pinv function
Usage
armaGinv(x, tol = NULL)
Arguments
x numeric matrix
tol numeric: maximum singular value to be considered
Value
Pseudo-inverse
12 arrMean3
Examples
mat <- matrix(rnorm(12),3,4)
pinvmat <- armaGinv(mat)
array2list reverts list2array, converting an array to a list of matrices
Description
reverts list2array, converting an array to a list of matrices
Usage
array2list(x)
Arguments
x array
Value
returns a list containing the matrices
arrMean3 calculate mean of an array
Description
calculate mean of a 3D-array (e.g. containing landmarks) (fast) using the Armadillo C++ Backend
Usage
arrMean3(arr)
Arguments
arr k x m x n dimensional numeric array
Value
matrix of dimensions k x m.
Note
this is the same as apply(arr, 1:2, mean), only faster for large configurations.
asymPermute 13
Examples
data(boneData)
proc <- ProcGPA(boneLM, silent = TRUE)
mshape <- arrMean3(proc$rotated)
asymPermute Assess differences in amount and direction of asymmetric variation

(only object symmetry)
Description
Assess differences in amount and direction of asymmetric variation (only object symmetry)
Usage
asymPermute(x, groups, rounds = 1000, which = NULL)
Arguments
x object of class symproc result from calling procSym with pairedLM specified
groups factors determining grouping.
rounds number of permutations
which select which factorlevels to use, if NULL, all pairwise differences will be as-
sessed after shuffling pooled data.
Value
dist difference between vector lengths of group means
angle angle (in radians) between vectors of group specific asymmetric deviation
means actual group averages
p.dist p-value obtained by comparing the actual distance to randomly acquired dis-
tances
p.angle p-value obtained by comparing the actual angle to randomly acquired angles
permudist vector containing differences between random group means’ vector lenghts
permuangle vector containing angles between random group means’ vectors
groupmeans array with asymmetric displacement per group
levels character vector containing the factors used
Note
This test is only sensible if between-group differences concerning directional asymmetry have been
established (e.g. by applying a MANOVA on the "asymmetric" PCscores (see also procSym) and
one wants to test whether these can be attributed to differences in amount and/or direction of asym-
metric displacement. Careful interpretation for very small amounts of directional asymmetry is
advised. The Null-Hypothesis is that we have the same directional asymmetry in both groups. If
you want to test whether the angle between groups is similar, please use angleTest.
14 barycenter
See Also
procSym
barycenter calculates the barycenters for all faces of a triangular mesh
Description
calculates the barycenters for all faces of a triangular mesh
Usage
barycenter(mesh)
Arguments
mesh triangular mesh of class ’mesh3d’
Value
k x 3 matrix of barycenters for all k faces of input mesh.
See Also
closemeshKD
Examples
data(nose)
bary <- barycenter(shortnose.mesh)
## Not run:
require(rgl)
##visualize mesh
wire3d(shortnose.mesh)
# visualize barycenters
points3d(bary, col=2)
## now each triangle is equipped with a point in its barycenter
## End(Not run)
bindArr 15
bindArr concatenate multiple arrays/matrices
Description
concatenate multiple 3-dimensional arrays and/or 2-dimensional matrices to one big array
Usage
bindArr(..., along = 1, collapse = FALSE)
Arguments
... matrices and/or arrays with appropriate dimensionality to combine to one array,
or a single list containing suitable matrices, or arrays).
along dimension along which to concatenate.
collapse logical: if the resulting array is shallow (only 1 dimension deep), it is converted
to a matrix.
Details
dimnames, if present and if differing between entries, will be concatenated, separated by a "_".
Value
returns array of combined matrices/arrays
See Also
cbind, rbind, array
Examples
A <- matrix(rnorm(18),6,3)
B <- matrix(rnorm(18),6,3)
C <- matrix(rnorm(18),6,3)
#combine to 3D-array
newArr <- bindArr(A,B,C,along=3)
#combine along first dimension
newArr2 <- bindArr(newArr,newArr,along=1)
16 CAC
boneData Landmarks and a triangular mesh
Description
Landmarks on the osseous human nose and a triangular mesh representing this structure.
Format
boneLM: A 10x3x80 array containing 80 sets of 3D-landmarks placed on the human osseous nose.
skull_0144_ch_fe.mesh: The mesh representing the area of the first individual of boneLM
CAC calculate common allometric component
Description
calculate common allometric component
Usage
CAC(x, size, groups = NULL, log = FALSE)
Arguments
x datamatrix (e.g. with PC-scores) or 3D-array with landmark coordinates
size vector with Centroid sizes
groups grouping variable
log logical: use log(size)
Value
CACscores common allometric component scores
CAC common allometric component
x (group-) centered data
sc CAC reprojected into original space by applying CAC %*% x
RSCscores residual shape component scores
RSC residual shape components
gmeans groupmeans
CS the centroid sizes (log transformed if log = TRUE)
cExtract 17
References
Mitteroecker P, Gunz P, Bernhard M, Schaefer K, Bookstein FL. 2004. Comparison of cranial
ontogenetic trajectories among great apes and humans. Journal of Human Evolution 46(6):679-97.
Examples
data(boneData)
pop.sex <- name2factor(boneLM,which=3:4)
cac <- CAC(proc$rotated,proc$size,pop.sex)
plot(cac$CACscores,cac$size)#plot scores against Centroid size
cor.test(cac$CACscores,cac$size)#check for correlation
#visualize differences between large and small on the sample's consensus
## Not run:
large <- restoreShapes(max(cac$CACscores),cac$CAC,proc$mshape)
small <- restoreShapes(min(cac$CACscores),cac$CAC,proc$mshape)
deformGrid3d(small,large,ngrid=0)
## End(Not run)
cExtract extract information about fixed landmarks, curves and patches from
and atlas generated by "landmark"
Description
After exporting the pts file of the atlas from "landmark" and importing it into R via "read.pts"
cExtract gets information which rows of the landmark datasets belong to curves or patches.
Usage
cExtract(pts.file)
Arguments
pts.file either a character naming the path to a pts.file or the name of an object imported
via read.pts.
Value
returns a list containing the vectors with the indices of matrix rows belonging to the in "landmark"
defined curves, patches and fix landmarks and a matrix containing landmark coordinates.
Author(s)
Stefan Schlager
See Also
read.lmdta ,read.pts
18 checkLM
checkLM Visually browse through a sample rendering its landmarks and corre-
sponding surfaces.
Description
Browse through a sample rendering its landmarks and corresponding surfaces. This is handy e.g. to
check if the landmark projection using placePatch was successful, and to mark specific specimen.
Usage
checkLM(
dat.array,
path = NULL,
prefix = "",
suffix = ".ply",
col = "white",
pt.size = NULL,
alpha = 1,
begin = 1,
render = c("w", "s"),
point = c("s", "p"),
add = FALSE,
meshlist = NULL,
Rdata = FALSE,
atlas = NULL,
text.lm = FALSE
)
Arguments
dat.array array or list containing landmark coordinates.
path optional character: path to files where surface meshes are stored locally. If not
specified only landmarks are displayed.
prefix prefix to attach to the filenames extracted from dimnames(dat.array)[[3]]
(in case of an array), or names(dat.array) (in case of a list)
suffix suffix to attach to the filenames extracted from dimnames(dat.array)[[3]] (in
case of an array), or names(dat.array) (in case of a list)
col mesh color
pt.size size of plotted points/spheres. If point="s". pt.size defines the radius of the
spheres. If point="p" it sets the variable size used in point3d.
alpha value between 0 and 1. Sets transparency of mesh 1=opaque 0= fully transpar-
ent.
begin integer: select a specimen to start with.
render if render="w", a wireframe will be drawn, else the meshes will be shaded.
checkLM 19
point how to render landmarks. "s"=spheres, "p"=points.

add logical: add to existing rgl window.
meshlist list holding meshes in the same order as dat.array (Overrides path).
Rdata logical: if the meshes are previously stored as Rdata-files by calling save(), these
are simply loaded and rendered. Otherwise it is assumed that the meshes are
stored in standard file formats such as PLY, STL or OBJ, that are then imported
with the function file2mesh.
atlas provide object generated by createAtlas to specify coloring of surface patches,
curves and landmarks
text.lm logical: number landmarks. Only applicable when atlas=NULL.
Value
returns an invisible vector of indices of marked specimen.
See Also
placePatch, createAtlas, plotAtlas,file2mesh
Examples
data(nose)
###create mesh for longnose
longnose.mesh <- tps3d(shortnose.mesh,shortnose.lm,longnose.lm,threads=1)
### write meshes to disk
save(shortnose.mesh, file="shortnose")
save(longnose.mesh, file="longnose")
## create landmark array

data <- bindArr(shortnose.lm, longnose.lm, along=3)
dimnames(data)[[3]] <- c("shortnose", "longnose")
## Not run:
checkLM(data, path="./",Rdata=TRUE, suffix="")
## End(Not run)
## now visualize by using an atlas:

atlas <- createAtlas(shortnose.mesh, landmarks =
shortnose.lm[c(1:5,20:21),],
patch=shortnose.lm[-c(1:5,20:21),])
if (interactive()){
checkLM(data, path="./",Rdata=TRUE, suffix="", atlas=atlas)
}
## remove data from disk
unlink("shortnose")
unlink("longnose")
20 classify
checkNA check for NA values in a matrix (of landmarks)
Description
check for NA values in a matrix (of landmarks)
Usage
checkNA(x)
Arguments
x matrix containing landmarks
Value
returns a vector with missin landmarks and a vector of length=0 if none are missing
classify classify specimen based on between-group PCA or CVA or typprob-

Class
Description
classify specimen based on between-group PCA, CVA or typprobClass
Usage
classify(x, cv = TRUE, ...)
## S3 method for class 'bgPCA'

classify(x, cv = TRUE, newdata = NULL, ...)
## S3 method for class 'CVA'

classify(x, cv = T, newdata = NULL, prior = NULL, ...)
## S3 method for class 'typprob'

classify(x, cv = TRUE, ...)
closemeshKD 21
Arguments
x result of groupPCA, CVA or typprobClass

cv logical: use cross-validated scores if available
... currently not used
newdata use new data to predict scores and evaluate group affinity
prior specify prior probability for CVA evaluation if NULL prior from CVA will be
used. Be m your number of groups then to set the prior equally for all groups set
prior=rep(1,m)/m.
Value
class classification result

groups original grouping variable, only available if newdata=NULL
posterior only for object of CVA and typprob, also the posterior probabilities are returned
See Also
CVA,groupPCA, typprobClass
closemeshKD Project coordinates onto a target triangular surface mesh.
Description
For a set of 3D-coordinates the closest matches on a target surface are determined and normals at
as well as distances to that point are calculated.
Usage
closemeshKD(
x,
mesh,
k = 50,
sign = FALSE,
barycoords = FALSE,
cores = 1,
method = 0,
...
)
22 closemeshKD
Arguments
x k x 3 matrix containing 3D-coordinates or object of class mesh3d.
mesh triangular surface mesh stored as object of class mesh3d.
k neighbourhood of kd-tree to search - the larger, the slower - but the more likely
the absolutely closest point is hit.
sign logical: if TRUE, signed distances are returned.
barycoords logical: if TRUE, barycentric coordinates of the hit points are returned.
cores integer: how many cores to use for the search algorithm.
method integer: either 0 or 1, if 0 ordinary Euclidean distance is used, if 1, the distance
suggested by Moshfeghi(1994) is calculated.
... additional arguments. currently unavailable.
Details
The search for the clostest point is designed as follows: Calculate the barycenter of each target
face. For each coordinate of x, determine the k closest barycenters and calculate the distances to
the closest point on these faces.
Value
returns an object of class mesh3d. with:
vb 4xn matrix containing n vertices as homolougous coordinates

normals 4xn matrix containing vertex normals
quality vector: containing distances to target. In case of method=1, this is not the Eu-
clidean distance but the distance of the reference point to the faceplane (orthog-
onally projected) plus the distance to the closest point on one of the face’s edges
(the target point). See the literature cited below for details.
it 4xm matrix containing vertex indices forming triangular faces.Only available,
when x is a mesh
Author(s)
Stefan Schlager
References
Baerentzen, Jakob Andreas. & Aanaes, H., 2002. Generating Signed Distance Fields From Triangle
Meshes. Informatics and Mathematical Modelling.
Moshfeghi M, Ranganath S, Nawyn K. 1994. Three-dimensional elastic matching of volumes IEEE
Transactions on Image Processing: A Publication of the IEEE Signal Processing Society 3:128-138.
See Also
ply2mesh
colors 23
Examples
data(nose)
out <- closemeshKD(longnose.lm,shortnose.mesh,sign=TRUE)
### show distances - they are very small because
###longnose.lm is scaled to unit centroid size.
hist(out$quality)
colors predefined colors for bone and skin
Description
predefined colors for bone and skin
Details
available colors are:
bone1
bone2
bone3
skin1
skin2
skin3
skin4
computeArea Compute area enclosed within an irregular polygon
Description
Compute area enclosed within an irregular polygon - i.e. defined by curves
Usage
computeArea(x)
Arguments
x k x 2 or k x 3 matrix containing ordered coordinates forming the boundary of
the area. For 3D-cases, the area should be closed to a 2D surface (see details
below).
24 computeTransform
Details
For 3D coordinates, a PCA is computed and only the first two PCs are used to compute the area.
This is a projection of the coordinates onto a 2D plane spanned by those PCs.
Value
returns a list containing
area size of the enclosed area

xpro2D projected coordinates of x in the 2D plane.
poly object of class sp as defined by the sp package.
xpro3D For 3D-cases, this contains the projected coordinates of x rotated back into the
original coordinate system
Note
in case custom planes are preferred, the data can first be projected onto such a custom defined plane
via points2plane first.
Examples
require(shapes)
require(sf)
myarea <- computeArea(gorf.dat[c(1,6:8,2:5),,1])
myarea$area
plot(myarea$poly)
## 3D example
data(boneData)
myarea3D <- computeArea(boneLM[c(4,2,3,7,5,6,8),,1])
plot(myarea3D$poly)
cent <- colMeans(myarea3D$xpro2D)
text(cent[1],cent[2],labels=paste0("Area=",round(myarea3D$area,digits=2)))
computeTransform calculate an affine transformation matrix
Description
calculate an affine transformation matrix

computeTransform 25
Usage
computeTransform(
x,
y,
type = c("rigid", "similarity", "affine", "tps"),
reflection = FALSE,
lambda = 1e-08,
weights = NULL,
centerweight = FALSE,
threads = 1
)
Arguments
x fix landmarks. Can be a k x m matrix or mesh3d.

y moving landmarks. Can be a k x m matrix or mesh3d.
type set type of affine transformation: options are "rigid", "similarity" (rigid + scale)
and "affine",
reflection logical: if TRUE "rigid" and "similarity" allow reflections.
lambda numeric: regularisation parameter of the TPS.
weights vector of length k, containing weights for each landmark (only used in type="rigid"
or "similarity").
centerweight logical or vector of weights: if weights are defined and centerweigths=TRUE,
the matrix will be centered according to these weights instead of the barycenter.
If centerweight is a vector of length nrow(x), the barycenter will be weighted
accordingly.
threads number of threads to use in TPS interpolation.
Details
x and y can also be a pair of meshes with corresponding vertices.
Value
returns a 4x4 (3x3 in 2D case) transformation matrix or an object of class "tpsCoeff" in case of
type="tps".
Note
all lines containing NA, or NaN are ignored in computing the transformation.
See Also
rotonto, link{rotmesh.onto}, tps3d

26 covDist
Examples
data(boneData)
trafo <- computeTransform(boneLM[,,1],boneLM[,,2])
transLM <- applyTransform(boneLM[,,2],trafo)
covDist calculates distances and PC-coordinates of covariance matrices
Description
calculates PC-coordinates of covariance matrices by using the Riemannian metric in their respective
space.
Usage
covDist(s1, s2)
covPCA(
data,
groups,
rounds = 1000,
bootrounds = 0,
lower.bound = 0.05,
upper.bound = 0.95
)
Arguments
s1 m x m covariance matrix
s2 m x m covariance matrix
data matrix containing data with one row per observation
groups factor: group assignment for each specimen
rounds integer: rounds to run permutation of distances by randomly assigning group
membership
bootrounds integer: perform bootstrapping to generate confidence intervals (lower bound-
ary, median and upper boundary) for PC-scores.
lower.bound numeric: set probability (quantile) for lower boundary estimate from bootstrap-
ping.
upper.bound numeric: set probability (quantile) for upper boundary estimate from bootstrap-
ping.
covDist 27
Details
covDist calculates the Distance between covariance matrices while covPCA uses a MDS (multidi-
mensional scaling) approach to obtain PC-coordinates from a distance matrix derived from multiple
groups. P-values for pairwise distances can be computed by permuting group membership and com-
paring actual distances to those obtained from random resampling. To calculate confidence intervals
for PC-scores, within-group bootstrapping can be performed.
Value
covDist returns the distance between s1 and s2
covPCA returns a list containing:
if scores = TRUE
PCscores PCscores
eigen eigen decomposition of the centered inner product
if rounds > 0
dist distance matrix

p.matrix p-values for pairwise distances from permutation testing
if bootrounds > 0
bootstrap list containing the lower and upper bound of the confidence intervals of PC-
scores as well as the median of bootstrapped values.
boot.data array containing all results generated from bootstrapping.
Author(s)
Stefan Schlager
References
Mitteroecker P, Bookstein F. 2009. The ontogenetic trajectory of the phenotypic covariance matrix,
with examples from craniofacial shape in rats and humans. Evolution 63:727-737.
Hastie T, Tibshirani R, Friedman JJH. 2013. The elements of statistical learning. Springer New
York.
See Also
prcomp
Examples
cpca <- covPCA(iris[,1:4],iris[,5])

cpca$p.matrix #show pairwise p-values for equal covariance matrices
## Not run:
28 covW
require(car)
sp(cpca$PCscores[,1],cpca$PCscores[,2],groups=levels(iris[,5]),
smooth=FALSE,xlim=range(cpca$PCscores),ylim=range(cpca$PCscores))
data(boneData)
pop <- name2factor(boneLM, which=3)
## compare covariance matrices for PCscores of Procrustes fitted data
cpca1 <- covPCA(proc$PCscores, groups=pop, rounds = 1000)
## view p-values:
cpca1$p.matrix # differences between covariance matrices
# are significant
## visualize covariance ellipses of first 5 PCs of shape
spm(proc$PCscores[,1:5], groups=pop, smooth=FALSE,ellipse=TRUE, by.groups=TRUE)
## covariance seems to differ between 1st and 5th PC
## for demonstration purposes, try only first 4 PCs
cpca2 <- covPCA(proc$PCscores[,1:4], groups=pop, rounds = 1000)
## view p-values:
cpca2$p.matrix # significance is gone
## End(Not run)
#do some bootstrapping 1000 rounds

cpca <- covPCA(iris[,1:4],iris[,5],rounds=0, bootrounds=1000)
#plot bootstrapped data of PC1 and PC2 for first group
plot(t(cpca$boot.data[1,1:2,]),xlim=range(cpca$boot.data[,1,]),
ylim=range(cpca$boot.data[,2,]))
points(t(cpca$PCscores[1,]),col="white",pch=8,cex=1.5)##plot actual values
for (i in 2:3) {
points(t(cpca$boot.data[i,1:2,]),col=i)##plot other groups
points(t(cpca$PCscores[i,]),col=1,pch=8,cex=1.5)##plot actual values
}
covW calculate the pooled within groups covariance matrix
Description
calculate the pooled within groups covariance matrix
Usage
covW(data, groups, robust = c("classical", "mve", "mcd"), ...)

createAtlas 29
Arguments
data a matrix containing data
groups grouping variables
robust character: determines covariance estimation methods in case sep=TRUE, when
covariance matrices and group means can be estimated robustly using MASS::cov.rob.
Default is the standard product-moment covariance matrix.
... additional parameters passed to MASS::cov.rob for robust covariance and mean
estimations.
Value
Returns the pooled within group covariance matrix. The attributes contain the entry means, con-
taining the respective group means.
Author(s)
Stefan Schlager
See Also
cov, typprobClass
Examples
data(iris)
poolCov <- covW(iris[,1:4],iris[,5])
createAtlas Create an atlas needed in placePatch
Description
Create an atlas needed in placePatch
Usage
createAtlas(
mesh,
landmarks,
patch,
corrCurves = NULL,
patchCurves = NULL,
keep.fix = NULL
)
30 CreateL
Arguments
mesh triangular mesh representing the atlas’ surface
landmarks matrix containing landmarks defined on the atlas, as well as on each specimen
in the corresponding sample.
patch matrix containing semi-landmarks to be projected onto each specimen in the
corresponding sample.
corrCurves a vector or a list containing vectors specifiyng the rowindices of landmarks
to be curves that are defined on the atlas AND each specimen. e.g. if land-
marks 2:4 and 5:10 are two distinct curves, one would specifiy corrCurves =
list(c(2:4), c(5:10)).
patchCurves a vector or a list containing vectors specifiyng the rowindices of landmarks to
be curves that are defined ONLY on the atlas. E.g. if coordinates 5:10 and
20:40 on the patch are two distinct curves, one would specifiy patchCurves =
list(c(5:10),c(20:40)).
keep.fix in case corrCurves are set, specify explicitly which landmarks are not allowed
to slide during projection (with placePatch)
Value
Returns a list of class "atlas". Its content is corresponding to argument names.
Note
This is a helper function of placePatch.
See Also
placePatch, plotAtlas
Examples
data(nose)
shortnose.lm[c(1:5,20:21),], patch=shortnose.lm[-c(1:5,20:21),])
CreateL Create Matrices necessary for Thin-Plate Spline
Description
Create (Bending Engergy) Matrices necessary for Thin-Plate Spline, and sliding of Semilandmarks
CreateL 31
Usage
CreateL(
matrix,
lambda = 1e-08,
output = c("K", "L", "Linv", "Lsubk", "Lsubk3"),
threads = 1
)
Arguments
matrix k x 3 or k x 2 matrix containing landmark coordinates.
lambda numeric: regularization factor
output character vector: select which matrices to create. Can be a vector containing
any combination of the strings: "K", "L","Linv","Lsubk", "Lsubk3".
threads threads to be used for parallel execution calculating K. sliding of semilandmarks.
Value
depending on the choices in output:
L Matrix K as specified in Bookstein (1989)

L Matrix L as specified in Bookstein (1989)
Linv Inverse of matrix L as specified in Bookstein (1989)
Lsubk uper left k x k submatrix of Linv
Lsubk3 Matrix used for sliding in slider3d and relaxLM
Note
This function is not intended to be called directly - except for playing around to grasp the mechan-
sims of the Thin-Plate Spline.
References
Gunz, P., P. Mitteroecker, and F. L. Bookstein. 2005. Semilandmarks in Three Dimensions, in
Modern Morphometrics in Physical Anthropology. Edited by D. E. Slice, pp. 73-98. New York:
Kluwer Academic/Plenum Publishers.
Bookstein FL. 1989. Principal Warps: Thin-plate splines and the decomposition of deformations.
IEEE Transactions on pattern analysis and machine intelligence 11(6).
See Also
tps3d
32 createMissingList
Examples
data(boneData)
L <- CreateL(boneLM[,,1])
## calculate Bending energy between first and second specimen:
be <- t(boneLM[,,2])%*%L$Lsubk%*%boneLM[,,2]
## calculate Frobenius norm
sqrt(sum(be^2))
## the amount is dependant on on the squared scaling factor
# scale landmarks by factor 5 and compute bending energy matrix
be2 <- t(boneLM[,,2]*5)%*%L$Lsubk%*%(boneLM[,,2]*5)
sqrt(sum(be2^2)) # exactly 25 times the result from above
## also this value is not symmetric:
L2 <- CreateL(boneLM[,,2])
be3 <- t(boneLM[,,1])%*%L2$Lsubk%*%boneLM[,,1]
sqrt(sum(be3^2))
createMissingList create a list with empty entries to be used as missingList in slider3d
Description
create a list with empty entries to be used as missingList in slider3d
Usage
createMissingList(x)
Arguments
x length of the list to be created
Value
returns a list of length x filled with numerics of length zero.
See Also
fixLMtps,fixLMmirror, slider3d
Examples
## Assume in a sample of 10, the 9th individual has (semi-)landmarks 10:50
# hanging in thin air (e.g. estimated using fixLMtps)
# while the others are complete.
## create empty list
missingList <- createMissingList(10)
missingList[[9]] <- 10:50
crossProduct 33
crossProduct calculate the orthogonal complement of a 3D-vector
Description
calculate the orthogonal complement of a 3D-vector
Usage
crossProduct(x, y, normalize = TRUE)
tangentPlane(x)
Arguments
x vector of length 3.
y vector of length 3.
normalize logical: if TRUE, the resulting vector is normalized
Details
calculate the orthogonal complement of a 3D-vector or the 3D-crossproduct, finding an orthogonal
vector to a plane in 3D.
Value
tangentPlane:
crossProduct: returns a vector of length 3.
y vector orthogonal to x
z vector orthogonal to x and y
Author(s)
Stefan Schlager
Examples
require(rgl)
x <- c(1,0,0)
y <- c(0,1,0)
#example tangentPlane
z <- tangentPlane(x)
#visualize result
## Not run:
34 cSize
lines3d(rbind(0, x), col=2, lwd=2)

## show complement
lines3d(rbind(z$y, 0, z$z), col=3, lwd=2)
## End(Not run)
# example crossProduct
z <- crossProduct(x, y)
# show x and y
## Not run:
lines3d(rbind(x, 0, y), col=2, lwd=2)
# show z
lines3d(rbind(0, z), col=3, lwd=2)
## End(Not run)
cSize calculate Centroid Size for a landmark configuration
Description
calculate Centroid Size for a landmark configuration
Usage
cSize(x)
Arguments
x k x 3 matrix containing landmark coordinates or mesh of class "mesh3d"
Value
returns Centroid size
Examples
data(boneData)
cSize(boneLM[,,1])
cutMeshPlane 35
cutMeshPlane cut a mesh by a hyperplane and remove parts above/below that plane
Description
cut a mesh by a hyperplane and remove parts above/below that plane
Usage
cutMeshPlane(mesh, v1, v2 = NULL, v3 = NULL, normal = NULL, keep.upper = TRUE)
Arguments
mesh triangular mesh of class "mesh3d"

v1 numeric vector of length=3 specifying a point on the separating plane
normal plane normal (overrides specification by v2 and v3)
keep.upper logical specify whether the points above or below the plane are should be kept
Details
see cutSpace for more details.
Value
mesh with part above/below hyperplane removed
cutSpace separate a 3D-pointcloud by a hyperplane
Description
separate a 3D-pointcloud by a hyperplane
Usage
cutSpace(pointcloud, v1, v2 = NULL, v3 = NULL, normal = NULL, upper = TRUE)

36 CVA
Arguments
pointcloud numeric n x 3 matrix
upper logical specify whether the points above or below the plane are to be reported as
TRUE.
Details
As above and below are specified by the normal calculated from (v2 − v1) × (v3 − v1), where
× denotes the vector crossproduct. This means the normal points "upward" when viewed from the
positon where v1, v2 and v3 are arranged counter-clockwise. Thus, which side is "up" depends on
the ordering of v1, v2 and v3.
Value
logical vector of length n. Reporting for each point if it is above or below the hyperplane
Examples
data(nose)
v1 <- shortnose.lm[1,]
pointcloud <- vert2points(shortnose.mesh)
upper <- cutSpace(pointcloud, v1, v2, v3)
## Not run:
require(rgl)
normal <- crossProduct(v2-v1,v3-v1)
zeroPro <- points2plane(rep(0,3),v1,normal)
## get sign of normal displacement from zero
sig <- sign(crossprod(-zeroPro,normal))
d <- sig*norm(zeroPro,"2")
planes3d(normal[1],normal[2],normal[3],d=d)
points3d(pointcloud[upper,])
## End(Not run)
CVA Canonical Variate Analysis
Description
performs a Canonical Variate Analysis.
CVA 37
Usage
CVA(
dataarray,
groups,
weighting = TRUE,
tolinv = 1e-10,
plot = TRUE,
rounds = 0,
cv = FALSE,
p.adjust.method = "none",
robust = c("classical", "mve", "mcd"),
prior = NULL,
...
)
Arguments
dataarray Either a k x m x n real array, where k is the number of points, m is the number
of dimensions, and n is the sample size. Or alternatively a n x m Matrix where
n is the numeber of observations and m the number of variables (this can be PC
scores for example)
groups a character/factor vector containgin grouping variable.
weighting Logical: Determines whether the between group covariance matrix and Grand-
mean is to be weighted according to group size.
tolinv Threshold for the eigenvalues of the pooled within-group-covariance matrix to
be taken as zero - for calculating the general inverse of the pooled withing groups
covariance matrix.
plot Logical: determins whether in the two-sample case a histogramm ist to be plot-
ted.
rounds integer: number of permutations if a permutation test of the Mahalanobis dis-
tances (from the pooled within-group covariance matrix) and Euclidean distance
between group means is requested If rounds = 0, no test is performed.
cv logical: requests a Jackknife Crossvalidation.
p.adjust.method
method to adjust p-values for multiple comparisons see p.adjust.methods for
options.
robust character: determines covariance estimation methods, allowing for robust esti-
mations using MASS::cov.rob
prior vector assigning each group a prior probability.
estimations
Value
CV A matrix containing the Canonical Variates
38 CVA
CVscores A matrix containing the individual Canonical Variate scores

Grandm a vector or a matrix containing the Grand Mean (depending if the input is an
array or a matrix)
groupmeans a matrix or an array containing the group means (depending if the input is an
array or a matrix)
Var Variance explained by the Canonical Variates
CVvis Canonical Variates projected back into the original space - to be used for visual-
ization purposes, for details see example below
Dist Mahalanobis Distances between group means - if requested tested by permuta-
tion test if the input is an array it is assumed to be superimposed Landmark Data
and Procrustes Distance will be calculated
CVcv A matrix containing crossvalidated CV scores
groups factor containing the grouping variable
class classification results based on posteriror probabilities. If cv=TRUE, this will be
done by a leaving-one-out procedure
posterior posterior probabilities
prior prior probabilities
Author(s)
Stefan Schlager
References
Cambell, N. A. & Atchley, W. R.. 1981 The Geometry of Canonical Variate Analysis: Syst. Zool.,
30(3), 268-280.
Klingenberg, C. P. & Monteiro, L. R. 2005 Distances and directions in multidimensional shape
spaces: implications for morphometric applications. Systematic Biology 54, 678-688.
See Also
groupPCA
Examples
## all examples are kindly provided by Marta Rufino
if (require(shapes)) {
# perform procrustes fit on raw data
alldat<-procSym(abind(gorf.dat,gorm.dat))
# create factors
groups<-as.factor(c(rep("female",30),rep("male",29)))
# perform CVA and test Mahalanobis distance
# between groups with permutation test by 100 rounds)
cvall<-CVA(alldat$orpdata,groups,rounds=10000)
## visualize a shape change from score -5 to 5:
CVA 39
cvvis5 <- 5*matrix(cvall$CVvis[,1],nrow(cvall$Grandm),ncol(cvall$Grandm))+cvall$Grandm

cvvisNeg5 <- -5*matrix(cvall$CVvis[,1],nrow(cvall$Grandm),ncol(cvall$Grandm))+cvall$Grandm
plot(cvvis5,asp=1)
points(cvvisNeg5,col=2)
for (i in 1:nrow(cvvisNeg5))
lines(rbind(cvvis5[i,],cvvisNeg5[i,]))
}
### Morpho CVA
data(iris)
vari <- iris[,1:4]
facto <- iris[,5]
cva.1=CVA(vari, groups=facto)
## get the typicality probabilities and resulting classifications - tagging
## all specimens with a probability of < 0.01 as outliers (assigned to no class)
typprobs <- typprobClass(cva.1$CVscores,groups=facto)
print(typprobs)
## visualize the CV scores by their groups estimated from (cross-validated)
## typicality probabilities:
if (require(car)) {
scatterplot(cva.1$CVscores[,1],cva.1$CVscores[,2],groups=typprobs$groupaffinCV,
smooth=FALSE,reg.line=FALSE)
}
# plot the CVA
plot(cva.1$CVscores, col=facto, pch=as.numeric(facto), typ="n",asp=1,
xlab=paste("1st canonical axis", paste(round(cva.1$Var[1,2],1),"%")),
ylab=paste("2nd canonical axis", paste(round(cva.1$Var[2,2],1),"%")))
text(cva.1$CVscores, as.character(facto), col=as.numeric(facto), cex=.7)
# add chull (merge groups)

for(jj in 1:length(levels(facto))){
ii=levels(facto)[jj]
kk=chull(cva.1$CVscores[facto==ii,1:2])
lines(cva.1$CVscores[facto==ii,1][c(kk, kk[1])],
cva.1$CVscores[facto==ii,2][c(kk, kk[1])], col=jj)
}
# add 80% ellipses

if (require(car)) {
for(ii in 1:length(levels(facto))){
dataEllipse(cva.1$CVscores[facto==levels(facto)[ii],1],
cva.1$CVscores[facto==levels(facto)[ii],2],
add=TRUE,levels=.80, col=c(1:7)[ii])}
}
# histogram per group
if (require(lattice)) {
histogram(~cva.1$CVscores[,1]|facto,
layout=c(1,length(levels(facto))),
xlab=paste("1st canonical axis", paste(round(cva.1$Var[1,2],1),"%")))
histogram(~cva.1$CVscores[,2]|facto, layout=c(1,length(levels(facto))),
xlab=paste("2nd canonical axis", paste(round(cva.1$Var[2,2],1),"%")))
}
40 data2platonic
# plot Mahalahobis
dendroS=hclust(cva.1$Dist$GroupdistMaha)
dendroS$labels=levels(facto)
par(mar=c(4,4.5,1,1))
dendroS=as.dendrogram(dendroS)
plot(dendroS, main='',sub='', xlab="Geographic areas",
ylab='Mahalahobis distance')
# Variance explained by the canonical roots:

cva.1$Var
# or plot it:
barplot(cva.1$Var[,2])
# another landmark based example in 3D:

data(boneData)
groups <- name2factor(boneLM,which=3:4)
cvall<-CVA(proc$orpdata,groups)
#' ## visualize a shape change from score -5 to 5:
cvvis5 <- 5*matrix(cvall$CVvis[,1],nrow(cvall$Grandm),ncol(cvall$Grandm))+cvall$Grandm
cvvisNeg5 <- -5*matrix(cvall$CVvis[,1],nrow(cvall$Grandm),ncol(cvall$Grandm))+cvall$Grandm
## Not run:
#visualize it
deformGrid3d(cvvis5,cvvisNeg5,ngrid = 0)
## End(Not run)
#for using (e.g. the first 5) PCscores, one will do:

cvall <- CVA(proc$PCscores[,1:5],groups)
#' ## visualize a shape change from score -5 to 5:
cvvis5 <- 5*cvall$CVvis[,1]+cvall$Grandm
cvvisNeg5 <- -5*cvall$CVvis[,1]+cvall$Grandm
cvvis5 <- restoreShapes(cvvis5,proc$PCs[,1:5],proc$mshape)
cvvisNeg5 <- restoreShapes(cvvisNeg5,proc$PCs[,1:5],proc$mshape)
## Not run:
#visualize it
deformGrid3d(cvvis5,cvvisNeg5,ngrid = 0)
## End(Not run)
data2platonic creates 3D shapes from data to be saved as triangular meshes
Description
creates 3D shapes from 3-dimensional data that can be saved as triangular meshes
deformGrid2d 41
Usage
data2platonic(
datamatrix,
shape = Rvcg::vcgSphere(),
col = "red",
scale = FALSE,
scalefactor = 1
)
Arguments
datamatrix k x 3 data matrix

shape a 3D shape
col color value
scale logical: whether to scale the data to unit sd.
scalefactor scale the resulting shapes.
Value
returns all shapes merged into a single mesh
Examples
mymesh <- data2platonic(iris[iris$Species=="setosa",1:3],scalefactor=0.1)

mymesh <- mergeMeshes(mymesh,data2platonic(iris[iris$Species=="versicolor",1:3],
shape=Rvcg::vcgIcosahedron(),scalefactor=0.1,col="green"))
mymesh <- mergeMeshes(mymesh,data2platonic(iris[iris$Species=="virginica",1:3],
shape=Rvcg::vcgTetrahedron(),scalefactor=0.1,col="blue"))
## Not run:
rgl::shade3d(mymesh)
## save to disk
Rvcg::vcgPlyWrite(mymesh,filename="3D_Data.ply")
## End(Not run)
deformGrid2d visualise differences between two superimposed sets of 2D landmarks
Description
visualise differences between two superimposed sets of 2D landmarks by deforming a square grid
based on a thin-plate spline interpolation
42 deformGrid2d
Usage
deformGrid2d(
matrix,
tarmatrix,
ngrid = 0,
lwd = 1,
show = c(1:2),
lines = TRUE,
lcol = 1,
lty = 2,
col1 = 2,
col2 = 3,
pcaxis = FALSE,
add = FALSE,
wireframe = NULL,
margin = 0.2,
gridcol = "grey",
gridlty = 1,
cex1 = 1,
cex2 = 1,
...
)
Arguments
matrix reference matrix containing 2D landmark coordinates or mesh of class "mesh3d"
tarmatrix target matrix containing 2D landmark coordinates or mesh of class "mesh3d"
ngrid number of grid lines to be plotted; ngrid=0 suppresses grid creation.
lwd width of lines connecting landmarks.
show integer (vector): if c(1:2) both configs will be plotted, show = 1 only plots the
reference and show = 2 the target. plotted. Options are combinations of 1,2 and
3.
lines logical: if TRUE, lines between landmarks will be plotted.
lcol color of lines
lty line type
col1 color of "matrix"
col2 color of "tarmat"
pcaxis logical: align grid by shape’s principal axes.
add logical: if TRUE, output will be drawn on existing plot.
wireframe list/vector containing row indices to be plotted as wireframe (see lineplot.)
margin margin around the bounding box to draw the grid
gridcol color of the grid
gridlty linetype for grid
deformGrid3d 43
cex1 control size of points belonging to matrix

cex2 control size of points belonging to tarmatrix
... additional parameters passed to plot
Value
if ngrid > 1 the coordinates of the displaced grid knots are returned.
Author(s)
Stefan Schlager
See Also
tps3d
Examples
proc <- procSym(gorf.dat)
deformGrid2d(proc$mshape,proc$rotated[,,1],ngrid=5,pch=19)
}
deformGrid3d visualise differences between two superimposed sets of 3D landmarks
Description
visualise differences between two superimposed sets of 3D landmarks by deforming a cubic grid
based on a thin-plate spline interpolation
Usage
deformGrid3d(
matrix,
tarmatrix,
ngrid = 0,
align = FALSE,
lwd = 1,
showaxis = c(1, 2),
show = c(1, 2),
lines = TRUE,
lcol = 1,
add = FALSE,
col1 = 2,
col2 = 3,
type = c("s", "p"),
44 deformGrid3d
size = NULL,
pcaxis = FALSE,
ask = TRUE,
margin = 0.2,
createMesh = FALSE,
slice1 = NULL,
slice2 = NULL,
slice3 = NULL,
gridcol = 1,
gridwidth = 1,
...
)
Arguments
matrix reference matrix containing 3D landmark coordinates or mesh of class "mesh3d"
tarmatrix target matrix containing 3D landmark coordinates or mesh of class "mesh3d"
ngrid number of grid lines to be plotted; ngrid=0 suppresses grid creation.
align logical: if TRUE, tarmatrix will be aligned rigidly to matrix
lwd width of lines connecting landmarks.
showaxis integer (vector): which dimensions of the grid to be plotted. Options are combi-
nations of 1,2 and 3.
show integer (vector): if c(1:2) both configs will be plotted, show = 1 only plots the
reference and show = 2 the target
lines logical: if TRUE, lines between landmarks will be plotted.
lcol color of lines
add logical: add to existing rgl window.
col1 color of "matrix"
col2 color of "tarmat"
type "s" renders landmarks as spheres; "p" as points - much faster for very large
pointclouds.
size control size/radius of points/spheres
pcaxis logical: align grid by shape’s principal axes.
ask logical: if TRUE for > 1000 coordinates the user will be asked to prefer points
over spheres.
margin margin around the bounding box to draw the grid
createMesh logical: if TRUE, a triangular mesh of spheres and displacement vectors (can
take some time depending on number of reference points and grid density).
slice1 integer or vector of integers: select slice(s) for the dimensions
gridcol define color of grid
gridwidth integer: define linewidth of grid
... additional parameters passed to rotonto in case align=TRUE
equidistantCurve 45
Value
if createMesh=TRUE, a mesh containing spheres of reference and target as well as the displacement
vectors is returned. Otherwise the knots of the displaced grid is returned.
Author(s)
Stefan Schlager
See Also
tps3d
Examples
if (interactive()){
data(nose)
deformGrid3d(shortnose.lm,longnose.lm,ngrid=10)
## select some slices

deformGrid3d(shortnose.lm,longnose.lm,showaxis=1:3,ngrid=10,slice1=2,slice2=5,slice3=7)
}
equidistantCurve make a curve equidistant (optionally up/downsampling)
Description
make a curve equidistant (optionally up/downsampling)
Usage
equidistantCurve(
x,
n = NULL,
open = TRUE,
subsample = 0,
increment = 2,
smoothit = 0,
mesh = NULL,
iterations = 1
)
Arguments
x k x m matrix containing the 2D or 3D coordinates
n integer: number of coordinates to sample. If NULL, the existing curve will be
made equidistant.
46 exVar
open logical: specifies whether the curve is open or closed.

subsample integer: number of subsamples to draw from curve for interpolation. For curves
with < 1000 points, no subsampling is required.
increment integer: if > 1, the curve is estimated iteratively by incrementing the original
points by this factor. The closer this value to 1, the smoother the line but possibly
farther away from the control points.
smoothit integer: smoothing iterations after each step
mesh specify mesh to project point to
iterations integer: how many iterations to run equidistancing.
Details
Equidistancy is reached by iteratively deforming (using TPS) a straight line with equidistantly
placed points to the target using control points with the same spacing as the actual curve. To avoid
singularity, the straight line containes a small amount of noise, which can (optionally) be accounted
for by smoothing the line by its neighbours.
Value
matrix containing equidistantly placed points
Note
if n » number of original points, the resulting curves can show unwanted distortions.
Examples
data(nose)
x <- shortnose.lm[c(304:323),]
xsample <- equidistantCurve(x,n=50,iterations=10,increment=2)
## Not run:
require(rgl)
points3d(xsample,size=5)
spheres3d(x,col=2,radius=0.3,alpha=0.5)
## End(Not run)
exVar calculate variance of a distribution stemming from prediction models
Description
calculates a quotient of the overall varriance within a predicted distribution to that from the original
one. This function calculates a naive extension of the univariate R^2-value by dividing the variance
in the predicted dat by the variance of the original data. No additional adjustments are made!!
exVar 47
Usage
exVar(model, ...)
## S3 method for class 'lm'

exVar(model, ...)
## S3 method for class 'mvr'

exVar(model, ncomp, val = FALSE, ...)
Arguments
model a model of classes "lm" or "mvr" (from the package "pls")

... currently unused additional arguments.
ncomp How many latent variables to use (only for mvr models)
val use cross-vaildated predictions (only for mvr models)
Value
returns the quotient.
Note
The result is only!! a rough estimate of the variance explained by a multivariate model. And the
result can be misleading - especially when there are many predictor variables involved. If one is
interested in the value each factor/covariate explains, we recommend a 50-50 MANOVA perfomed
by the R-package "ffmanova", which reports this value factor-wise.
Author(s)
Stefan Schlager
References
Langsrud O, Juergensen K, Ofstad R, Naes T. 2007. Analyzing Designed Experiments with Multi-
ple Responses Journal of Applied Statistics 34:1275-1296.
Examples
lm1 <- lm(as.matrix(iris[,1:4]) ~ iris[,5])

exVar(lm1)
48 fastKmeans
fastKmeans fast kmeans clustering for 2D or 3D point clouds
Description
fast kmeans clustering for 2D or 3D point clouds - with the primary purpose to get a spatially
equally distributed samples
Usage
fastKmeans(x, k, iter.max = 10, project = TRUE, threads = 0)
Arguments
x matrix containing coordinates or mesh3d
k number of clusters
iter.max maximum number of iterations
project logical: if x is a triangular mesh, the centers will be projected onto the surface.
threads integer number of threads to use
Value
selected coordinates closest to the final centers
centers cluster center
class vector with cluster association for each coordinate
Examples
require(Rvcg)
data(humface)
set.seed(42)
clust <- fastKmeans(humface,k=1000,threads=1)
## Not run:
require(rgl)
## plot the cluster centers

spheres3d(clust$centers)
## now look at the vertices closest to the centers

wire3d(humface)
spheres3d(vert2points(humface)[clust$selected,],col=2)
## End(Not run)
file2mesh 49
file2mesh Import 3D surface mesh files
Description
Import 3D surface mesh files
Usage
file2mesh(filename, clean = TRUE, readcol = FALSE)
obj2mesh(filename, adnormals = TRUE)
ply2mesh(
filename,
adnormals = TRUE,
readnormals = FALSE,
readcol = FALSE,
silent = FALSE
)
Arguments
filename character: path to file

clean Logical: Delete dumpfiles.
readcol Logical: Import vertex colors (if available).
adnormals Logical: If the file does not contain normal information, they will be calculated
in R: Can take some time.
readnormals Logical: Import vertex normals (if available), although no face information is
present.
silent logical: suppress messages.
Details
imports 3D mesh files and store them as an R .object of class mesh3d
Value
mesh list of class mesh3d - see rgl manual for further details, or a matrix containing
vertex information or a list containing vertex and normal information
50 find.outliers
Examples
data(nose)
mesh2ply(shortnose.mesh)
mesh <- ply2mesh("shortnose.mesh.ply")
mesh2obj(shortnose.mesh)
mesh2 <- obj2mesh("shortnose.mesh.obj")
## cleanup
unlink(c("shortnose.mesh.obj","shortnose.mesh.ply"))
find.outliers Graphical interface to find outliers and/or to switch mislabeld land-

marks
Description
Graphical interface to find outliers and/or to switch mislabeld landmarks
Usage
find.outliers(
A,
color = 4,
lwd = 1,
lcol = 2,
mahalanobis = FALSE,
PCuse = NULL,
text = TRUE,
reflection = FALSE
)
Arguments
A Input k x m x n real array, where k is the number of points, m is the number of
dimensions, and n is the sample size.
color color of Landmarks points to be plotted
lwd linewidth visualizing distances of the individual landmarks from mean.
lcol color of lines visualizing distances of the individual landmarks from mean.
mahalanobis logical: use mahalanobis distance to find outliers.
PCuse integer: Restrict mahalanobis distance to the first n Principal components.
text logical: if TRUE, landmark labels (rownumbers) are displayed
reflection logical: specify whether reflections are allowed for superimpositioning.
find.outliers 51
Details
This function performs a procrustes fit and sorts all specimen according to their distances (either
Procrustes or Mahalanobis-distance) to the sample’s consensus. It provides visual help for rearrang-
ing landmarks and/or excluding outliers.
Value
data.cleaned array (in original coordinate system) containing the changes applied and outliers
eliminated
outlier vector with integers indicating the positions in the original array that have been
marked as outliers
dist.sort table showing the distance to mean for each observation - decreasing by distance
type what kind of distance was used
Author(s)
Stefan Schlager
See Also
typprob,typprobClass
Examples
data(boneData)
## look for outliers using the mahalanobis distance based on the first
# 10 PCscores
# to perform the example below, you need,of course, uncomment the answers
if (interactive()){
outliers <- find.outliers(boneLM, mahalanobis= TRUE, PCuse=10)
# n # everything is fine
# n # proceed to next
# s # let's switch some landmarks (3 and 4)
# 3
# 4
# n # we are done
# y # yes, because now it is an outlier
# s #enough for now
}
52 fixLMmirror
fixLMmirror estimate missing landmarks from their bilateral counterparts
Description
estimate missing landmarks from their bilateral counterparts
Usage
fixLMmirror(x, pairedLM, ...)
## S3 method for class 'array'


Arguments
x a matrix or an array containing landmarks (3D or 2D)
pairedLM a k x 2 matrix containing the indices (rownumbers) of the paired LM. E.g. the
left column contains the lefthand landmarks, while the right side contains the
corresponding right hand landmarks.
... additional arguments
Details
the configurations are mirrored and the relabled version is matched onto the original using a thin-
plate spline deformation. The missing landmark is now estimated using its bilateral counterpart.
If one side is completely missing, the landmarks will be mirrored and aligned by the unilateral
landmarks.
Value
a matrix or array with fixed missing bilateral landmarks.
Note
in case both landmarks of a bilateral pair are missing a message will be issued. As well if there are
missing landmarks on the midsaggital plane are detected.
Examples
data(boneData)
left <- c(4,6,8)
## determine corresponding Landmarks on the right side:
# important: keep same order
right <- c(3,5,7)
fixLMtps 53
pairedLM <- cbind(left, right)

exampmat <- boneLM[,,1]
exampmat[4,] <- NA #set 4th landmark to be NA
fixed <- fixLMmirror(exampmat, pairedLM=pairedLM)
## Not run:
deformGrid3d(fixed, boneLM[,,1],ngrid=0)
## result is a bit off due to actual asymmetry
## End(Not run)
## example with one side completely missing
oneside <- boneLM[,,1]
oneside[pairedLM[,1],] <- NA
onesidefixed <- fixLMmirror(oneside,pairedLM)
## Not run:
deformGrid3d(onesidefixed, boneLM[,,1],ngrid=0)
## result is a bit off due to actual asymmetry
## End(Not run)
fixLMtps estimate missing landmarks
Description
Missing landmarks are estimated by deforming a sample average or a weighted estimate of the
configurations most similar onto the deficient configuration. The deformation is performed by a
Thin-plate-spline interpolation calculated by the available landmarks.
Usage
fixLMtps(data, comp = 3, weight = TRUE, weightfun = NULL)
Arguments
data array containing landmark data
comp integer: select how many of the closest observations are to be taken to calculate
an initial estimate.
weight logical: requests the calculation of an estimate based on the procrustes distance.
Otherwise the sample’s consensus is used as reference.
weightfun custom function that operates on a vector of distances (see examples) and gen-
erates weights accordingly.
Details
This function tries to estimate missing landmark data by mapping weighted averages from complete
datasets onto the missing specimen. The weights are the inverted Procrustes (see proc.weight)
distances between the ’comp’ closest specimen (using the available landmark configuration).
54 fixLMtps
Value
out array containing all data, including fixed configurations - same order as input
mshape meanshape - calculated from complete datasets
checklist list containing information about missing landmarks
check vector containing position of observations in data where at least one missing
coordinate was found
Note
Be aware that these estimates might be grossly wrong when the missing landmark is quite far off
the rest of the landmarks (due to the radial basis function used in the Thin-plate spline interpolation.
Author(s)
Stefan Schlager
References
Bookstein FL. 1989. Principal Warps: Thin-plate splines and the decomposition of deformations
IEEE Transactions on pattern analysis and machine intelligence 11.
See Also
proc.weight, tps3d
Examples
data <- gorf.dat
### set first landmark of first specimen to NA
data[1,,1] <- NA
repair <- fixLMtps(data,comp=5)
### view difference between estimated and actual landmark
plot(repair$out[,,1],asp=1,pch=21,cex=0.7,col=2)#estimated landmark
points(gorf.dat[,,1],col=3,pch=20)#actual landmark
}
## 3D-example:
data(boneData)
data <- boneLM
### set first and 5th landmark of first specimen to NA
data[c(1,5),,1] <- NA
repair <- fixLMtps(data,comp=10)
## view difference between estimated and actual landmark
## Not run:
deformGrid3d(repair$out[,,1], boneLM[,,1],ngrid=0)
## End(Not run)
## Now use a gaussian kernel to compute the weights and use all other configs
gaussWeight <- function(r,sigma=0.05) {
getFaces 55
sigma <- 2*sigma^2

return(exp(-r^2/ sigma))
}
repair <- fixLMtps(data,comp=79,weightfun=gaussWeight)
getFaces find indices of faces that contain specified vertices
Description
find indices of faces that contain specified vertices
Usage
getFaces(mesh, index)
Arguments
index vector containing indices of vertices
Value
vector of face indices
getMeaningfulPCs get number of meaningful Principal components
Description
get number of meaningful Principal components
Usage
getMeaningfulPCs(values, n, expect = 2, sdev = FALSE)
Arguments
values eigenvalues from a PCA
n sample size
expect expectation value for chi-square distribution of df=2
sdev logical: if TRUE, it is assumed that the values are square roots of eigenvalues.
56 getOuterViewpoints
Details
This implements the method suggested by Bookstein (2014, pp. 324), to determine whether a PC is
entitled to interpretation. I.e. a PC is regarded meaningful (its direction) if the ratio of this PC and
its successor is above a threshold based on a log-likelihood ratio (and dependend on sample size).
Value
tol threshold of ratio specific for n
good integer vector specifying the meaningful Principal Components
References
Bookstein, F. L. Measuring and reasoning: numerical inference in the sciences. Cambridge Univer-
sity Press, 2014
See Also
getPCtol
Examples
data(boneData)
getMeaningfulPCs(proc$eigenvalues,n=nrow(proc$PCscores))
## the first 3 PCs are reported as meaningful
## show barplot that seem to fit the bill
barplot(proc$eigenvalues)
getOuterViewpoints Get viewpoints on a sphere around a 3D mesh
Description
Get viewpoints on a sphere around a 3D mesh to be used with virtualMeshScan
Usage
getOuterViewpoints(
x,
n,
inflate = 1.5,
radius = NULL,
subdivision = 3,
PCA = FALSE
)
getPCscores 57
Arguments
x triangular mesh of class ’mesh3d’
n number of viewpoint to generate
inflate factor for the size of the sphere: inflate=1 means that the sphere around the
object just touches the point farthest away from the mesh’s centroid.
radius defines a fix radius for the sphere (overrides arg inflate).
subdivision parameter passed to vcgSphere
PCA logical: if TRUE, the sphere will be deformed to match the principle axes of the
mesh. NOTE: this may result in the sphere not necessarily completely enclosing
the mesh.
Value
a list containing
viewpoints n x 3 matrix containing viewpoints.

sphere sphere from which the points are sampled
radius radius of the sphere
Examples
data(boneData)
vp <- getOuterViewpoints(skull_0144_ch_fe.mesh,n=100)
## Not run:
require(rgl)
shade3d(skull_0144_ch_fe.mesh,col="white")
spheres3d(vp$viewpoints)
wire3d(vp$sphere)
## End(Not run)
### Fit to principal axes
vppca <- getOuterViewpoints(skull_0144_ch_fe.mesh,n=100,PCA=TRUE,inflate=1.5)
## Not run:
require(rgl)
shade3d(skull_0144_ch_fe.mesh,col="white")
spheres3d(vppca$viewpoints)
wire3d(vppca$sphere)
## End(Not run)
getPCscores Obtain PC-scores for new landmark data
Description
Obtain PC-scores for new landmark data
58 getPCtol
Usage
getPCscores(x, PC, mshape)
Arguments
x landmarks aligned (e.g. using align2procSym to the meanshape of data the PCs
are derived from.
PC Principal components (eigenvectors of the covariance matrix)
mshape matrix containing the meanshape’s landmarks (used to center the data)
Value
returns a matrix containing the PC scores
See Also
restoreShapes
Examples
data(boneData)
proc <- procSym(boneLM[,,-c(1:2)])
newdata <- boneLM[,,c(1:2)]
newdataAlign <- align2procSym(proc,newdata)
scores <- getPCscores(newdataAlign,proc$PCs,proc$mshape)
getPCtol determine the minimum ratio for two subsequent eigenvalues to be

considered different
Description
determine the minimum ratio for two subsequent eigenvalues to be considered different
Usage
getPCtol(n, expect = 2)
Arguments
n sample size
expect expectation value for chi-square distribution of df=2
Value
returns the minimum ratio between two subsequent subsequent eigenvalues to be considered differ-
ent.
getPLSCommonShape 59
References
Bookstein, F. L. Measuring and reasoning: numerical inference in the sciences. Cambridge Univer-
sity Press, 2014
See Also
getMeaningfulPCs
Examples
## reproduce the graph from Bookstein (2014, p. 324)
## and then compare it to ratios for values to be considered
## statistically significant
myseq <- seq(from=10,to = 50, by = 2)
myseq <- c(myseq,seq(from=50,to=1000, by =20))
ratios <- getPCtol(myseq)
plot(log(myseq),ratios,cex=0,xaxt = "n",ylim=c(1,5.2))
ticks <- c(10,20,50,100,200,300,400,500,600,700,800,900,1000)
axis(1,at=log(ticks),labels=ticks)
lines(log(myseq),ratios)
abline(v=log(ticks), col="lightgray", lty="dotted")
abline(h=seq(from=1.2,to=5, by = 0.2), col="lightgray", lty="dotted")
## now we raise the bar and compute the ratios for values
## to be beyond the 95th percentile of
## the corresponding chi-square distribution:
ratiosSig <- getPCtol(myseq,expect=qchisq(0.95,df=2))
lines(log(myseq),ratiosSig,col=2)
getPLSCommonShape Get the linear combinations associated with the common shape change
in each latent dimension of a pls2B
Description
Get the linear combinations associated with the common shape change in each latent dimension of
a pls2B
Usage
getPLSCommonShape(pls)
Arguments
pls object of class "pls2B"
60 getPLSfromScores
Value
shapevectors matrix with each containing the shapevectors (in column- major format) of com-
mon shape change associated with each latent dimension
XscoresScaled Xscores scaled according to shapevectors
YscoresScaled Yscores scaled according to shapevectors
commoncenter Vector containing the common mean
lmdim dimension of landmarks
References
Mitteroecker P, Bookstein F. 2007. The conceptual and statistical relationship between modularity
and morphological integration. Systematic Biology 56(5):818-836.
See Also
plsCoVarCommonShape
Examples
data(boneData)
pls <- pls2B(proc$orpdata[1:4,,],proc$orpdata[5:10,,])
commShape <- getPLSCommonShape(pls)
## get common shape for first latent dimension at +-2 sd of the scores
## (you can do this much more convenient using \code{\link{plsCoVarCommonShape}}
scores <- c(-2,2) * sd(c(commShape$XscoresScaled[,1],commShape$YscoresScaled[,1]))
pred <- restoreShapes(scores,commShape$shapevectors[,1],matrix(commShape$commoncenter,10,3))
## Not run:
deformGrid3d(pred[,,1],pred[,,2])
## End(Not run)
getPLSfromScores compute changes associated with 2-Block PLS-scores
Description
compute changes associated with 2-Block PLS-scores
Usage
getPLSfromScores(pls, x, y)
getPLSscores 61
Arguments
pls output of pls2B
x scores associated with dataset x in original pls2B
y scores associated with dataset y in original pls2B
Details
other than predictPLSfromScores, providing Xscores will not compute predictions of y, but the
changes in the original data x that is associated with the specific scores
Value
returns data in the original space associated with the specified values.
getPLSscores compute 2-Block PLS scores for new data
Description
compute 2-Block PLS scores for new data from an existing pls2B
Usage
getPLSscores(pls, x, y)
Arguments
pls output of pls2B
x matrix or vector representing new dataset(s) - same kind as in original pls2B
y matrix or vector representing new dataset(s) - same kind as in original pls2B
Value
returns a vector of pls-scores
Note
either x or y must be missing
See Also
pls2B, predictPLSfromScores,predictPLSfromData
62 getSides
getPointAlongOutline Get a point along a line with a given distance from the start of the line
Description
Get a point along a line with a given distance from the start of the line
Usage
getPointAlongOutline(mat, dist = 15, reverse = FALSE)
Arguments
mat matrix with rows containing sequential coordinates
dist numeric: distance from the first point on the line.
reverse logical: if TRUE start from the end of the line
Value
returns a vector containing the resulting coordinate
getSides try to identify bilateral landmarks and sort them by side
Description
try to identify bilateral landmarks and sort them by side
Usage
getSides(x, tol = 3, pcAlign = TRUE, icpiter = 100, ...)
Arguments
x matrix containing landmarks (see details)
tol maximal distance allowed between original and mirrored set.
pcAlign logical: if TRUE orginal and mirrored landmarks will be initally aligned by their
PC-axes
icpiter integer: number of iterations in ICP alignment.
... more arguments passed to mirror.
getTrafo4x4 63
Details
This function mirrors the landmark set and aligns it to the original. Then it tries to find pairs. If you
have a sample, run a Procrustes registration first (without scaling to unit centroid size, or you later
have to adapt tol - see examples) and then use the mean as it is usually more symmetrical.
Value
side1 integer vector containing indices of landmarks on one side

side2 integer vector containing indices of landmarks on the other side
unilat integer vector containing indices unilateral landmarks
Examples
data(boneData)
proc <- procSym(boneLM,CSinit=FALSE)
mysides <- getSides(proc$mshape)
if (interactive()){
#visualize bilateral landmarks
deformGrid3d(boneLM[mysides$side1,,1],boneLM[mysides$side2,,1])
## visualize unilateral landmarks
rgl::spheres3d(boneLM[mysides$unilat,,1],radius=0.5)
}
getTrafo4x4 get 4x4 Transformation matrix
Description
get 4x4 Transformation matrix
Usage
getTrafo4x4(x)
## S3 method for class 'rotonto'

getTrafo4x4(x)
Arguments
x object of class "rotonto"
Value
returns a 4x4 transformation matrix
64 getVisibleVertices
Examples
data(boneData)
rot <- rotonto(boneLM[,,1],boneLM[,,2])
trafo <- getTrafo4x4(rot)
getTrafoRotaxis compute a 4x4 Transformation matrix for rotation around an arbitrary

axis
Description
compute a 4x4 Transformation matrix for rotation around an arbitrary axis
Usage
getTrafoRotaxis(pt1, pt2, theta)
Arguments
pt1 numeric vector of length 3, defining first point on the rotation axis.
pt2 numeric vector of length 3, defining second point on the rotation axis.
theta angle to rotate in radians. With pt1 being the viewpoint, the rotation is counter-
clockwise.
Note
the resulting matrix can be used in applyTransform
getVisibleVertices find vertices visible from a given viewpoints
Description
find vertices visible from a given viewpoints
Usage
getVisibleVertices(mesh, viewpoints, offset = 0.001, cores = 1)
Arguments
mesh triangular mesh of class ’mesh3d’
viewpoints vector or k x 3 matrix containing a set of viewpoints
offset value to generate an offset at the meshes surface (see notes)
cores integer: number of cores to use (not working on windows)
groupPCA 65
Value
a vector with (1-based) indices of points visible from at least one of the viewpoints
Note
The function tries to filter out all vertices where the line connecting each vertex with the viewpoints
intersects with the mesh itself. As, technically speaking this always occurs at a distance of value=0,
a mesh with a tiny offset is generated to avoid these false hits.
Examples
SCP1 <- file2mesh(system.file("extdata","SCP1.ply",package="Morpho"))
viewpoints <- read.fcsv(system.file("extdata","SCP1_Endo.fcsv",package="Morpho"))
visivert <- getVisibleVertices(SCP1,viewpoints)
groupPCA Perform PCA based of the group means’ covariance matrix
Description
Calculate covariance matrix of the groupmeans and project all observations into the eigenspace of
this covariance matrix. This displays a low dimensional between group structure of a high dimen-
sional problem.
Usage
groupPCA(
dataarray,
groups,
rounds = 10000,
tol = 1e-10,
cv = TRUE,
mc.cores = parallel::detectCores(),
weighting = TRUE
)
Arguments
dataarray Either a k x m x n real array, where k is the number of points, m is the number
of dimensions, and n is the sample size. Or alternatively a n x m Matrix where
n is the numeber of observations and m the number of variables (this can be PC
scores for example)
groups a character/factor vector containgin grouping variable.
rounds integer: number of permutations if a permutation test of the euclidean distance
between group means is requested.If rounds = 0, no test is performed.
tol threshold to ignore eigenvalues of the covariance matrix.
66 groupPCA
cv logical: requests leaving-one-out crossvalidation

mc.cores integer: how many cores of the Computer are allowed to be used. Default is
use autodetection by using detectCores() from the parallel package. Parallel
processing is disabled on Windows due to occasional errors.
weighting logical:weight between groups covariance matrix according to group sizes.
Value
eigenvalues Non-zero eigenvalues of the groupmean covariance matrix

groupPCs PC-axes - i.e. eigenvectors of the groupmean covariance matrix
Variance table displaying the between-group variance explained by each between group
PC - this only reflects the variability of the group means and NOT the variability
of the data projected into that space
Scores Scores of all observation in the PC-space
probs p-values of pairwise groupdifferences - based on permuation testing
groupdists Euclidean distances between groups’ averages
groupmeans matrix with rows containing the Groupmeans, or a k x m x groupsize array if the
input is a k x m x n landmark array
Grandmean vector containing the Grand mean, or a matrix if the input is a k x m x n landmark
array
CV Cross-validated scores
groups grouping Variable
resPCs PCs orthogonal to the between-group PCs
resPCscores Scores of the residualPCs
resVar table displaying the residual variance explained by each residual PC.
Author(s)
Stefan Schlager
References
Mitteroecker P, Bookstein F 2011. Linear Discrimination, Ordination, and the Visualization of

Selection Gradients in Modern Morphometrics. Evolutionary Biology 38:100-114.
Boulesteix, A. L. 2005: A note on between-group PCA, International Journal of Pure and Applied
Mathematics 19, 359-366.
See Also
CVA
histGroup 67
Examples
data(iris)
vari <- iris[,1:4]
facto <- iris[,5]
pca.1 <-groupPCA(vari,groups=facto,rounds=100,mc.cores=1)
### plot scores

if (require(car)) {
scatterplotMatrix(pca.1$Scores,groups=facto, ellipse=TRUE,
by.groups=TRUE,var.labels=c("PC1","PC2","PC3"))
}
## example with shape data
data(boneData)
pop_sex <- name2factor(boneLM, which=3:4)
gpca <- groupPCA(proc$orpdata, groups=pop_sex, rounds=0, mc.cores=2)
## Not run:
## visualize shape associated with first between group PC
dims <- dim(proc$mshape)
## calculate matrix containing landmarks of grandmean
grandmean <-gpca$Grandmean
## calculate landmarks from first between-group PC
# (+2 and -2 standard deviations)
gpcavis2sd<- restoreShapes(c(-2,2)*sd(gpca$Scores[,1]), gpca$groupPCs[,1], grandmean)
deformGrid3d(gpcavis2sd[,,1], gpcavis2sd[,,2], ngrid = 0,size=0.01)
require(rgl)
## visualize grandmean mesh
grandm.mesh <- tps3d(skull_0144_ch_fe.mesh, boneLM[,,1],grandmean,threads=1)

wire3d(grandm.mesh, col="white")
spheres3d(grandmean, radius=0.01)
## End(Not run)
histGroup plot histogram for multiple groups.
Description
plot a histogram for multiple groups, each group colored individually
Usage
histGroup(
data,
groups,
68 histGroup
main = paste("Histogram of", dataname),

xlab = dataname,
ylab,
col = NULL,
alpha = 0.5,
breaks = "Sturges",
legend = TRUE,
legend.x = 80,
legend.y = 80,
legend.pch = 15,
freq = TRUE
)
Arguments
data vector containing data.
groups grouping factors
main, xlab, ylab
these arguments to title have useful defaults here.
col vector containing color for each group. If NULL, the function "rainbow" is
called.
alpha numeric between 0 and 1. Sets the transparency of the colors
breaks one of:
• a vector giving the breakpoints between histogram cells,
• a single number giving the number of cells for the histogram,
• a character string naming an algorithm to compute the number of cells (see
‘Details’),
• a function to compute the number of cells.
In the last three cases the number is a suggestion only.
legend logical: if TRUE, a legend is plotted
legend.x x position of the legend from the upper left corner
legend.y y position of the legend from the upper left corners
legend.pch integer: define the symbol to visualise group colors (points)
freq logical: if TRUE, the histogram graphic is a representation of frequencies, the
counts component of the result; if FALSE, probability densities are plotted for
each group.
Details
Just a wrapper for the function hist from the "graphics" package
Author(s)
Stefan Schlager
icpmat 69
See Also
hist
Examples
data(iris)
histGroup(iris$Petal.Length,iris$Species)
icpmat match two landmark configurations using iteratively closest point

search
Description
match two landmark configurations using iteratively closest point search
Usage
icpmat(
x,
y,
iterations,
mindist = 1e+15,
subsample = NULL,
type = c("rigid", "similarity", "affine"),
weights = NULL,
threads = 1,
centerweight = FALSE
)
Arguments
x moving landmarks
y target landmarks
iterations integer: number of iterations
mindist restrict valid points to be within this distance
subsample use a subsample determined by kmean clusters to speed up computation
type character: select the transform to be applied, can be "rigid","similarity" or "affine"
weights vector of length nrow(x) containing weights for each row in x
threads integer: number of threads to use.
centerweight logical: if weights are defined and centerweigths=TRUE, the matrix will be
centered according to these weights instead of the barycenter.
70 invertFaces
Value
returns the rotated landmarks
Examples
data(nose)
icp <- icpmat(shortnose.lm,longnose.lm,iterations=10)
## example using weights

## we want to assign high weights to the first three cordinates
icpw <- icpmat(shortnose.lm,longnose.lm,iterations=10,
weights=c(rep(100,3),rep(1,620)),centerweight = TRUE)
## the RMSE between those four points and the target is now smaller:
require(Rvcg)
RMSE <- sqrt(sum(vcgKDtree(longnose.lm,icp[1:3,],k=1)$distance^2))
RMSEW<- sqrt(sum(vcgKDtree(longnose.lm,icpw[1:3,],k=1)$distance^2))
barplot(c(RMSE,RMSEW),names.arg=c("RMSE weighted","RMSE unweighted"))
## Not run:
## plot the differences between unweighted and weighted icp
deformGrid3d(icp,icpw)
## plot the first four coordinates from the icps:
spheres3d(icp[1:3,],col="red",radius = 0.5)
spheres3d(icpw[1:3,],col="green",radius = 0.5)
## plot the target
spheres3d(longnose.lm,col="yellow",radius = 0.2)
## End(Not run)
##2D example using icpmat to determine point correspondences
## we scramble rows to show that this is independent of point order
moving <- gorf.dat[sample(1:8),,1]
plot(moving,asp=1) ## starting config
icpgorf <- icpmat(moving,gorf.dat[,,2],iterations = 20)
points(icpgorf,asp = 1,col=2)
points(gorf.dat[,,2],col=3)## target
## get correspondences using nearest neighbour search

index <- mcNNindex(icpgorf,gorf.dat[,,2],k=1,cores=1)
icpsort <- icpgorf[index,]
for (i in 1:8)
lines(rbind(icpsort[i,],gorf.dat[i,,2]))
}
invertFaces invert faces’ orientation of triangular mesh
Description
inverts faces’ orientation of triangular mesh and recomputes vertex normals
kendalldist 71
Usage
invertFaces(mesh)
Arguments
mesh triangular mesh of class mesh3d
Value
returns resulting mesh
Author(s)
Stefan Schlager
See Also
updateNormals
Examples
data(nose)
## Not run:
rgl::shade3d(shortnose.mesh,col=3)
## End(Not run)
noseinvert <- invertFaces(shortnose.mesh)
## show normals
## Not run:
plotNormals(noseinvert,long=0.01)
## End(Not run)
kendalldist Calculates the Riemannian distance between two superimposed land-

mark configs.
Description
Calculates the Riemannian distance between two superimposed landmark configs.
Usage
kendalldist(x, y)
72 line2plane
Arguments
x Matrix containing landmark coordinates.
y Matrix containing landmark coordinates.
Value
returns Riemannian distance
Examples
if(require(shapes)) {
OPA <- rotonto(gorf.dat[,,1],gorf.dat[,,2])
kendalldist(OPA$X,OPA$Y)
}
line2plane get intersection between a line and a plane
Description
get intersection between a line and a plane
Usage
line2plane(ptLine, ptDir, planePt, planeNorm)
Arguments
ptLine vector of length 3: point on line
ptDir vector of length 3: direction vector of line
planePt vector of length 3: point on plane
planeNorm vector of length 3: plane normal vector
Value
hit point
Note
in case you only have three points on a plane (named pt1, pt2, pt3 you can get the plane’s normal
by calling crossProduct(pt1-pt2,pt1-pt3).
lineplot 73
lineplot plot lines between landmarks
Description
add lines connecting landmarks to visualise a sort of wireframe
Usage
lineplot(
x,
point,
col = 1,
lwd = 1,
line_antialias = FALSE,
lty = 1,
add = TRUE
)
Arguments
x matrix containing 2D or 3D landmarks

point vector or list of vectors containing rowindices of x, determining which land-
marks to connect.
col color of lines
lwd line width
line_antialias logical: smooth lines
lty line type (only for 2D case)
add logical: add to existing plot
Note
works with 2D and 3D configurations
Author(s)
Stefan Schlager
See Also
pcaplot3d
74 LPS2RAS
Examples
##2D example
plot(gorf.dat[,,1],asp=1)
lineplot(gorf.dat[,,1],point=c(1,5:2,8:6,1),col=2)
}
##3D example
## Not run:
require(rgl)
data(nose)
points3d(shortnose.lm[1:9,])
lineplot(shortnose.lm[1:9,],point=list(c(1,3,2),c(3,4,5),c(8,6,5,7,9)),col=2)
## End(Not run)
list2array converts a list of matrices to an array
Description
converts a list of matrices to an array
Usage
list2array(x)
Arguments
x a list containing matrices of the same dimensionality
Value
returns an array concatenating all matrices
LPS2RAS convert data from LPS to RAS space and back
Description
convert data from LPS to RAS space and back
Usage
LPS2RAS(x)
mcNNindex 75
Arguments
x mesh of class mesh3d or a matrix with 3D Landmarks
Details
As e.g. the Slicer versions >= 4.11 are using LPS space, it might be needed to transform data like
fiducials and surface models from and back to that space.
Value
returns the rotated data
mcNNindex find nearest neighbours for 2D and 3D point clouds
Description
find nearest neighbours for point clouds using a kd-tree search. This is just a wrapper of the func-
tion vcgKDtree from package Rvcg. Wwraps the function vcgKDtree from package ’Rvcg’ (for
backward compatibility )
Usage
mcNNindex(target, query, cores = parallel::detectCores(), k = k, ...)
Arguments
target k x m matrix containing data which to search.

query l x m matrix containing data for which to search.
cores integer: amount of CPU-cores to be used. Only available on systems with
OpenMP support.
k integer: how many closest points are sought.
... additional arguments - currently unused.
Value
l x k matrix containing indices of closest points.
See Also
closemeshKD
76 mergeMeshes
Examples
require(rgl)
data(nose)
# find closest vertex on surface for each landmark
clost <- mcNNindex(vert2points(shortnose.mesh),shortnose.lm, k=1,
mc.cores=1)
## Not run:
spheres3d(vert2points(shortnose.mesh)[clost,],col=2,radius=0.3)
spheres3d(shortnose.lm,radius=0.3)
## End(Not run)
mergeMeshes merge multiple triangular meshes into a single one
Description
merge multiple triangular meshes into a single one, preserving color and vertex normals.
Usage
mergeMeshes(...)
Arguments
... triangular meshes of class 'mesh3d' to merge or a list of triangular meshes.
Value
returns the meshes merged into a single one.
See Also
mesh2ply, file2mesh, ply2mesh
Examples
require(rgl)
data(boneData)
data(nose)
mergedMesh <- mergeMeshes(shortnose.mesh, skull_0144_ch_fe.mesh)
## Not run:
require(rgl)
shade3d(mergedMesh, col=3)
## End(Not run)
mesh2grey 77
mesh2grey convert a colored mesh to greyscale.
Description
convert the colors of a colored mesh to greyscale values
Usage
mesh2grey(mesh)
Arguments
mesh Object of class mesh3d
Value
returns a mesh with material$color replaced by greyscale rgb values.
Author(s)
Stefan Schlager
See Also
ply2mesh,file2mesh
mesh2obj export mesh objects to disk
Description
export mesh objects to disk.
Usage
mesh2obj(x, filename = dataname, writeNormals = TRUE)
mesh2ply(x, filename = dataname, col = NULL, writeNormals = FALSE)

78 mesh2obj
Arguments
x object of class mesh3d - see rgl documentation for further details or a matrix
containing vertices, this can either be a k x 3 or a 3 x k matrix, with rows or
columns containing vertex coordinates.
filename character: Path/name of the requested output - extension will be added atuomat-
ically. If not specified, the file will be named as the exported object.
writeNormals logical: if TRUE, existing normals of a mesh are written to file - can slow things
down for very large meshes.
col Writes color information to ply file. Can be either a single color value or a vector
containing a color value for each vertex of the mesh.
Details
export an object of class mesh3d or a set of coordinates to a common mesh file.
Note
meshes containing quadrangular faces will be converted to triangular meshes by splitting the faces.
Additionally, mesh2obj is now simply a wrapper of Rvcg::vcgObjWrite.
Author(s)
Stefan Schlager
See Also
ply2mesh, quad2trimesh
Examples
require(rgl)
vb <- c(-1.8,-1.8,-1.8,1.0,1.8,-1.8,-1.8,1.0,-1.8,1.8,-1.8,1.0,1.8,
1.8,-1.8,1.0,-1.8,-1.8,1.8,1.0,1.8,
-1.8,1.8,1.0,-1.8,1.8,1.8,1.0,1.8,1.8,1.8,1.0)
it <- c(2,1,3,3,4,2,3,1,5,5,7,3,5,1,2,2,6,5,6,8,7,7,5,6,7,8,4,4,3,7,4,8,6,6,2,4)
vb <- matrix(vb,4,8) ##create vertex matrix
it <- matrix(it,3,12) ## create face matrix
cube<-list(vb=vb,it=it)
class(cube) <- "mesh3d"
## Not run:
shade3d(cube,col=3) ## view the green cube
## End(Not run)
mesh2ply(cube,filename="cube") # write cube to a file called cube.ply
unlink("cube.ply")
meshcube 79
meshcube calculate the corners of a mesh’s bouning box
Description
calculate the corners of a mesh’s bouning box
Usage
meshcube(x)
Arguments
x object of class ’mesh3d’
Value
returns a 8 x 3 matrix with the coordinates of the corners of the bounding box.
Examples
require(rgl)
data(boneData)
mc <- meshcube(skull_0144_ch_fe.mesh)
## Not run:
spheres3d(mc)
wire3d(skull_0144_ch_fe.mesh)
## End(Not run)
meshDist calculates and visualises distances between surface meshes or 3D co-

ordinates and a surface mesh.
Description
calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh.
80 meshDist
Usage
meshDist(x, ...)

meshDist(
x,
mesh2 = NULL,
distvec = NULL,
from = NULL,
to = NULL,
steps = 20,
ceiling = FALSE,
rampcolors = colorRamps::blue2green2red(steps - 1),
NAcol = "white",
file = "default",
imagedim = "100x800",
uprange = 1,
ray = FALSE,
raytol = 50,
raystrict = FALSE,
save = FALSE,
plot = TRUE,
sign = TRUE,
tol = NULL,
tolcol = "green",
displace = FALSE,
shade = TRUE,
method = c("vcglib", "morpho"),
add = FALSE,
scaleramp = TRUE,
threads = 1,
titleplot = "Distance in mm",
...
)

meshDist(
x,
mesh2 = NULL,
distvec = NULL,
from = NULL,
to = NULL,
steps = 20,
ceiling = FALSE,
rampcolors = colorRamps::blue2green2red(steps - 1),
NAcol = "white",
uprange = 1,
plot = TRUE,
meshDist 81
sign = TRUE,
tol = NULL,
tolcol = "green",
type = c("s", "p"),
radius = NULL,
displace = FALSE,
add = FALSE,
scaleramp = FALSE,
...
)
Arguments
x reference mesh; object of class "mesh3d" or a n x 3 matrix containing 3D coor-
dinates.
... additional arguments passed to shade3d. See material3d for details.
mesh2 target mesh: either object of class "mesh3d" or a character pointing to a surface
mesh (ply, obj or stl file)
distvec vector: optional, a vector containing distances for each vertex/coordinate of x,
if distvec != NULL, mesh2 will be ignored.
from numeric: minimum distance to be colorised; default is set to 0 mm
to numeric: maximum distance to be colorised; default is set to the maximum
distance
steps integer: determines break points for color ramp: n steps will produce n-1 colors.
ceiling logical: if TRUE, the next larger integer of "to" is used
rampcolors character vector: specify the colors which are used to create a colorramp.
NAcol character: specify color for values outside the range defined by from and to.
file character: filename for mesh and image files produced. E.g. "mydist" will
produce the files mydist.ply and mydist.png
imagedim character of type 100x200 where 100 determines the width and 200 the height
of the image.
uprange numeric between 0 and 1: restricts "to" to a quantile of "to", if to is NULL.
ray logical: if TRUE, the search is along vertex normals.
raytol maximum distance to follow a normal.
raystrict logical: if TRUE, only outward along normals will be sought for closest points.
save logical: save a colored mesh.
plot logical: visualise result as 3D-plot and distance charts
sign logical: request signed distances. Only meaningful, if mesh2 is specified or
distvec contains signed distances.
tol numeric: threshold to color distances within this threshold green.
tolcol a custom color to color vertices below a threshold defined by tol. Default is
green.
82 meshDist
displace logical: if TRUE, displacement vectors between original and closest points are
drawn colored according to the distance.
shade logical: if FALSE, the rendering of the colored surface will be supressed.
method accepts: "vcglib" and "morpho" (and any abbreviation). vcglib uses a command
line tool using vcglib headers, morpho uses fortran routines based on a kd-tree
search for closest triangles.
add logical: if TRUE, visualization will be added to the rgl window currently in
focus
scaleramp logical: if TRUE, the colorramp will be symmetrical for signed distances: span-
ning from -max(from,to) to max(from,to).
threads integer: number of threads to use. 0 = let system decide.
titleplot character: axis description of heatmap.
type character: "s" shows coordinates as spheres, while "p" shows 3D dots.
radius determines size of spheres; if not specified, optimal radius size will be estimated
by centroid size of the configuration.
Details
calculates the distances from a mesh or a set of 3D coordinates to another at each vertex; either
closest point or along the normals
Value
Returns an object of class "meshDist" if the input is a surface mesh and one of class "matrixDist" if
input is a matrix containing 3D coordinates.
colMesh object of mesh3d with colors added

dists vector with distances
cols vector with color values
params list of parameters used
Author(s)
Stefan Schlager
References
Detection of inside/outside uses the algorithm proposed in:
Meshes. Informatics and Mathematical Modelling, .
See Also
render.meshDist, , export.meshDist, shade3d
meshPlaneIntersect 83
Examples
data(nose)##load data
##warp a mesh onto another landmark configuration:
longnose.mesh <- tps3d(shortnose.mesh, shortnose.lm, longnose.lm,threads=1)
## Not run:
mD <- meshDist(longnose.mesh, shortnose.mesh)
##now change the color ramp
render(mD,rampcolors = c("white","red"))
## End(Not run)
#use unsigned distances and a ramp from blue to red
#color distances < 0.01 green:
## Not run:
meshDist(longnose.mesh, shortnose.mesh, rampcolors = c("blue", "red"),sign=FALSE, tol=0.5)
## End(Not run)
meshPlaneIntersect get intersections between mesh and a plane
Description
get intersections between mesh and a plane
Usage
meshPlaneIntersect(mesh, v1, v2 = NULL, v3 = NULL, normal = NULL)
Arguments

Value
returns the intersections of edges and the plane

84 meshres
Examples
data(nose)
intersect <- meshPlaneIntersect(shortnose.mesh,v1,v2,v3)
## Not run:
require(rgl)
spheres3d(shortnose.lm[1:3,],col=2)#the plane
spheres3d(intersect,col=3,radius = 0.2)#intersections
## End(Not run)
meshres calculate average edge length of a triangular mesh
Description
calculate average edge length of a triangular mesh, by iterating over all faces.
Usage
meshres(mesh)
Arguments
mesh triangular mesh stored as object of class "mesh3d"
Value
returns average edge length (a.k.a. mesh resolution)
Author(s)
Stefan Schlager
Examples
data(boneData)
mres <- meshres(skull_0144_ch_fe.mesh)
mirror 85
mirror mirror landmarks or triangular mesh in place
Description
mirror landmarks or triangular mesh in place
Usage
mirror(
x,
icpiter = 50,
subsample = NULL,
pcAlign = FALSE,
mirroraxis = 1,
initPC = TRUE,
initCenter = TRUE,
v1 = NULL,
v2 = NULL,
v3 = NULL,
normal = NULL,
mc.cores = 2
)

mirror(
x,
icpiter = 50,
subsample = NULL,
pcAlign = FALSE,
mirroraxis = 1,
initPC = TRUE,
initCenter = TRUE,
v1 = NULL,
v2 = NULL,
v3 = NULL,
normal = NULL,
mc.cores = 2
)

mirror(
x,
icpiter = 50,
subsample = NULL,
pcAlign = FALSE,
mirroraxis = 1,
86 mirror
initPC = TRUE,
initCenter = TRUE,
v1 = NULL,
v2 = NULL,
v3 = NULL,
normal = NULL,
mc.cores = 2
)
Arguments
x k x 3 matrix or mesh3d
icpiter integer: number of iterations to match reflected configuration onto original one
subsample integer: use only a subset for icp matching
pcAlign if TRUE, the icp will be preceeded by an alignment of the principal axis (only
used if icpiter > 0), currently only works for 3D data.
mirroraxis integer: which axis to mirror at
initPC logical: if TRUE the data will be prealigned by its principal axes.
initCenter logical: if TRUE and initPC=FALSE, x will be translated to its centroid before
mirroring.
v1 point on plane
v2 if normal=NULL, the plane will be defined by three points v1, v2, v3
v3 if normal=NULL, the plane will be defined by three points v1, v2, v3
mc.cores use parallel processing to find best alignment to original shape.
Details
reflect a mesh configuration at the plane spanned by its first 2 principal axis, then try to rigidily
register the reflected configuration onto the original one using iterative closest point search to es-
tablish correspondences. Also, if a reflection plane is defined, pcAlign, initPC, initCenter and
mirroraxis will be ignored and the object will be mirrored on the defined plane (and optionally
aligned using an ICP approach).
Value
returns the reflected object
Examples
data(boneData)
boneMir <- mirror(boneLM[,,1],icpiter=50,mc.cores=2,mirroraxis=3)
### mirror on 3 midsaggital landmarks and then optimize it with an ICP

boneMirPlane <- mirror(boneLM[,,1],v1=boneLM[1,,1],v2=boneLM[2,,1],v3=boneLM[9,,1])
## 2D Example:
mirror2plane 87
gorfMir <- mirror(gorf.dat[,,1],mirroraxis=2,pcAlign=TRUE,icpiter = 0)
plot(gorfMir,asp = 1)
points(gorf.dat[,,1],col=3)
}
## Not run:
## now mirror a complete mesh
require(rgl)
skullMir <- mirror(skull_0144_ch_fe.mesh,icpiter=10,subsample = 30,
mc.cores=2,mirroraxis=3,pcAlign=TRUE)
###compare result to original
wire3d(skull_0144_ch_fe.mesh,col=3)
wire3d(skullMir,col=2)
## End(Not run)
mirror2plane mirror points or mesh on an arbitrary plane
Description
mirror points or mesh on an arbitrary plane
Usage
mirror2plane(x, v1, normal = NULL, v2 = NULL, v3 = NULL)


Arguments
x x 3D-vector or a k x 3 matrix with 3D vectors stored in rows. Or a triangular
mesh of class mesh3d
v1 point on plane
v2 if pNorm=NULL, the plane will be defined by three points v1, v2, v3
Value
mirrored coordinates mesh
88 name2factor
Examples
# mirror mesh on plane spanned by 3 midsagital landmarks
data(boneData)
mirrmesh <- mirror2plane(skull_0144_ch_fe.mesh,v1=boneLM[1,,1],v2=boneLM[9,,1],v3=boneLM[10,,1])
name2factor extract data from array names
Description
extract data from array names
Usage
name2factor(x, sep = "_", which, collapse = sep, as.factor = TRUE)
name2num(x, sep = "_", which, collapse = sep, dif = TRUE)
Arguments
x data, can be a three-dimensional array, a matrix, a named list or a vector con-
taining names to split
sep character by which to split the strings
which integer or vector of integers, if more entries are selected, they will be concate-
nated by the string specified with the option ’collapse’.
collapse character by which to collapse data if two strings are to be concatenated
as.factor logical: if TRUE, a factor vector will be returned, strings otherwise.
dif logical: calculate difference if two fields containing numbers are selected.
Details
extract data from array names and convert to factors or numbers
If an array is used as input, the data info is expected to be in the 3rd dimension, for a matrix,
rownames are used.
Value
returns a vector containing factors or numbers
Author(s)
Stefan Schlager
NNshapeReg 89
Examples
data <- matrix(rnorm(200),100,2)

id <- paste("id",1:100,sep="")
pop <- c(rep("pop1",50),rep("pop2",50))
sex <- c(rep("male",50),rep("female",50))
age <- floor(rnorm(100,mean=50,sd=10))
rownames(data) <- paste(id,pop,sex,age,sep="_")
infos <- data.frame(pop=name2factor(data,which=2))
infos$age <- name2num(data,which=4)
infos$pop.sex <- name2factor(data,which=2:3)
NNshapeReg Estimate the shape by averaging the shape of the nearest neighbours.
Description
Estimate the shape of one set of landmarks by averaging the shape of the nearest neighbours ob-
tained by a second set of landmarks. Weights are calculated either form Mahalanobis or Procrustes
distances. This can be useful for data with missing landmarks.
Usage
NNshapeReg(
x,
y = NULL,
n = 3,
mc.cores = parallel::detectCores()
)
Arguments
x an array or matrix (one row per specim) with data used for estimating weights.
y an array or matrix (one row per specim) with landmark data on which the weighted
averaging is applied for prediction. If NULL, x will be used for both tasks.
n amount of nearest neighbours to consider
mahalanobis logical: use mahalanobis distance
mc.cores integer: amount of cores used for parallel processing.
Details
This function calculates weights from one set of shape data and then estimates the shape of another
(or same) set of landmarks. CAUTION: landmark data has to be registered beforehand.
90 pcAlign
Value
matrix or array of estimates.
See Also
proc.weight, fixLMtps
Examples
#use the closest 3 specimen based on the first 4 landmarks
#to estimate the shape
estim <- NNshapeReg(proc$rotated[1:4,,],proc$rotated,n=3,mc.cores=1)
#compare estimation and true config
plot(proc$rotated[,,1],asp=1)
points(estim[,,1],col=2)
}
nose landmarks and a triangular mesh representing a human nose
Description
triangular mesh representing a human nose and two matrices containing landmark data
Format
shortnose.mesh: A triangular mesh of class ’mesh3d’.
shortnose.lm: matrix containing example landmark data placed on shortnose.mesh.
longnose.lm: matrix containing example landmark data representing a caricaturesquely deformed
human nose.
pcAlign align two 3D-pointclouds/meshes by their principal axes
Description
align two 3D-pointclouds/meshes by their principal axes
pcAlign 91
Usage
pcAlign(x, y, optim = TRUE, subsample = NULL, iterations = 10, mc.cores = 2)


Arguments
x matrix or mesh3d
y matrix or mesh3d, if missing, x will be centered by its centroid and aligned by
its princial axis.
optim logical if TRUE, the RMSE between reference and target will be minimized
testing all possible axes alignments and (if iterations > 0) followed by a rigid
ICP procedure.
subsample integer: use subsampled points to decrease computation time of optimization.
iterations integer: number of iterations for optimization (the higher the more accurate but
also more time consuming).
mc.cores use parallel processing to find best alignment to original shape.
Details
x and y will first be centered and aligned by their PC-axes. If optim=TRUE,all possible 8 ordinations
of PC-axes will be tested and the one with the smallest RMSE between the transformed version of
x and the closest points on y will be used. Then the rotated version of x is translated to the original
center of mass of y.
Value
rotated and translated version of x to the center and principal axes of y.
Examples
data(boneData)
blm1 <- pcAlign(boneLM[,,1],boneLM[,,2])
## Not run:
require(rgl)
spheres3d(boneLM[,,1])#original position
spheres3d(blm1,col=2)#aligned configuration
spheres3d(boneLM[,,2],col=3)#target
## End(Not run)
92 pcaplot3d
pcaplot3d visualization of shape variation
Description
visualization of shape change
Usage
pcaplot3d(x, ...)
## S3 method for class 'symproc'

pcaplot3d(
x,
pcshow = c(1, 2, 3),
mag = 3,
color = 4,
lwd = 1,
sym = TRUE,
legend = TRUE,
type = c("spheres", "points"),
...
)
## S3 method for class 'nosymproc'

pcaplot3d(
x,
pcshow = c(1, 2, 3),
mag = 3,
color = 4,
lwd = 1,
legend = TRUE,
type = c("spheres", "points"),
...
)
Arguments
x a object derived from the function procSym calculated on 3D coordinates.
... Additional parameters which will be passed to the methods.
pcshow a vector containing the PCscores to be visualized.
mag a vector or an integer containing which standard deviation of which PC has to
be visualized.
color color of the 3d points/spheres.
lwd width of the lines representing the shape change.
PCdist 93
sym logical: if TRUE the symmetric component of shape is displayed. Otherwise the
asymmetric one.
legend logical: if TRUE a legend explaining the color coding of the PCs is plotted.
type character: for type="spheres", the landmarks will be rendered using rgl’s
spheres3d function and for type="points" by points3d respectivly.
Details
visualization of the shape changes explained by Principal components
Value
returns an invisible array containing the shapes associated with the Principal components selected.
See Also
procSym
Examples
## Not run:
data(boneData)
pcaplot3d(proc,pcshow=1:3,mag=-3)#only one PC available
## End(Not run)
PCdist correlation between a reduced space and the original space
Description
Calculates the correlation between distances in a reduced space and the original space
Usage
PCdist(PCs, PCscores, x = 5, plot.type = "b")
Arguments
PCs m x k matrix of Principal Components where m is the k is the number of PCs.
PCscores n x m matrix of Principal Component scores where n is the number of observa-
tions.
x integer: increment for every x-th PC the subspace to fullspace correlation will
be calculated.
plot.type "b"=barplot of correlation values, "s"=line between correlation values.
94 permudist
Value
a vector of R-squared values between subspace and fullspace distances and a barplot depicting the
correlations belonging to the subspace.
Author(s)
Stefan Schlager
Examples
a <- procSym(gorf.dat)
PCdist(a$PCs, a$PCscores, x = 2)
}
permudist performs permutation testing for group differences.
Description
This function compares the distance between two groupmeans to the distances obtained by random
assignment of observations to this groups.
Usage
permudist(
data,
groups,
rounds = 1000,
which = NULL,
p.adjust.method = "none",
median = FALSE
)
Arguments
data array or matrix containing data
groups factors determining grouping.
rounds number of permutations
which integer (optional): in case the factor levels are > 2 this determins which factor-
levels to use
p.adjust.method
method to adjust p-values for multiple comparisons see p.adjust.methods for
options.
median logical: if TRUE, comparison will be median instead of mean.
permuvec 95
Value
dist distance matrix with distances between actual group means

p.adjust.method
method used for p-value adjustion
p.value distance matrix containing pairwise p-values obtained by comparing the actual
distance to randomly acquired distances
Examples
data(boneData)
groups <- name2factor(boneLM,which=3)
perm <- permudist(proc$PCscores[,1:10], groups=groups, rounds=10000)
## now we concentrate only on sex dimorphism between Europeans

groups <- name2factor(boneLM,which=3:4)
levels(groups)
perm1 <- permudist(proc$PCscores, groups=groups,which=3:4, rounds=10000)
permuvec perfom permutation testing on angles and distances between sub-

groups of two major groups.
Description
perform permutation test on length and angle of the vectors connecting the subgroup means of two
groups: e.g. compare if length and angle between sex related differences in two populations differ
significantly.
Usage
permuvec(
data,
groups,
subgroups = NULL,
rounds = 9999,
scale = TRUE,
tol = 1e-10,
mc.cores = parallel::detectCores()
)
96 permuvec
Arguments
data array or matrix containing data.
groups factors of firs two grouping variables.
subgroups factors of the subgrouping.
rounds number of requested permutation rounds
scale if TRUE: data will be scaled by pooled within group covarivance matrix. Other-
wise Euclidean distance will be used for calculating distances.
tol threshold for inverting covariance matrix.
mc.cores integer: determines how many cores to use for the computation. The default
is autodetect. But in case, it doesn’t work as expected cores can be set manu-
ally.Parallel processing is disabled on Windows due to occasional errors.
Details
This function calculates means of all four subgroups and compares the residual vectors of the major
grouping variables by angle and distance.
Value
angle angle between the vectors of the subgroups means
dist distances between subgroups
meanvec matrix containing the means of all four subgroups
permutangles vector containing angles (in radians) from random permutation
permudists vector containing distances from random permutation
p.angle p-value of angle between residual vectors
p.dist p-value of length difference between residual vectors
subdist length of residual vectors connecting the subgroups
means.
Examples
data(boneData)
pop <- name2factor(boneLM,which=3)
sex <- name2factor(boneLM,which=4)
## use non scaled distances by setting \code{scale = FALSE}
## and only use first 10 PCs
perm <- permuvec(proc$PCscores[,1:10], groups=pop, subgroups=sex,
scale=FALSE, rounds=100, mc.cores=2)
## visualize if the amount of sexual dimorphism differs between

# (lenghts of vectors connecting population specific sex's averages)
# differs between European and Chines
placePatch 97
hist(perm$permudist, xlim=c(0,0.1),main="measured vs. random distances",

xlab="distances")
points(perm$dist,10,col=2,pch=19)#actual distance
text(perm$dist,15,label=paste("actual distance\n
(p=",perm$p.dist,")"))
## not significant!!
## visualize if the direction of sexual dimorphism

# (angle between vectors connecting population specific sex's averages)
# differs between European and Chines
hist(perm$permutangles, main="measured vs. random angles",
xlab="angles")
points(perm$angle,10,col=2,pch=19)#actual distance
text(perm$angle,15,label=paste("actual distance\n
(p=",perm$p.angle,")"))
## also non-significant
placePatch Project semi-landmarks from a predefined atlas onto all specimen in a

sample
Description
Project semi-landmarks from a predefined atlas onto all specimen in a sample. Various mechanisms
are implemented to avoid errorneous placement on the wrong surface layer (e.g. inside the bone).
Usage
placePatch(
atlas,
dat.array,
path,
prefix = NULL,
fileext = ".ply",
ray = TRUE,
inflate = NULL,
tol = inflate,
relax.patch = TRUE,
keep.fix = NULL,
rhotol = NULL,
silent = FALSE,
mc.cores = 1
)
Arguments
atlas object of class "atlas" created by createAtlas
98 placePatch
dat.array k x 3 x n array containing reference landmarks of the sample or a matrix in case

of only one target specimen.
path character: specify the directory where the surface meshes of the sample are
stored.
prefix character: prefix to the specimens names (stored in dimnames(dat.array)[[3]])
to match the corresponding file names. If dat.array has no dimnames (e.g. be-
cause it is a matrix - see example below), this can also be a character vector
containing the filenames to which fileext will be appended.
fileext character: file extension of the surface meshes.
ray logical: projection will be along surface normals instead of simple closest point
search.
inflate inflate (or deflate - if negative sign) the semilandmarks along the normals of the
deformed atlas to make sure that they stay on the outside (inside) of the target
mesh.
tol numeric: threshold to follow the ray back after inflation. See details below. If
no surface is hit after tol mm, the simple closest point will be used.
relax.patch logical: request relaxation minimising bending energy toward the atlas.
keep.fix integer: rowindices of those landmarks that are not allowed to be relaxed in
case relax.patch=TRUE. If not specified, all landmarks will be kept fix. This
is preferably set during atlas creation with createAtlas: In case you specified
corrCurves on the atlas, you should define explicitly which landmarks (also on
the curves) are supposed to fix to prevent them from sliding.
rhotol numeric: maximum amount of deviation a hit point’s normal is allowed to de-
viate from the normal defined on the atlas. If relax.patch=TRUE, those points
exceeding this value will be relaxed freely (i.e. not restricted to tangent plane).
silent logical: suppress messages.
mc.cores run in parallel (experimental stuff now even available on Windows). On win-
dows this will only lead to a significant speed boost for many configurations,
as all required packages (Morpho and Rvcg) need to be loaded by each newly
spawned process.
Details
This function allows the (relatively) easy projection of surface points defined on an atlas onto all
surface of a given sample by Thin-Plate Spline deformation and additional mechanisms to avoid
distortions. The algorithm can be outlined as followed.
1. relax curves (if specified) against atlas.
2. deform atlas onto targets by TPS based on predefined landmarks (and curves).
3. project coordinates on deformed atlas onto target mesh
4. ’inflate’ or ’deflate’ configuration along their normals to make sure all coordinates are on the
outside/inside
5. Project inflated points back onto surface along these normals.
6. Check if normals are roughly pointing into the same direction as those on the (deformed) atlas.
7. Relax all points against atlas.
8. the predefined coordinates will note change afterwards!
placePatch 99
Value
array containing the projected coordinates appended to the data.array specified in the input. In case
dat.array is a matrix only a matrix is returned.
Author(s)
Stefan Schlager
References
de/volltexte/9181/.
See Also
createAtlas, relaxLM, checkLM,slider3d, tps3d
Examples
## Not run:
data(nose)
require(rgl)
## create atlas
fix <- c(1:5,20:21)
shortnose.lm[fix,], patch=shortnose.lm[-c(1:5,20:21),])
## view atlas
plotAtlas(atlas)
## create landmark array with only fix landmarks

data <- bindArr(shortnose.lm[fix,], longnose.lm[fix,], along=3)

mesh2ply(shortnose.mesh, filename="shortnose")
mesh2ply(longnose.mesh, filename="longnose")
patched <- placePatch(atlas, data, path="./", inflate=5)

## now browse through placed patches
checkLM(patched, path="./", atlas=atlas)
## same example with only one target specimen

data <- longnose.lm[fix, ]
patched <- placePatch(atlas, data, prefix="longnose", path="./", inflate=5)

wire3d(longnose.mesh,col=3)
100 plot.slider3d
spheres3d(patched)
## End(Not run)
plot.slider3d plot the result of slider3d
Description
plot the result of slider3d
Usage
## S3 method for class 'slider3d'

plot(
x,
cols = 2:4,
pt.size = NULL,
point = c("sphere", "point"),
specimen = 1,
add = TRUE,
...
)
Arguments
x result of slider3d call

cols vector containing colors for each coordinate type cols[1]=landmarks, cols[2]=surface
landmarks, cols[3]=outlines.
point how to render landmarks.
specimen integer: select the specimen to plot
add logical: if TRUE, a new rgl window is opened.
... additonal, currently unused parameters
plotAtlas 101
plotAtlas visualize an atlas defined by createAtlas
Description
visualize an atlas defined by createAtlas
Usage
plotAtlas(
atlas,
pt.size = NULL,
alpha = 1,
render = c("w", "s"),
point = c("s", "p"),
meshcol = "white",
add = TRUE,
legend = TRUE,
cols = 2:5
)
Arguments
atlas object of class atlas created by createAtlas.
alpha value between 0 and 1. Sets transparency of mesh 1=opaque 0= fully transpar-
ent.
render if render="w", a wireframe will be drawn, if render="s", the mesh will be
shaded.
point how to render landmarks. "s"=spheres, "p"=points.
meshcol color to render the atlas mesh
add logical: if TRUE, a new rgl window is opened.
legend logical: request plot of legend specifying landmark coloring.
cols vector containing colors for each coordinate type cols[1]=landmarks, cols[2]=patch,
cols[3]=corrCurves, cols[4]=patchCurves.
Details
If legend=TRUE, a plot with a legend will open where coloring of the 3D-spheres is specified.
Value
returns invisible vector containing rgl.id of rendered objects.
102 plotNormals
See Also
placePatch, createAtlas
Examples
data(nose)
shortnose.lm[c(1:5,20:21),], patch=shortnose.lm[-c(1:5,20:21),])
## Not run:
plotAtlas(atlas)
## End(Not run)
plotNormals plots the normals of a triangular surface mesh.
Description
visualises the vertex normals of a triangular surface mesh of class mesh3d. If no normals are
contained, they are computed.
Usage
plotNormals(x, length = 1, lwd = 1, col = 1, ...)
Arguments
x object of class "mesh3d"
length either a single numeric value or a numeric vector defining per-normals lenght
(default is 1)
lwd width of the normals
col color of the normals
... addtional parameters, currently not in use.
Author(s)
Stefan Schlager
Examples
## Not run:
require(rgl)
data(nose)
plotNormals(shortnose.mesh,col=4,length=0.01)
shade3d(shortnose.mesh,col=3)
pls2B 103
## End(Not run)
pls2B Two-Block partial least square regression.
Description
Performs a Two-Block PLS on two sets of data and assesses the significance of each score by
permutation testing
Usage
pls2B(
x,
y,
tol = 1e-12,
same.config = FALSE,
rounds = 0,
useCor = FALSE,
cv = FALSE,
cvlv = NULL,
...
)
Arguments
x array containing superimposed landmark data second block.Matrices are also
allowed but the option ’same.config’ will not work.
y array containing superimposed landmark data of the first block. Matrices are
also allowed but the option ’same.config’ will not work.
tol threshold for discarding singular values.
same.config logical: if TRUE each permutation includes new superimposition of permuted
landmarks. This is necessary if both blocks originate from landmarks that are
superimposed together.
rounds rounds of permutation testing.
useCor if TRUE, the correlation matrix instead of the covariance matrix is used.
cv logical: if TRUE, a leave-one-out cross-validation is performed
cvlv integer: number of latent variables to test
mc.cores integer: determines how many cores to use for the
... arguments passed to ProcGPA computation. The default is autodetect. But in
case, it doesn’t work as expected cores can be set manually. Parallel processing
is disabled on Windows due to occasional errors.
104 pls2B
Details
The Two-Block PLS tries to find those linear combinations in each block maximising the covariance
between blocks. The significance of each linear combination is assessed by comparing the singu-
lar value to those obtained from permuted blocks. If both blocks contain landmarks superimposed
TOGETHER, the option same.config=TRUE requests superimposition of the permuted configura-
tions (i.e. where the the landmarks of block x are replaced by corresponding landmarks of other
specimen.
Value
svd singular value decomposition (see svd) of the ’common’ covariance block
Xscores PLS-scores of x
Yscores PLS-scores of y
CoVar Dataframe containing singular values, explained covariation, correlation coef-
fictient between PLS-scores and p-values for singular values obtained from per-
mutation testing
xlm linear model: lm(Xscores ~ Yscores - 1)
ylm linear model: lm(Yscores ~ Xscores - 1)
predicted.x array containing matrices of cross-validated predictions for x(landmarks arrays
will be vectorized using vecx)
predicted.y array containing matrices of cross-validated predictions for y (landmarks arrays
will be vectorized using vecx)
rv RV-coefficient
p.value.RV p-value for RV-coefficient determined by permutation testing
Author(s)
Stefan Schlager
References
Rohlf FJ, Corti M. 2000. Use of two-block partial least-squares to study covariation in shape.
Systematic Biology 49:740-753.
See Also
plsCoVar, getPLSfromScores, predictPLSfromScores, getPLSscores, predictPLSfromData,svd
, plsCoVarCommonShape, getPLSCommonShape
Examples
### very arbitrary test:
### check if first 4 landmarks covaries with the second 4
## we do only 50 rounds to minimize computation time
plsCoVar 105
## Not run: #same.config takes too long for CRAN check

pls1 <- pls2B(proc$rotated[1:4,,],proc$rotated[5:8,,],
same.config=TRUE,rounds=50,mc.cores=2)
## End(Not run)
pls1 <- pls2B(proc$rotated[1:4,,],proc$rotated[5:8,,],
same.config=FALSE,rounds=50,mc.cores=1)
pls1
layout(matrix(1:4,2,2,byrow=TRUE))
for(i in 1:4)
plot(pls1$Xscores[,i]~pls1$Yscores[,i])
## predict first 4 landmarks from second 4 for first config

layout(1)
predPLS <- predictPLSfromData(pls1,y=proc$rotated[5:8,,1])
## show differences between prediction and original
deformGrid2d(predPLS,proc$rotated[1:4,,1],pch=19)
##plot the complete first config
points(proc$rotated[,,1])
##show effects of first latent variable

plsEffects <- plsCoVar(pls1,i=1)
deformGrid2d(plsEffects$x[,,1],plsEffects$x[,,2])##show on x
deformGrid2d(plsEffects$y[,,1],plsEffects$y[,,2],add=TRUE,pch=19)##show on y
##show effects of 2nd latent variable

plsEffects2 <- plsCoVar(pls1,i=2)
deformGrid2d(plsEffects2$x[,,1],plsEffects2$x[,,2])##show on x
deformGrid2d(plsEffects2$y[,,1],plsEffects2$y[,,2],add=TRUE,pch=19)##show on y
}
plsCoVar Get the shape changes from pls2B associated with each latent variable
Description
Get the shape changes from pls2B associated with each latent variable
Usage
plsCoVar(pls, i, sdx = 3, sdy = 3)
Arguments
pls output of pls2B
i integer: which latent variable to show. E.g. i=3 will show the changes associated
with the 3rd latent variable.
sdx standard deviation on the xscores. sdx=3 will show the effecs of -3sd vs +3sd
sdy standard deviation on the yscores. sdy=3 will show the effecs of -3sd vs +3sd
106 plsCoVarCommonShape
Value
x matrix/array with reconstructed x
y matrix/array with reconstructed y, with each prediction named accordingly: e.g.
neg_x_sd_3 means the prediction of x at a score of -3*sd(Xscores)
.
See Also
pls2B, getPLSfromScores, predictPLSfromScores, getPLSscores, predictPLSfromData,svd,
plsCoVarCommonShape
plsCoVarCommonShape Compute the shape changes along the common axis of deformations
Description
Compute the shape changes between two blocks of 2D or 3D shape coordiantes along the common
axis of deformations defined by each dimension of the latent space
Usage
plsCoVarCommonShape(pls, i, sdcommon = 1)
Arguments
pls object of class "pls2B"
i integer: dimension of latent space to show shape changes for
sdcommon standard deviations derived from scores scaled to a consensus scale
Value
returns an k x m x 2 array with the common shape changes associated with +-sdcommon SD of the
i-th latent dimension
Note
this give the same results as plsCoVar, however, using common shape vectors as suggested by
Mitteroecker and Bookstein (2007)
References
Mitteroecker P, Bookstein F. 2007. The conceptual and statistical relationship between modularity
and morphological integration. Systematic Biology 56(5):818-836.
points2plane 107
See Also
pls2B, getPLSfromScores, predictPLSfromScores, getPLSscores, predictPLSfromData,svd,

plsCoVar, getPLSCommonShape
Examples
data(boneData)
pls <- pls2B(proc$orpdata[1:4,,],proc$orpdata[5:10,,])
commShape <- getPLSCommonShape(pls)
## get common shape for first latent dimension at +-2 sd of the scores
pred <- plsCoVarCommonShape(pls,1,2)
## Not run:
deformGrid3d(pred[,,1],pred[,,2])
## End(Not run)
points2plane projects a 3D coordinate orthogonally onto a plane
Description
projects a 3D coordinate orthogonally onto a plane
Usage
points2plane(x, v1, normal = NULL, v2 = NULL, v3 = NULL)
Arguments
x 3D-vector or a k x 3 matrix with 3D vectors stored in rows

v1 point on plane
Value
projected point
108 prcompfast
Examples
data(boneData)
##project rhinion onto plane spanned by Nasion and both Nariales
rpro <- points2plane(boneLM[10,,1],v1=boneLM[9,,1],v2=boneLM[3,,1],v3=boneLM[4,,1])
## Not run:
require(rgl)
#visualize
wire3d(skull_0144_ch_fe.mesh,col="white")
##get plane normal
normal <- crossProduct(boneLM[3,,1]-boneLM[9,,1],boneLM[4,,1]-boneLM[9,,1])
#' ## get plane offset
d <- norm(points2plane(c(0,0,0),v1=boneLM[9,,1],normal=normal),"2")
spheres3d(boneLM[,,1],radius=0.5)
spheres3d(boneLM[c(3,4,9),,1],radius=0.6,col=3)
##original position of Rhinion
spheres3d(boneLM[10,,1],radius=0.6,col=2)
##projected onto plane
spheres3d(rpro,radius=0.9,col=6)
lines3d(rbind(rpro,boneLM[10,,1]),lwd=3)
##plot plane
planes3d(normal[1],normal[2],normal[3],d=d,col=2,alpha=0.5)
##now we project all points onto that plane:

spheres3d(points2plane(boneLM[,,1],v1=boneLM[9,,1],v2=boneLM[3,,1],v3=boneLM[4,,1]),col=3)
## and finally project the vertices of the mesh onto the plane
meshpro <- points2plane(vert2points(skull_0144_ch_fe.mesh),v1=boneLM[9,,1],normal=normal)
points3d(meshpro,col=2)
## End(Not run)
prcompfast fast Principal Component Analysis (PCA)
Description
fast Principal Component Analysis (PCA)
Usage
prcompfast(x, retx = TRUE, center = TRUE, scale. = FALSE, tol = NULL, ...)
Arguments
x a numeric or complex matrix (or data frame) which provides the data for the
principal components analysis.
retx a logical value indicating whether the rotated variables should be returned
predict.bgPCA 109
center a logical value indicating whether the variables should be shifted to be zero
centered. Alternately, a vector of length
scale. a logical value indicating whether the variables should be scaled to have unit
variance before the analysis takes place. The default is FALSE for consistency
with S, but in general scaling is advisable. Alternatively, a vector of length equal
the number of columns of x can be supplied. The value is passed to scale. equal
the number of columns of x can be supplied. The value is passed to scale.
tol a value indicating the magnitude below which components should be omitted.
(Components are omitted if their standard deviations are less than or equal to
tol times the standard deviation of the first component.) With the default null
setting, no components are omitted. Other settings for tol could be tol = 0
or tol = sqrt(.Machine$double.eps), which would omit essentially constant
components.
... arguments passed to or from other methods.
Value
prcomp returns a list with class prcomp containing the followin components:
sdev the standard deviations of the principal components (i.e., the square roots of
the eigenvalues of the covariance/correlation matrix, though the calculation is
actually done with the singular values of the data matrix).
rotation: the matrix of variable loadings (i.e., a matrix whose columns contain the eigen-
vectors). The function princomp returns this in the element loadings.
x: if retx is true the value of the rotated data (the centred (and scaled if requested)
data multiplied by the rotation matrix) is returned. Hence, cov(x) is the di-
agonal matrix diag(sdev^2). For the formula method, napredict() is applied
to handle the treatment of values omitted by the na.action.
center, scale: the centering and scaling used, or FALSE
. pcafast <- prcompfast(iris[,1:4]) pcadefault <- prcompfast(iris[,1:4]) ## check if both results are
idential (ignoring the sign) all.equal(lapply(pcafast,abs),lapply(pcadefault,abs))
Note
this function returns the same results as prcomp (apart from sign differences) but uses smarter matrix
decompositions making it faster for nrow(x) » ncol(x) and nrow(x) « ncol(x).
predict.bgPCA Compute between-group-PC scores from new data
Description
Compute between-group-PC scores from new data
110 predict.CVA
Usage
## S3 method for class 'bgPCA'
predict(object, newdata, ...)
Arguments
object object of class bgPCA returned from groupPCA
newdata matrix or 3D array containing data in the same format as originally used to
compute groupPCA
... currently not used.
Value
returns the between-group-PC scores for new data
Examples
data(boneData)
boneLMPart <- boneLM[,,-(1:2)]

procPart <- procSym(boneLMPart)
pop_sex <- name2factor(boneLMPart, which=3:4)
## compute group PCA without first 2 specimens
gpcaPart <- groupPCA(procPart$orpdata, groups=pop_sex, rounds=0, mc.cores=2,cv=FALSE)
## align new data to Procrustes analysis
newdata <- align2procSym(procPart,boneLM[,,1:2])
## get scores for new data
newscores <- predict(gpcaPart,newdata)
predict.CVA Compute CV-scores from new data
Description
Compute CV-scores from new data
Usage
## S3 method for class 'CVA'
predict(object, newdata, ...)
Arguments
object object of class CVA
newdata matrix or 3D array containing data in the same format as originally used to
compute CVA
... currently not used.
predictPLSfromData 111
Value
returns the CV-scores for new data
predictPLSfromData predict 2 Block-PLS from new data
Description
predict 2 Block-PLS from new data
Usage
predictPLSfromData(pls, x, y, ncomp = NULL)
Arguments
pls output of pls2B

x data in the same format as in original pls2B (for landmarks this can be an array
or a matrix and for other data a matrix of a vector)
y data in the same format as in original pls2B (for landmarks this can be an array
or a matrix and for other data a matrix of a vector)
ncomp number of (latent) components to use for prediction.
Value
returns an array/matrix/vector of predictions - depending on input for computing pls
Note
either x or y must be missing
See Also
pls2B, getPLSscores,predictPLSfromScores
Examples
##see examples in pls2B
112 predictRelWarps
predictPLSfromScores predict data from 2-Block PLS-scores
Description
predict data from 2-Block PLS-scores
Usage
predictPLSfromScores(pls, x, y)
Arguments
pls output of pls2B
x scores associated with dataset x in original pls2B
y scores associated with dataset y in original pls2B
Value
returns an array/matrix of landmarks or original values, depending on input for computing pls
Note
either x or y must be missing. If x-scores are provided, the yscores will be estimated and the
predictions calculated.
See Also
pls2B, getPLSscores,predictPLSfromData
predictRelWarps predict relative warps for data not included in the training data set
Description
predict relative warps for data not included in the training data set
Usage
predictRelWarps(x, newdata, noalign = FALSE)
Arguments
x output from relWarps
newdata k x m x n array holding new landmark data
noalign logical: if TRUE, data is assumed to be already aligned to training data and
alignment is skipped.
predictShape.lm 113
Details
This function aligns the new data to the mean from x and transforms it into the relative warp space
computed from the training data.
Value
bescores relative warp scores (PC-scores if alpha = 0)
uniscores uniform scores, NULL if alpha = 0
Examples
data(boneData)
set.seed(42)
training <- sample(1:80,size=60)
rW1 <- relWarps(boneLM[,,training], alpha = -1)
## predict scores for the entire sample
predAll <- predictRelWarps(rW1,boneLM)
## now compare the scores predicted scores to the original ones

layout(matrix(1:4,2,2))
for (i in 1:2) {
plot(rW1$bescores[,i],predAll$bescores[training,i],main=paste("RW",i))
plot(rW1$uniscores[,i],predAll$uniscores[training,i],main=paste("UC",i))
}
predictShape.lm Predict shapes based on linear models calculated from PCscores
Description
Predict shapes based on linear models calculated from PCscores.
Usage
predictShape.lm(fit, datamod, PC, mshape)
Arguments
fit model of class lm where the PCscores are fitted onto
datamod a one-sided "model" formula, of the form ~ x1 + x2 + ... + xk, corresponding
to the right hand term in the model used in fit. If omitted, the predicted shapes
of all specimen are calculated based on the fitted values.
PC Matrix/vector containing Principal components (rotation matrix) corresponding
to PC-scores used in fit.
mshape matrix of the meanshape’s landmarks by which the data was centered before
rotation in covariance eigenspace.
114 predictShape.lm
Details
This function predicts the landmarks based on models calculated from PCscores.
Value
predicted array or matrix containing predicted landmark coordinates
predictedPC matrix containing predicted PC-scores
Warning
Make sure that the levels of the variables used in datamod correspond exactly to those used in fit.
Otherwise model matrix will be calculated erroneous.
See Also
model.matrix, lm, formula
Examples
data(boneData)
##easy model with only one factor based on the first four PCs
fit <- lm(proc$PCscores[,1:4] ~ pop)
## get shape for Europeans only
datamod <- ~as.factor(levels(pop))[2]
Eu <- predictShape.lm(fit,datamod, proc$PCs[,1:4],proc$mshape)
## get shape for Europeans and Chinese

datamod <- ~as.factor(levels(pop))
pred <- predictShape.lm(fit,datamod, proc$PCs[,1:4],proc$mshape)
## Not run:
deformGrid3d(pred$predicted[,,1], pred$predicted[,,2], ngrid = 0)
## End(Not run)
## more complicated model
sex <- name2factor(boneLM,which=4)

fit <- lm(proc$PCscores[,1:4] ~ pop*sex)
## predict female for chinese and European
datamod <- ~(as.factor(levels(pop))*rep(as.factor(levels(sex))[1],2))
## predict female and malefor chinese and European

popmod <- factor(c(rep("eu",2),rep("ch",2)))
sexmod <- rep(as.factor(levels(sex)),2)
datamod <- ~(popmod*sexmod)
proc.weight 115
## add some (randomly generated) numeric covariate

somevalue <- rnorm(80,sd=10)
fit <- lm(proc$PCscores[,1:4] ~ pop+somevalue)
probs <- quantile(somevalue, probs=c(0.05, 0.95))
## make model for European at 5% and 95% quantile
popmod <- rep(factor(levels(pop))[2],2)
datamod <- ~(popmod+probs)
proc.weight calculate weights inverse to the distances from the specified observa-
tion.
Description
for calculation of a shape model by averaging the observations neighbouring the configuration in
question, it is necessary to calculate weights by similarity.
Usage
proc.weight(
data,
number,
ref,
report = TRUE,
reg = 0,
log = FALSE,
weightfun = NULL
)
Arguments
data array containing landmark configurations
number integer: how many of the neighbours are to be involved.
ref integer: position in the array that is used as reference.
report logical: require report about name of the reference.
reg numeric: regularise mahalanobis distance by adding reg to the diagonal of eigen-
values of the covariance matrix.
log logical: use the logarithm of the distances.
mahalanobis logical: use mahalanobis distance.
weightfun custom function that operates on a vector of distances (see examples) and gen-
erates weights accordingly.
116 procAOVsym
Details
distances of zero will get a weight of 1e12 (this is scaled to all weights summing to one), thus
weights for observations further away are converging to zero.
Value
data dataframe containing id, procrustes/mahalanobis distance and weight according
to the reference
reference returns observations’ names if available
rho.all dataframe containing distances to references of all observations
Examples
##get weights for the the four specimen closest to the first observation.
weights <- proc.weight(proc$rotated,4,1)
##estimate the first specimen by weighted neighbour shapes.

estim <- proc$mshape*0;
for (i in 1:4)
{estim <-estim+proc$rotated[,,weights$data$nr[i]]*weights$data$weight[i]}
### visualise
plot(estim,asp=1)## show estimation
points(proc$rotated[,,1],col=3)##show original
## use a gaussian smoother to compute weights using a bandwidth of 0.05

gaussWeight <- function(r,sigma=0.05) {
sigma <- 2*sigma^2
return(exp(-r^2/ sigma))
}
weights <- proc.weight(proc$rotated,4,1,weightfun=gaussWeight)
}
procAOVsym Procrustes ANOVA for structures with object symmetry
Description
Procrustes ANOVA for structures with object symmetry, currently only supporting the factors ’spec-
imen’, ’side’ and the interaction term.
Usage
procAOVsym(symproc, indnames = NULL)
procAOVsym 117
Arguments
symproc object returned by procSym, where pairedLM is specified

indnames vector containing specimen identifiers. Only necessary, if data does not contain
dimnames containing identifiers
Details
performs a Procrustes ANOVA for configurations with object symmetry (as described in Klingen-
berg et al. 2002).
Value
returns a dataframe containing Sums of Squares for each factor.
Note
In future releases the implementation of support for bilateral symmetry and more factors is intended.
Author(s)
Stefan Schlager
References
Klingenberg CP, Barluenga M, Meyer A. 2002. Shape analysis of symmetric structures: quantifying
variation among individuals and asymmetry. Evolution 56:1909-20.
See Also
procSym
Examples
data(boneData)
left <- c(4,6,8)
right <- c(3,5,7)
pairedLM <- cbind(left,right)
symproc <- procSym(boneLM, pairedLM=pairedLM)
procAOVsym(symproc)
118 ProcGPA
ProcGPA Workhorse function for procSym, responsible for Procrustes registra-

tion
Description
Workhorse function for procSym, responsible for Procrustes registration
Usage
ProcGPA(
dat.array,
tol = 1e-05,
scale = TRUE,
CSinit = FALSE,
silent = TRUE,
weights = NULL,
reflection = TRUE,
pcAlign = TRUE
)
Arguments
dat.array Input k x m x n real array, where k is the number of points, m is the number of
tol numeric: Threshold for convergence during iterative superimpositioning.
scale logical: indicating if scaling is requested
CSinit logical: if TRUE, all configurations are initially scaled to Unit Centroid Size.
silent logical: suppress output of elapsed time.
weights numeric vector: assign per landmark weights.
centerweight logical: if TRUE, the landmark configuration is scaled according to weights
during the rotation process, instead of being scaled to the Centroid size.
reflection logical: allow reflections.
pcAlign logical: if TRUE, the shapes are aligned by the principal axis of the first speci-
men, otherwise the orientation of the first specimen is used.
Value
returns a list with
rotated k x m x n array of the rotated configurations

mshape sample meanshape
procSym 119
Author(s)
Stefan Schlager
References
Goodall C. 1991. Procrustes methods in the statistical analysis of shape. Journal of the Royal
Statistical Society. Series B. Statistical Methodology 53:285-239.
Dryden IL, Mardia KV. 1998. Statistical shape analysis. John Wiley and sons, Chichester.
See Also
procSym, rotonto
Examples
data(boneData)
proc <- ProcGPA(boneLM, CSinit=TRUE, silent=TRUE)
#now we landmarks 5 - 9 double the weight as the others
weights <- c(rep(1,4),rep(2,5),1)
proc.wt <- ProcGPA(boneLM, CSinit=TRUE, weights=weights, silent=TRUE)
procSym Procrustes registration
Description
procSym performs Procrustes superimposition including sliding of semi-landmarks on curves/outlines
in 2D and 3D.
Usage
procSym(
dataarray,
scale = TRUE,
reflect = TRUE,
CSinit = TRUE,
orp = TRUE,
proctol = 1e-05,
tol = 1e-05,
pairedLM = NULL,
sizeshape = FALSE,
use.lm = NULL,
center.part = FALSE,
weights = NULL,
120 procSym
pcAlign = TRUE,
distfun = c("angle", "riemann"),
SMvector = NULL,
outlines = NULL,
deselect = FALSE,
recursive = TRUE,
iterations = 0,
initproc = FALSE,
bending = TRUE,
stepsize = 1
)
Arguments
dataarray Input k x m x n real array, where k is the number of points, m is the number of
scale logical: indicating if scaling is requested to minimize the General Procrustes
distance. To avoid all scaling, one has to set CSinit=FALSE, too.
reflect logical: allow reflections.
CSinit logical: if TRUE, all configurations are initially scaled to Unit Centroid Size.
orp logical: if TRUE, an orthogonal projection at the meanshape into tangent space
is performed.
proctol numeric: Threshold for convergence in the alignment process
tol numeric: Threshold for convergence in the sliding process
pairedLM A X x 2 matrix containing the indices (rownumbers) of the paired LM. E.g. the
sizeshape Logical: if TRUE, a log transformed variable of Centroid Size will be added to
the shapedata as first variable before performing the PCA.
use.lm vector of integers to define a subset of landmarks to be used for Procrustes reg-
istration.
center.part Logical: if TRUE, the data superimposed by the subset defined by use.lm will
be centered according to the centroid of the complete configuration. Otherwise
orp will be set to FALSE to avoid erroneous projection into tangent space.
weights numeric vector: assign per landmark weights.
centerweight logical: if TRUE, the landmark configuration is scaled according to weights
during the rotation process, instead of being scaled to the Centroid size.
men
distfun character: "riemann" requests a Riemannian distance for calculating distances
to mean, while "angle" uses an approximation by calculating the angle between
rotated shapes on the unit sphere.
SMvector A vector containing the landmarks on the curve(s) that are allowed to slide
procSym 121
outlines A vector (or if threre are several curves) a list of vectors (containing the rowindices)
of the (Semi-)landmarks forming the curve(s) in the successive position on the
curve - including the beginning and end points, that are not allowed to slide.
deselect Logical: if TRUE, the SMvector is interpreted as those landmarks, that are not
allowed to slide.
recursive Logical: if TRUE, during the iterations of the sliding process, the outcome of
the previous iteration will be used. Otherwise the original configuration will be
used in all iterations.
iterations integer: select manually how many iterations will be performed during the slid-
ing process (usefull, when there is very slow convergence). 0 means iteration
until convergence.
initproc Logical: indicating if the first Relaxation step is performed against the mean of
an initial Procrustes superimposition. Symmetric configurations will be relaxed
against a perfectly symmetrical mean.
bending if TRUE, bending energy will be minimized, Procrustes distance otherwise (not
suggested with large shape differences)
stepsize integer: dampening factor for the sliding. Useful to keep semi-landmarks from
sliding too far off the surface. The displacement is calculated as
stepsize * displacement.
Details
This function performs Procrustes registration, allowing a variety of options, including scaling, or-
thogonal projection into tangentspace and relaxation of semi-landmarks on curves (without repro-
jection onto the surface/actual outline). It also allows the superimpositioning to be performed using
only a subset of the available landmark. For taking into account object symmetry, pairedLM needs
to be set. This generates an object of class "symproc". Otherwise an object of class "nosymproc".
Value
size a vector containing the Centroid Size of the configurations
rotated k x m x n array of the rotated configurations
Sym k x m x n array of the Symmetrical component - only available for the "Symmetry"-
Option (when pairedLM is defined)
Asym k x m x n array of the Asymmetrical component. It contains the per-landmark
asymmetric displacement for each specimen. Only available for the "Symmetry"-
Option (when pairedLM is defined)
asymmean k x m matrix of mean asymmetric deviation from symmetric mean
mshape sample meanshape
symmean meanshape of symmetrized configurations
tan if orp=TRUE: Residuals in tangentspace else, Procrustes residuals - only avail-
able without the "Symmetrie"-Option
PCs Principal Components - if sizeshape=TRUE, the first variable of the PCs is size
information (as log transformed Centroid Size)
122 procSym
PCsym Principal Components of the Symmetrical Component

PCasym Principal Components of the Asymmetrical Component
PCscores PC scores
PCscore_sym PC scores of the Symmetrical Component
PCscore_asym PC scores of the Asymmetrical Component
eigenvalues eigenvalues of the Covariance matrix
eigensym eigenvalues of the "Symmetrical" Covariance matrix
eigenasym eigenvalues of the "Asymmetrical" Covariance matrix
Variance Table of the explained Variance by the PCs
SymVar Table of the explained "Symmetrical" Variance by the PCs
AsymVar Table of the explained "Asymmetrical" Variance by the PCs
orpdata k x m x n array of the rotated configurations projected into tangent space
rho vector of Riemannian distance from the mean
dataslide array containing slidden Landmarks in the original space - not yet processed by
a Procrustes analysis. Only available if a sliding process was requested
meanlogCS mean log-transformed centroid size
Note
For processing of surface landmarks or including the reprojection of slid landmarks back onto 3D-
surface representations, the usage of slider3d is recommended.
Author(s)
Stefan Schlager
References
Dryden IL, and Mardia KV. 1998. Statistical shape analysis. Chichester.
Klingenberg CP, Barluenga M, and Meyer A. 2002. Shape analysis of symmetric structures: quan-
tifying variation among individuals and asymmetry. Evolution 56(10):1909-1920.
See Also
slider3d
projRead 123
Examples
require(rgl)
data(boneData)
### do an analysis of symmetric landmarks

## visualize landmarks on surface
## Not run:
spheres3d(boneLM[,,1])
wire3d(skull_0144_ch_fe.mesh,col=3)
## get landmark numbers
text3d(boneLM[,,1],text=paste(1:10),adj = 1, cex=3)
## End(Not run)
## determine paired Landmarks left side:
left <- c(4,6,8)
right <- c(3,5,7)
symproc <- procSym(boneLM, pairedLM=pairedLM)
## Not run:
## visualize first 3 PCs of symmetric shape
pcaplot3d(symproc, sym=TRUE)
## visualize first 3 PCs of asymmetric shape
pcaplot3d(symproc, sym=FALSE)
## visualze distribution of symmetric PCscores population

pop <- name2factor(boneLM, which=3)
if (require(car)) {
spm(~symproc$PCscore_sym[,1:5], groups=pop)
## visualze distribution of asymmetric PCscores population
spm(~symproc$PCscore_asym[,1:5], groups=pop)
}
## End(Not run)
projRead Project points onto the closest point on a mesh
Description
project points onto a given surface and return projected points and normals.
Usage
projRead(lm, mesh, readnormals = TRUE, smooth = FALSE, sign = TRUE, ...)
124 projRead
Arguments
lm m x 3 matrix containing 3D coordinates.

mesh character: specify path to mesh file.
readnormals logical: return normals of projected points.
smooth logical: rerturn smoothed normals.
sign logical: request signed distances.
... additional arguments currently not used.
Value
if readnormals = FALSE, a m x 3 matrix containing projected points is returned, otherwise a list,

where
vb 3 x m matrix containing projected points

normals 3 x m matrix containing normals
quality vector containing distances
Author(s)
Stefan Schlager
References
Detection of inside/outside uses the algorithm proposed in:

Meshes. Informatics and Mathematical Modelling.
See Also
closemeshKD
Examples
data(nose)
## Not run:
repro <- projRead(shortnose.lm,shortnose.mesh)
## End(Not run)
qqmat 125
qqmat Q-Q plot to assess normality of data
Description
qqmat plots Mahalanobisdistances of a given sample against those expected from a Gaussian distri-
bution
Usage
qqmat(x, output = FALSE, square = FALSE)
Arguments
x sample data: matrix or vector
output logical: if TRUE results are returned
square plot in a square window - outliers might be cut off.
Value
if output=TRUE, the following values are returned
x distances from an expected Gaussian distribution

y observed distances - sorted
d observed distances - unsorted
Author(s)
Stefan Schlager
See Also
qqplot
Examples
require(MASS)
### create normally distributed data
data <- mvrnorm(100,mu=rep(0,5),Sigma = diag(5:1))
qqmat(data)
###create non normally distributed data

data1 <- rchisq(100,df=3)
qqmat(data1,square=FALSE)
126 r2morphoj
quad2trimesh converts a mesh containing quadrangular faces into one only consist-
ing of triangles
Description
converts a mesh containing quadrangular faces into one only consisting of triangles
Usage
quad2trimesh(mesh, updateNormals = TRUE)
Arguments
mesh object of class "mesh3d"
updateNormals logical: request recalculation of (angle weighted) vertex normals.
Value
triangular mesh with updated normals
Examples
Sigma <- diag(3:1) #create a 3D-covariance matrix

require(rgl)
quadmesh <- ellipse3d(Sigma)##create quadmesh
trimesh <- quad2trimesh(quadmesh)# convert to trimesh
r2morphoj Export data to MorphoJ and Morphologika
Description
Export data to MorphoJ and Morphologika
Usage
r2morphoj(x, file, id.string = NULL)
r2morphologika(x, file = file, labels = NULL, labelname = NULL, ...)

ray2mesh 127
Arguments
x 3-dimensionla array containing landmark data. E.g. the input/output from procSym.
file character: name the output file
id.string a string with ids or factors to append
labels character vector specify labels to create for Morphologika
labelname character: name the labels for Morphologika.
... unused at the moment
Details
Export data to MorphoJ and Morphologika
Examples
r2morphoj(gorf.dat,file="gorf.dat")
data <- bindArr(gorf.dat, gorm.dat, along=3)

datalabels <- c(rep("female",dim(gorf.dat)[3]),
rep("male",dim(gorm.dat)[3]))
labelname <- "sex"
r2morphologika(data, labels=datalabels, labelname= labelname, file="data.dat")
## cleanup
unlink(c("gorf.dat","data.dat"))
}
ray2mesh projects the vertices of a mesh along its normals onto the surface of
another one.
Description
projects the vertices of a mesh onto the surface of another one by searching for the closest point
along vertex normals on the target by for each vertex.
Usage
ray2mesh(mesh1, tarmesh, tol = 1e+12, inbound = FALSE, mindist = FALSE, ...)
Arguments
mesh1 mesh to project. Can be an object of class "mesh3d" or path to an external mesh
file (ply, obj, stl).
tarmesh mesh to project onto. Can be an object of class "mesh3d" or path to an external
mesh file (ply, obj, stl).
128 read.csv.folder
tol numeric: maximum distance to search along ray, closest Euclidean distance will
be used, if tol is exceeded.
inbound inverse search direction along rays.
mindist search both ways (ray and -ray) and select closest point.
... additional arguments not used at the moment.
Value
returns projected mesh with additional list entries:
quality integer vector containing a value for each vertex of x: 1 indicates that a ray has
intersected ’tarmesh’ within the given threshold, while 0 means not
distance numeric vector: distances to intersection
Author(s)
Stefan Schlager
See Also
ply2mesh, closemeshKD
read.csv.folder batch import data from files
Description
imports all data files contained in a specified folder.
Usage
read.csv.folder(
folder,
x,
y = 2:4,
rownames = NULL,
header = TRUE,
dec = ".",
sep = ";",
pattern = "csv",
addSpec = NULL,
back = TRUE
)
read.fcsv 129
Arguments
folder character: path to folder
x either a vector specifiing which rows are to be imported, or character vector
containing variable names to be sought for.
y a vector specifiing, which columns of the speradsheet ist to be imported.
rownames integer: specifies columns, where variable names are stored.
header logical : if spreadsheet contains header-row.
dec character: defines decimal sepearator.
sep character: defines column seperator.
pattern character: specify file format (e.g. csv).
addSpec character: add a custom specifier to the dimnames of the array.
back logical: where to place the specifier.
Value
arr array containing imported data
NAs vector containing position of observations with NAs
NA.list list: containing vectors containing information which LMs are missing in which
observation
Author(s)
Stefan Schlager
See Also
read.table
read.fcsv read fiducials from slicer4
Description
read fiducials from slicer4
Usage
read.fcsv(x, na = NULL, lps2ras = FALSE)
Arguments
x filename
na value to be replaced by NA
lps2ras logical: if the coordinate system is LPS and lps2ras=TRUE, the data will be
rotated into the RAS space by inverting the first two dimensions using LPS2RAS.
130 read.mpp
Value
a k x 3 matrix with landmarks
read.lmdta read dta files
Description
reads .dta files created by the software Landmark http://graphics.idav.ucdavis.edu/research/EvoMorph
Usage
read.lmdta(file = "x", na = 9999)
Arguments
file a dta file
na specifies a value that indicates missing values
Value
arr array containing landmarks dimnames will be Information of ID and landmark
names specified in Landmark
info Information extracted from the header of the dta file
idnames character vector containing the names of the individuals as specified in the dta
file
read.mpp Read saved pick-points from meshlab
Description
imports pick points selected with meshlab
Usage
read.mpp(file, info = FALSE)
Arguments
file file to import
info logical: if TRUE, addtional infos are returned
read.pts 131
Value
if info=FALSE:
a matrix containing picked-points coordinates (only those tagged as active).
if info=TRUE: a list containing
data matrix containing coordinates - including points tagged as inactive
info additional info contained in file.
Author(s)
Stefan Schlager
See Also
read.pts
read.pts reads pts files
Description
reads Landmark data exported from the software Landmark from http://graphics.idav.ucdavis.edu/research/EvoMorph
Usage
read.pts(file = "x", na = 9999)
Arguments
file pts file
na specifies a value that indicates missing values
Value
matrix matrix containing landmark information rownames will be the names given to
the landmarks in Landmark
See Also
read.pts
Examples
data(nose)
write.pts(shortnose.lm, filename="shortnose")
data <- read.pts("shortnose.pts")
132 readallTPS
read.slicerjson read Landmarks from Slicer in Json format
Description
read Landmarks from Slicer in Json format
Usage
read.slicerjson(x, lps2ras = FALSE, na = NULL)
Arguments
x path to json file
lps2ras logical: if the coordinate system is LPS and lps2ras=TRUE, the data will be
rotated into the RAS space by inverting the first two dimensions using LPS2RAS.
na value to be replaced by NA
Value
returns matrix or list of matrices with imported landmark coordinates
readallTPS Import landmarks and outlines from TPS files
Description
Imports outlines and landmarks from files generated by tpsdig2
Usage
readallTPS(file, scale = TRUE)
Arguments
file A TPS-file generated by tpsdig2
scale logical: if TRUE the data will be scaled according to the SCALE entry.
Value
ID Specimen IDs read from TPS file
LM list of landmarks contained in the TPS-file
outlines a list containing sublists for each specimen with all the outlines read from TPS
file
SCALE vector containing the scale factors for each landmark config.
readLandmarks.csv 133
Note
currently only landmarks, ID and outlines are read from the TPS-file
Author(s)
Stefan Schlager
References
http://life.bio.sunysb.edu/ee/rohlf/software.html
See Also
read.lmdta, read.pts
readLandmarks.csv import landmark data from csv files
Description
import landmark data from csv files
Usage
readLandmarks.csv(
file,
x,
y = 2:4,
rownames = NULL,
header = TRUE,
dec = ".",
sep = ";"
)
Arguments
file character: path to file containing landmark data.
x either a vector specifiing which rows are to be imported, or character vector
containing variable names to be sought for.
y a vector specifiing, which columns of the speradsheet ist to be imported.
rownames integer: specifies columns, where variable names are stored.
header logical : if spreadsheet contains header-row.
dec character: defines decimal sepearator.
sep character: defines column seperator.
134 regdist
Value
LM matrix containing imported data
NAs vector containing rows containing NAs
Author(s)
Stefan Schlager
See Also
read.table
regdist correlation between shape space and tangent space
Description
performs a partial Procrustes superimposition of landmark data and calculates the correlation be-
tween tangent and shape space.
Usage
regdist(dataarray, plot = TRUE, main = "", rho = "angle", dist.mat.out = FALSE)
Arguments
dataarray Input k x m x n real array, where k is the number of points, m is the number of
plot Logical: whether to plot the distances between observations.
main character string: Title of the plot.
rho chose how to calculate distances in shape space. Options: "riemdist"=Riemannian
distance (function from the shapes package-takes along time to calculate), "an-
gle"=calculates the angle between shape vectors, "sindist"=sinus of length of
residual vector between shape vectors.
dist.mat.out Logical: If TRUE, output will contain distance matrices.
Value
cor correlation coefficient between distances in shape space and tangent space
procSS Procrustes Sums of Squares (of full procrustes distance)
tanSS Tangent Sums of Squares
rhoSS Procrustes Sums of Squares (of angle)
euc.dist distance matrix of euclidean distance in Tangent space
proc.dist distance matrix of Procrustes distance in Shape space
RegScore 135
Author(s)
Stefan Schlager
See Also
regdist
Examples
regdist(gorf.dat)
}
RegScore calulate regression scores for linear model
Description
calulate regression scores for linear model as specified in Drake & Klingenberg(2008)
Usage
RegScore(model, x = NULL)
Arguments
model linear model
x optional: matrix containing fitted data to be projected onto the regression lines.
If omitted the model’s fitted values will be used.
Details
the data are orthogonally projected onto the regression lines associated with each factor.
Value
returns a n x m matrix containing the regression scores for each specimen.
Warning
if model contains factors with more than 2 levels, R calculates one regression line per 2 factors.
Check the colnames of the returned matrix to select the appropriate one. See examples for details.
References
Drake, AG. & Klingenberg, CP. The pace of morphological change: historical transformation of
skull shape in St Bernard dogs. Proceedings of the Royal Society B: Biological Sciences, The
Royal Society, 2008, 275, 71-76.
136 relaxLM
Examples
model <- lm(as.matrix(iris[,1:3]) ~ iris[,4])
rs <- RegScore(model)
plot(rs,iris[,4])
##now use a random subsample for model fitting

rand <- sample(nrow(iris))
x <- iris[rand[1:100],4]
newmod <- lm(as.matrix(iris[rand[1:100],1:3]) ~ x)
##predict the rest of data and get their regression scores
rsPred <- RegScore(newmod,as.matrix(iris[rand[101:150],1:3]))
plot(rsPred,iris[rand[101:150],4])
## Not run:
data(boneData)
pop.sex <- name2factor(boneLM,which=3:4) # generate a factor with 4 levels
lm.ps.size <- lm(proc$PCscores ~ pop.sex+proc$size)
rs <- RegScore(lm.ps.size)
colnames(rs) # in this case, the last column contains the regression
# scores associated with proc$size
## validate by using a subsample for fitting
rand <- sample(dim(boneLM)[3])
lm.ps.size0 <- lm(proc$PCscores[rand[1:50],] ~ proc$size[rand[1:50]])
rs0 <- RegScore(lm.ps.size0,proc$PCscores[rand[-c(1:50)],] )
plot(rs0,proc$size[rand[-c(1:50)]])
## End(Not run)
relaxLM relax one specific landmark configuration against a reference
Description
relax one specific landmark configuration against a reference (e.g. a sample mean)
Usage
relaxLM(lm, ...)

relaxLM(
lm,
reference,
SMvector,
outlines = NULL,
surp = NULL,
sur.name = NULL,
mesh = NULL,
relaxLM 137
tol = 1e-05,
deselect = FALSE,
inc.check = TRUE,
iterations = 0,
fixRepro = TRUE,
missing = NULL,
bending = TRUE,
stepsize = ifelse(bending, 1, 0.5),
use.lm = NULL,
silent = FALSE,
...
)

relaxLM(
lm,
reference,
tol = 1e-05,
deselect = FALSE,
inc.check = TRUE,
iterations = 0,
fixRepro = TRUE,
missing = NULL,
bending = FALSE,
use.lm = NULL,
silent = FALSE,
...
)
Arguments
lm k x 3 or k x 2 matrix containing landmark data to be slidden - or a triangular
mesh of class "mesh3d". See details
... additonal arguments - currently unused
reference k x 3 or k x 2 matrix containing landmark of the reference, or a mesh with the
same amount of vertices as there are landmarks in lm.
SMvector A vector containing the row indices of (semi-) landmarks on the curve(s) that
are allowed to slide
surp integer vector containing the row indices of semi-landmarks positioned on sur-
faces.
sur.name character: containing the filename of the corresponding surface.When specified,
mesh has to be NULL. If sur.name=NULL and mesh=NULL, the tangent planes
will be estimated from the point cloud.
138 relaxLM
mesh triangular mesh of class "mesh3d" loaded into the R workspace, when specified,
"sur.name" has to be NULL.
tol numeric: Threshold for convergence in the sliding proces. Full Procrustes dis-
tance between actual result and previous iteration.
allowed to slide.
inc.check Logical: if TRUE, the program stops when convergence criterion starts increas-
ing and reports result from last iteration.
iterations integer: maximum amounts the algorithm runs - even when ’tol’ is not reached.
When iterations=0, the algorithm runs until convergence.
fixRepro logical: if TRUE, fix landmarks will also be projected onto the surface. If you
have landmarks not on the surface, select fixRepro=FALSE
missing vector of integers, specifying row indices of missing (semi-)landmarks. They
will be relaxed freely in 3D and not projected onto the target (works only for 2D
data).
bending if TRUE, bending energy will be minimized, Procrustes distance otherwise (not
suggested with large shape differences)
stepsize integer: dampening factor for the amount of sliding. Useful to keep semi-
landmarks from sliding too far off the surface. The displacement is calculated
as Υ = Υ0 + stepsize ∗ U T . Default is set to 1 for bending=TRUE and 0.5 for
bending=FALSE.
use.lm indices specifying a subset of (semi-)landmarks to be used in the rotation step -
only used if bending=FALSE.
silent logical: if TRUE, console output is suppressed.
Details
if lm is a surface mesh, all vertices will be treated as semilandmarks and a allowed to freely slide
along the surface.
Value
returns kx3 matrix of slidden landmarks
Author(s)
Stefan Schlager
References
See Also
slider3d
relaxLM 139
Examples
require(rgl)
data(nose)
### relax shornose against longnose
# define fix landmarks

fix <- c(1:5,20:21)
# define surface patch by specifying row indices of matrices
# all except those defined as fix
surp <- c(1:dim(shortnose.lm)[1])[-fix]
relax <- relaxLM(shortnose.lm,

longnose.lm, mesh=shortnose.mesh, iterations=1,
SMvector=fix, deselect=TRUE, surp=surp)
## example minimizing Procrustes distance when displacement is not

## dampened by stepsize
relaxProcD <- relaxLM(shortnose.lm,
longnose.lm, mesh=shortnose.mesh, iterations=1,
SMvector=fix, deselect=TRUE, surp=c(1:623)[-fix],bending=FALSE,stepsize=1)
## Not run:
# visualize differences red=before and green=after sliding
deformGrid3d(shortnose.lm, relax, ngrid=0)
# visualize differences minimizing Procrusted distances red=before and green=after sliding
deformGrid3d(shortnose.lm, relaxProcD, ngrid=0)

## no smooth displacement, now let's check the distances:
rot2ref <- rotonto(relaxProcD,longnose.lm)
angle.calc(rot2ref$X,rot2ref$Y)
# 0.2492027 Procrustes distance between reference and slided shape
# (minimizing Procrustes distance)
rot2refBend <- rotonto(relax,longnose.lm)
angle.calc(rot2refBend$X,rot2refBend$Y)
# 0.2861322 Procrustes distance between reference and slided shape
# (minimizing bending energy)
rot2refOrig <- rotonto(shortnose.lm,longnose.lm)

angle.calc(rot2refOrig$X,rot2refOrig$Y)
# 0.3014957 Procrustes distance between reference and original shape
##result: while minimizing Procrustes distance, displacement is not
##guaranteed to be smooth
# add surface
wire3d(shortnose.mesh, col="white")
## finally relax two meshes with corresponding vertices:

140 relWarps
mediumnose.mesh <- tps3d(shortnose.mesh,shortnose.lm, (shortnose.lm+longnose.lm)/2,threads=1)

## we use Procrustes distance as criterion as bending energy is pretty slow because
## of too many coordinates (more than 3000 is very unreasonable).
relaxMesh <- relaxLM(shortnose.mesh,mediumnose.mesh,iterations=2,bending=FALSE,stepsize=0.05)
## End(Not run)
relWarps calculate relative Warp analysis
Description
After Procrustes registration the data is scaled by the bending energy or its inverse to emphasize
global/local differences when exploring a sample’s shape.
Usage
relWarps(
data,
scale = TRUE,
CSinit = TRUE,
alpha = 1,
tol = 1e-10,
orp = TRUE,
pcAlign = TRUE,
computeBasis = TRUE,
noalign = FALSE
)
Arguments
data Input k x m x n real array, where k is the number of points, m is the number of
scale Logical: indicating if scaling is requested
CSinit Logical: if TRUE, all configurations are initially scaled to Unit Centroid Size.
alpha integer: power of the bending energy matrix. If alpha = 0 then standard Pro-
crustes PCA is carried out. If alpha = 1 then large scale differences are empha-
sized, if alpha = -1 then small scale variations are emphasised.
tol tolerance for the eigenvalues of the bending energy matrix to be zero
orp logical: request orthogonal projection into tangent space.
men
computeBasis logical: whether to compute the basis of the resulting vector space (takes a lot
of memory and time for configurations with > 1000 coordinates.
noalign logical: if TRUE, data is assumed to be already aligned and alignment and or-
thogonal projection are skipped.
relWarps 141
Value
bescores relative warp scores (PC-scores if alpha = 0)
uniscores uniform scores, NULL if alpha = 0
Var non-affine variation explained by each relative warp
mshape sample’s conensus shape
rotated Procrustes superimposed data
bePCs vector basis of nonaffine shape variation- relative warps (plain PCs if alpha =
0)
uniPCs vector basis of affine shape variation - uniform component. NULL if alpha = 0
Author(s)
Stefan Schlager
References
Bookstein FL 1989. Principal Warps: Thin-plate splines and the decomposition of deformations.
IEEE Transactions on pattern analysis and machine intelligence 11.
Bookstein FL, 1991. Morphometric tools for landmark data. Geometry and biology. Cambridge
Univ. Press, Cambridge.
Rohlf FJ, Bookstein FL 2003. Computing the Uniform Component of Shape Variation. Systematic
Biology 52:66-69.
Examples
data(boneData)
rW <- relWarps(boneLM, alpha = -1)
## Not run:
if (require(car)) {
# plot first 5 relative warps scores grouped by population
spm(rW$bescores[,1:5],group=pop)
# plot uniform component scores grouped by population
spm(rW$uniscores[,1:5],group=pop)
}
##plot non-affine variance associated with each relative warp
barplot(rW$Var[,2], xlab="relative Warps")
## visualize first relative warp +-3 sd of the scores
rw1 <- restoreShapes(as.matrix(c(-3,3)*sd(rW$bescores[,1])),rW$bePCs[,1,drop=FALSE],rW$mshape)
deformGrid3d(rw1[,,1],rw1[,,2],ngrid=5)
## 2D example:
data <- bindArr(gorf.dat, gorm.dat, along=3)
sex <- factor(c(rep("fem", dim(gorf.dat)[3]), rep("male",dim(gorm.dat)[3])))
rW <- relWarps(data, alpha = -1)
if (require(car)) {
142 render
# plot first 3 relative warps scores grouped by population

spm(rW$bescores[,1:3],group=sex)
# plot uniform component scores grouped by population
spm(rW$uniscores[,1:2],group=sex)
}
##plot non-affine variance associated with each relative warp
barplot(rW$Var[,2], xlab="relative Warps")
## visualize first relative warp +-3 sd of the scores
rw1 <- restoreShapes(as.matrix(c(-3,3)*sd(rW$bescores[,1])),rW$bePCs[,1,drop=FALSE],rW$mshape)
deformGrid2d(rw1[,,1],rw1[,,2],ngrid=10)
}
## End(Not run)
render plot or save the results of meshDist
Description
plot or save the results of meshDist
Usage
render(x, ...)
## S3 method for class 'meshDist'

render(
x,
from = NULL,
to = NULL,
steps = NULL,
ceiling = NULL,
uprange = NULL,
tol = NULL,
tolcol = NULL,
rampcolors = NULL,
NAcol = NULL,
displace = FALSE,
shade = TRUE,
sign = NULL,
add = FALSE,
scaleramp = NULL,
...
)
## S3 method for class 'matrixDist'

render(
render 143
x,
from = NULL,
to = NULL,
steps = NULL,
ceiling = NULL,
uprange = NULL,
tol = NULL,
tolcol = NULL,
type = c("s", "p"),
radius = NULL,
rampcolors = NULL,
NAcol = NULL,
displace = FALSE,
sign = NULL,
add = FALSE,
scaleramp = FALSE,
...
)
export(x, ...)
## S3 method for class 'meshDist'

export(
x,
file = "default",
...
)
Arguments
x object of class meshDist
... for render.meshDist: additional arguments passed to shade3d. See material3d
for details.
from numeric: minimum distance to color; default is set to 0 mm
to numeric: maximum distance to color; default is set to the maximum distance
steps integer: determines how many intermediate colors the color ramp has.
ceiling logical: if TRUE, the next larger integer of "to" is used
uprange numeric between 0 and 1: restricts "to" to a quantile of "to", if to is NULL.
tol numeric: threshold to color distances within this threshold according to tolcol.
tolcol a custom color to color vertices below a threshold defined by tol. Default is
green.
rampcolors character vector: specify the colors which are used to create a colorramp.
NAcol character: specify color for values outside the range defined by from and to.
144 resampleCurve
displace logical: if TRUE, displacement vectors between original and closest points are
drawn colored according to the distance.
shade logical: if FALSE, the rendering of the colored surface will be supressed.
sign logical: request signed distances to be visualised.
add logical: if TRUE, visualization will be added to the rgl window currently in
focus
scaleramp if TRUE the ramp colors get scaled symmetrically into positive and negative
direction.
titleplot character: axis description of heatmap.
type character: "s" shows coordinates as spheres, while "p" shows 3D dots.
radius determines size of spheres; if not specified, optimal radius size will be estimated
by centroid size of the configuration.
file character: filename for mesh and image files produced. E.g. "mydist" will
produce the files mydist.ply and mydist.png
imagedim character of pattern "100x200" where 100 determines the width and 200 the
height of the image.
Details
Visualise or save the results of meshDist to disk.
render.meshDist renders the colored mesh and displays the color ramp and returns an object of class
"meshDist". export.meshDist exports the colored mesh as ply file and the color chart as png file.
Author(s)
Stefan Schlager
See Also
meshDist, shade3d
resampleCurve Resample a curve equidistantly
Description
Resample a curve equidistantly (optionally with smoothing)
Usage
resampleCurve(x, n, smooth = FALSE, smoothn = n, open = TRUE)
restoreFromPCA 145
Arguments
x matrix containing coordinates
n number of resulting points on the resampled curve
smooth logical: if TRUE, the resulting curve will be smoothed by using bezier curves.
smoothn integer: define the refinement of the bezier curve. The higher this value, the
closer the final curve will be to the original.
open logical: define whether it is a closed curve or not.
Value
returns a matrix containing the resampled curve
Examples
data(nose)
x <- shortnose.lm[c(304:323),]
xsample <- resampleCurve(x,n=50)
restoreFromPCA restore original data from PCA
Description
restore original data from PCA by reverting rotation and centering
Usage
restoreFromPCA(scores, rotation, center)
Arguments
scores matrix containing the PC-scores
rotation matrix containing the PCs
center vector containing the center
Examples
myirispca <- prcomp(iris[,1:4])
myirisRecovered <- restoreFromPCA(myirispca$x,myirispca$rotation,myirispca$center)
all.equal(myirisRecovered,as.matrix(iris[,1:4]))
146 restoreShapes
restoreShapes restore shapes from PC-Scores or similar projections
Description
restore shapes from PC-Scores or similar projections
Usage
restoreShapes(
scores,
PC,
mshape,
sizeshape = FALSE,
origsize = FALSE,
meanlogCS
)
Arguments
scores vector of PC-scores, or matrix with rows containing PC-scores
PC Principal components (eigenvectors of the covariance matrix) associated with
’scores’.
mshape matrix containing the meanshape’s landmarks (used to center the data by the
PCA)
sizeshape logical: if TRUE, it is assumed that the data is the output of procSym run with
sizeshape=TRUE.
origsize logical: if sizeshape = TRUE, this will apply the scaling to the original size from
the corresponding entry from the PC basis matrix.
meanlogCS numeric: provide the average log Centroid Size of the original sample (see ex-
amples below). Only needed if sizeshape = TRUE and origsize = TRUE
Details
Rotates and translates PC-scores (or similar) derived from shape data back into configuration space.
Value
returns matrix or array containing landmarks
Author(s)
Stefan Schlager
retroDeform3d 147
See Also
prcomp, procSym
getPCscores
Examples
## generate landmarks using
##the first PC-score of the first specimen

lm <- restoreShapes(proc$PCscores[1,1],proc$PCs[,1],proc$mshape)
plot(lm,asp=1)
##now the first 3 scores

lm2 <- restoreShapes(proc$PCscores[1,1:3],proc$PCs[,1:3],proc$mshape)
points(lm2,col=2)
## Now restore some sizeshape data

procSize <- procSym(gorf.dat,sizeshape=TRUE)
est1 <- restoreShapes(range(procSize$PCscores[,1]),procSize$PCs[,1],procSize$mshape,
sizeshape=TRUE,origsize=TRUE,meanlogCS=procSize$meanlogCS)
}
retroDeform3d symmetrize a bilateral landmark configuration
Description
symmetrize a bilateral landmark configuration by removing bending and stretching
Usage
retroDeform3d(mat, pairedLM, hmult = 5, alpha = 0.01)
Arguments
mat matrix with bilateral landmarks
pairedLM 2-column integer matrix with the 1st columns containing row indices of left side
landmarks and 2nd column the right hand landmarks
hmult factor controlling the bandwidth for calculating local weights (which will be
hmult * average distance between landmarks and their closest neighbour).
alpha factor controlling spacing along x-axis
148 retroDeformMesh
Value
deformed matrix containing deformed landmarks
orig matrix containing original landmarks
References
Ghosh, D.; Amenta, N. & Kazhdan, M. Closed-form Blending of Local Symmetries. Computer
Graphics Forum, Wiley-Blackwell, 2010, 29, 1681-1688
retroDeformMesh symmetrize a triangular mesh
Description
symmetrize a triangular mesh
Usage
retroDeformMesh(
mesh,
mat,
pairedLM,
hmult = 5,
alpha = 0.01,
rot = TRUE,
lambda = 1e-08,
threads = 0
)
Arguments
mesh triangular mesh of class mesh3d
mat matrix with bilateral landmarks
pairedLM 2-column integer matrix with the 1st columns containing row indices of left side
landmarks and 2nd column the right hand landmarks
hmult damping factor for calculating local weights which is calculated as humult times
the average squared distance between a landmark and its closest neighbor (on
each side).
alpha factor controlling spacing along x-axis
rot logical: if TRUE the deformed landmarks are rotated back onto the original ones
lambda control parameter passed to tps3d
threads integer: number of threads to use for TPS deform
rotaxis3d 149
Details
this function performs retroDeform3d and deforms the mesh accordingly using the function tps3d.
Value
mesh symmetrized mesh
landmarks a list containing the deformed and original landmarks
rotaxis3d Rotate an object (matrix or mesh) around an arbitrary axis in 3D
Description
Rotate an object around an arbitrary axis in 3D
Usage
rotaxis3d(x, pt1, pt2 = c(0, 0, 0), theta)


Arguments
x k x 3 matrix containing 3D-coordinates or a triangular mesh of class "mesh3d".
pt1 numeric vector of length 3, defining first point on the rotation axis.
pt2 numeric vector of length 3, defining second point on the rotation axis.
theta angle to rotate in radians. With pt1 being the viewpoint, the rotation is counter-
clockwise.
Details
Rotate an object (matrix or triangular mesh) around an 3D-axis defined by two points.
Value
returns rotated object (including updated normals for mesh3d objects)
Author(s)
Stefan Schlager
150 rotaxisMat
References
http://en.wikipedia.org/wiki/Rotation_matrix
See Also
rotonto, rotmesh.onto
Examples
require(rgl)
data(nose)
shrot.rot <- rotaxis3d(shortnose.mesh,pt1=c(1,1,1),theta=pi)
## Not run:
shade3d(shortnose.mesh,col=3,specular=1)
shade3d(shrot.rot,col=2)
###print rotation axis

#' lines3d(rbind(rep(-0.1,3),rep(0.1,3)))
## End(Not run)
rotaxisMat calculate a rotation matrix around an arbitrary axis through the origin
in 3D
Description
calculate a rotation matrix around an arbitrary axis in 3D
Usage
rotaxisMat(u, theta, homogeneous = FALSE)
Arguments
u a vector around which to rotate
theta angle in radians to rotate
homogeneous logical: if TRUE a 4x4 rotation matrix is returned
Value
returns 3x3 rotation matrix
References
http://en.wikipedia.org/wiki/Rotation_matrix
rotmesh.onto 151
See Also
rotaxis3d
rotmesh.onto rotate ,scale and translate a mesh based on landmark information.
Description
rotates and reflects a mesh onto by calculating the transformation from two sets of referenced land-
marks.
Usage
rotmesh.onto(
mesh,
refmat,
tarmat,
adnormals = FALSE,
scale = FALSE,
reflection = FALSE,
...
)
Arguments
mesh object of class mesh3d.
refmat k x m matrix with landmarks on the mesh
tarmat k x m matrix as target configuration
adnormals logical - if TRUE, vertex normals will be recomputed after rotation. If mesh has
normals and adnormals=FALSE, the existing normals are rotated by the same
rotation matrix as the mesh’s vertices.
scale logical: if TRUE the mesh will be scaled according to the size of the target.
reflection logical: allow reflection.
... additional parameters passed on to rotonto.
Value
mesh rotated mesh
yrot rotated refmat
trafo 4x4 transformation matrix
Author(s)
Stefan Schlager
152 rotonmat
See Also
file2mesh,tps3d ,rotonto,mesh2ply
Examples
require(rgl)
data(boneData)
## rotate, translate and scale the mesh belonging to the first specimen
## onto the landmark configuration of the 10th specimen
rotmesh <- rotmesh.onto(skull_0144_ch_fe.mesh,boneLM[,,1],
boneLM[,,10], scale=TRUE)
## Not run:
## render rotated mesh and landmarks
shade3d(rotmesh$mesh, col=2, specular=1)
## render original mesh
shade3d(skull_0144_ch_fe.mesh, col=3, specular=1)
## End(Not run)
rotonmat rotate matrix of landmarks
Description
rotate matrix of landmarks by using a rotation determined by two matrices.
Usage
rotonmat(
X,
refmat,
tarmat,
scale = TRUE,
reflection = FALSE,
weights = NULL,
getTrafo = FALSE
)
Arguments
X Matrix to be rotated
refmat reference matrix used to estimate rotation parameters
tarmat target matrix used to estimate rotation parameters
rotonmat 153
scale logical: requests scaling to minimize sums of squared distances

reflection logical: if TRUE, reflections are allowed.
weights vector of length k, containing weights for each landmark.
centerweight logical: if weights are defined and centerweigths=TRUE, the matrix will be
centered according to these weights instead of the barycenter.
getTrafo logical: if TRUE, a 4x4 transformation matrix will also be returned.
Details
A matrix is rotated by rotation parameters determined by two different matrices. This is usefull, if
the rotation parameters are to be estimated by a subset of landmark coordinates.
Value
if getTrafo=FALSE the transformed X will be returned, else alist containing:
Xrot the transformed matrix X

trafo a 4x4 transformation matrix
Author(s)
Stefan Schlager
See Also
rotonto,rotmesh.onto
Examples
data(nose)
shortnose.rot <-
rotonmat(shortnose.lm,shortnose.lm[1:9,],longnose.lm[1:9,])
##view result
## Not run:
deformGrid3d(shortnose.rot,shortnose.lm,ngrid=0)
## End(Not run)
154 rotonto
rotonto rotates, translates and scales one matrix onto an other using Pro-
crustes fitting
Description
rotates, translates and scales one matrix onto an other using Procrustes fitting
Usage
rotonto(
x,
y,
scale = FALSE,
signref = TRUE,
reflection = TRUE,
weights = NULL,
...
)
rotreverse(mat, rot)


Arguments
x k x m matrix to be rotated onto (targetmatrix)
y k x m matrix which will be rotated (reference matrix)
scale logical: scale matrix to minimize sums of squares
signref logical: report if reflections were involved in the rotation
reflection allow reflections.
weights vector of length k, containing weights for each landmark.
centerweight logical or vector of weights: if weights are defined and centerweigths=TRUE,
the matrix will be centered according to these weights instead of the barycenter.
If centerweight is a vector of length nrow(x), the barycenter will be weighted
accordingly.
... currently not used
mat matrix on which the reverse transformations have to be applied
rot an object resulting from the former application of rotonto
rotonto 155
Details
rotate a matrix onto an other without loosing information about the location of the targetmatrix and
reverse this transformations using rotreverse
Value
yrot rotated and translated matrix
Y centred and rotated reference matrix
X centred target matrix
trans vector between original position of target and centered reference (during rotation
process)
transy vector between original position of reference and centered reference (during
rotation process)
gamm rotation matrix
bet scaling factor applied
reflect if reflect = 1, reflections are involved in the superimposition. Else, reflect = 0
Note
all lines containing NA, or NaN are ignored in computing the transformation.
Author(s)
Stefan Schlager
References
Lissitz, R. W., Schoenemann, P. H., & Lingoes, J. C. (1976). A solution to the weighted Procrustes
problem in which the transformation is in agreement with the loss function. Psychometrika, 41,547-
550.
See Also
rotmesh.onto
Examples
lims <- c(min(gorf.dat[,,1:2]),max(gorf.dat[,,1:2]))
rot <- rotonto(gorf.dat[,,1],gorf.dat[,,2]) ### rotate the second onto the first config
plot(rot$yrot,pch=19,xlim=lims,ylim=lims) ## view result
points(gorf.dat [,,2],pch=19,col=2) ## view original config
rev1 <- rotreverse(rot$yrot,rot)
points(rev1,cex=2) ### show inversion by larger circles around original configuration
}
156 scalemesh
scalemesh scale a mesh of class "mesh3d"
Description
scales (the vertices of a mesh by a scalar
Usage
scalemesh(mesh, size, center = c("bbox", "mean", "none"))
Arguments
mesh object of class "mesh3d"
size numeric: scale factor
center character: method to position center of mesh after scaling: values are "bbox",
and "mean". See Details for more info.
Details
The mesh’s center is determined either as mean of the bounding box (center="bbox") or mean of ver-
tex coordinates (center="mean") and then scaled according to the scaling factor. If center="none",
vertex coordinates will simply be multiplied by "size".
Value
returns a scaled mesh
Author(s)
Stefan Schlager
See Also
rotmesh.onto
Examples
data(nose)
#inflate mesh by factor 4
largenose <- scalemesh(shortnose.mesh,4)
slider2d 157
slider2d slides Semilandmarks along curves 2D by minimising bending energy

of a thin-plate spline deformation.
Description
slides Semilandmarks along curves 2D. The positions are sought by minimising bending energy (of
a thin-plate spline deformation) or Procrustes distance
Usage
slider2d(
dataframe,
SMvector,
outlines,
tol = 1e-05,
deselect = FALSE,
recursive = TRUE,
iterations = 0,
initproc = FALSE,
pairedLM = NULL,
bending = TRUE,
stepsize = 1,
silent = FALSE
)
Arguments
dataframe Input k x 2 x n real array, where k is the number of points and n is the sample
size. Ideally the
SMvector A vector containing the row indices of (semi-) landmarks on the curve(s) and
surfaces that are allowed to slide
allowed to slide.
iterations integer: select manually the max. number of iterations that will be performed
during the sliding process (usefull, when there is very slow convergence). 0
means iteration until convergence.
initproc requests initial Procrustes fit before sliding.
158 slider3d
pairedLM A X x 2 numeric matrix with the indices of the rows containing paired Land-
marks. E.g. the left column contains the lefthand landmarks, while the right
side contains the corresponding right hand landmarks. - This will ideally create
symmetric mean to get rid of assymetry.
bending if TRUE, bending energy will be minimized, Procrustes distance otherwise.
bending=FALSE.
Value
returns an array containing slided coorndinates in the original space - not yet processed by a Pro-
crustes analysis.
Warning
Depending on the amount of landmarks this can use an extensive amount of your PC’s resources,
especially when running in parallel. As the computation time and RAM usage of matrix algebra
involved is quadratic to the amount of landmarks used, doubling the amount of semi-landmarks will
quadruple computation time and system resource usage. You can easily stall you computer with this
function with inappropriate data.
Author(s)
Stefan Schlager
See Also
relaxLM, slider3d
slider3d slides Semilandmarks along curves and surfaces in 3D by minimising

bending energy of a thin-plate spline deformation.
Description
slides Semilandmarks along curves and surfaces in 3D. The positions on the surface are sought
which minimise bending energy (of a thin-plate spline deformation)
slider3d 159
Usage
slider3d(
dat.array,
SMvector,
outlines = NULL,
surp = NULL,
sur.path = NULL,
sur.name = NULL,
meshlist = NULL,
ignore = NULL,
sur.type = "ply",
tol = 1e-05,
deselect = FALSE,
inc.check = TRUE,
recursive = TRUE,
iterations = 0,
initproc = TRUE,
fullGPA = FALSE,
pairedLM = 0,
bending = TRUE,
fixRepro = TRUE,
missingList = NULL,
use.lm = NULL,
smoothnormals = FALSE,
silent = FALSE
)
Arguments
dat.array Input k x m x n real array, where k is the number of points, m is the number of
dimensions, and n is the sample size. Ideally the dimnames[[3]] vector contains
the names of the surface model (without file extension) - e.g. if the model is
named "surface.ply", the name of the corresponding matrix of the array would
be "surface"
SMvector A vector containing the row indices of (semi-) landmarks on the curve(s) and
surfaces that are allowed to slide
surp integer vector containing the row indices of semi-landmarks positioned on sur-
faces.
sur.path Path to the surface models (e.g. ply, obj, stl files)
sur.name character vector: containing the filenames of the corresponding surfaces - e.g.
if the dat.array[„i] belongs to surface_i.ply, sur.name[i] would be surface_i.ply.
Only necessary if dat.array does not contain surface names.
160 slider3d
meshlist list containing triangular meshes of class ’mesh3d’, for example imported with
mesh2ply or file2mesh in the same order as the specimen in the array (see
examples below).
ignore vector containing indices of landmarks that are to be ignored. Indices of out-
lines/surfaces etc will be updated automatically.
sur.type character:if all surfaces are of the same file format and the names stored in
dat.array, the file format will be specified here.
allowed to slide.
inc.check Logical: if TRUE, the program stops when convergence criterion starts increas-
ing and reports result from last iteration.
iterations integer: select manually the max. number of iterations that will be performed
during the sliding process (usefull, when there is very slow convergence). 0
means iteration until convergence.
initproc requests initial Procrustes fit before sliding.
fullGPA Logical: if FALSE, only a partial procrustes fit will be performed.
pairedLM A X x 2 numeric matrix with the indices of the rows containing paired Land-
marks. E.g. the left column contains the lefthand landmarks, while the right
side contains the corresponding right hand landmarks. - This will ideally create
symmetric mean to get rid of assymetry.
bending if TRUE, bending energy will be minimized, Procrustes distance otherwise.
bending=FALSE.
mc.cores integer: determines how many cores to use for the computation. The default is
autodetect. But in case, it doesn’t work as expected cores can be set manually.
fixRepro logical: if TRUE, fix landmarks will also be projected onto the surface. If you
have landmarks not on the surface, select fixRepro=FALSE
missingList a list of length samplesize containing integer vectors of row indices specifying
missing landmars for each specimen. For specimens without missing landmarks
enter numeric(0).
use.lm indices specifying a subset of (semi-)landmarks to be used in the rotation step -
only used if bending=FALSE.
smoothnormals logical: if TRUE, tangent planes will be computed from locally smoothed nor-
mals
slider3d 161
Value
dataslide array containing slidden Landmarks in the original space - not yet processed by
a Procrustes analysis
vn.array array containing landmark normals
Warning
Depending on the size of the suface meshes and especially the amount of landmarks this can use an
extensive amount of your PC’s resources, especially when running in parallel. As the computation
time and RAM usage of matrix algebra involved is quadratic to the amount of landmarks used, dou-
bling the amount of semi-landmarks will quadruple computation time and system resource usage.
You can easily stall you computer with this function with inappropriate data.
Note
if sur.path = NULL and meshlist = NULL, surface landmarks are relaxed based on a surface nor-
mals approximated by the pointcloud, this can lead to bad results for sparse sets of semilandmarks.
Obviously, no projection onto the surfaces will be occur and landmarks will likely be off the original
surface.
Author(s)
Stefan Schlager
References
Schlager S. 2012. Sliding semi-landmarks on symmetric structures in three dimensions. American
Journal of Physical Anthropology, 147(S52):261. URL: http://dx.doi.org/10.1002/ajpa.21502.
de/volltexte/9181/.
See Also
relaxLM, createMissingList
Examples
## Not run:
data(nose)
162 slider3d
mesh2ply(shortnose.mesh, filename="shortnose")
mesh2ply(longnose.mesh, filename="longnose")
## create landmark array

data <- bindArr(shortnose.lm, longnose.lm, along=3)
# define fix landmarks

fix <- c(1:5,20:21)
# define surface patch by specifying row indices of matrices
# all except those defined as fix
surp <- c(1:nrow(shortnose.lm))[-fix]
slide <- slider3d(data, SMvector=fix, deselect=TRUE, surp=surp,

sur.path=".",iterations=1,mc.cores=1)
# sur.path="." is the current working directory
# now one example with meshes in workspace
meshlist <- list(shortnose.mesh,longnose.mesh)
slide <- slider3d(data, SMvector=fix, deselect=TRUE, surp=surp,

iterations=1, meshlist=meshlist,
mc.cores=1,fixRepro=FALSE)
require(rgl)
## visualize sliding
deformGrid3d(slide$dataslide[,,1],shortnose.lm,ngrid = 0)
## these are fix
spheres3d(slide$dataslide[fix,,1],col=4,radius=0.7)
###finally an example with missing landmarks:

## we assume that coordinates 185:189, 205:209 and 225:229 are in the second config are missing
missingList <- createMissingList(2)
missingList[[2]] <- c(185:189,205:209,225:229)
slideMissing <- slider3d(data, SMvector=fix, deselect=TRUE, surp=surp,
iterations=1, meshlist=meshlist,
mc.cores=1,fixRepro=FALSE,missingList=missingList)
## example with two curves

## Example with surface semilandmarks and two curves
fix <- c(1:5,20:21)
outline1 <- c(304:323)
outline2 <- c(604:623)
outlines <- list(outline1,outline2)
surp <- c(1:623)[-c(fix,outline1,outline2)]
slideWithCurves <- slider3d(data, SMvector=fix, deselect=TRUE, surp=surp,
meshlist=meshlist,iterations=1,mc.cores=1,outlines=outlines)
deformGrid3d(slideWithCurves$dataslide[,,1],shortnose.lm,ngrid = 0)
plot(slideWithCurves)
## finally an example with sliding without meshes by estimating the surface from the
## semi-landmarks
solutionSpace 163
slideWithCurvesNoMeshes <- slider3d(data, SMvector=fix, deselect=TRUE, surp=surp,

iterations=1,mc.cores=1,outlines=outlines)
## compare it to the data with surfaces
deformGrid3d(slideWithCurves$dataslide[,,1],slideWithCurvesNoMeshes$dataslide[,,1],ngrid = 0)
## not too bad, only lonely surface semi-landmarks are a bit off
## End(Not run)
solutionSpace returns the solution space (basis and translation vector) for an equa-
tion system
Description
returns the solution space (basis and translation vector) for an equation system
Usage
solutionSpace(A, b)
Arguments
A numeric matrix
b numeric vector
Details
For a linear equationsystem, Ax = b, the solution space then is
x = A∗ b + (I − A∗ A)y
where A∗ is the Moore-Penrose pseudoinverse of A. The QR decomposition of I −A∗ A determines
the dimension of and basis of the solution space.
Value
basis matrix containing the basis of the solution space
translate translation vector
Examples
A <- matrix(rnorm(21),3,7)
b <- c(1,2,3)
subspace <- solutionSpace(A,b)
dims <- ncol(subspace$basis) # we now have a 4D solution space
## now pick any vector from this space. E.g
y <- 1:dims
solution <- subspace$basis%*%y+subspace$translate # this is one solution for the equation above
A%*%solution ## pretty close
164 sortCurve
sortCurve sort curvepoints by using the subsequent neighbours
Description
sort curvepoints by using the subsequent neighbours
Usage
sortCurve(x, k = 5, start = NULL)
Arguments
x k x m matrix containing the 2D or 3D coordinates
k number of nearest neighbours to look at. Set high for very irregularly clustered
curves.
start integer: which row of x to use as a starting point. If NULL, it is assumed that the
curve is open and the point where the angle between the two nearest neighbours
is closest will be chosen.
Value
xsorted matrix with coordinates sorted along a curve
index vector containing the sorting indices
Examples
## generate a curve from a polynome

x <- c(32,64,96,118,126,144,152.5,158)
y <- c(99.5,104.8,108.5,100,86,64,35.3,15)
fit <- lm(y~poly(x,2,raw=TRUE))
xx <- seq(30,160, length=50)
layout(matrix(1:3,3,1))
curve <- cbind(xx,predict(fit, data.frame(x=xx)))
## permute order
set.seed(42)
plot(curve);lines(curve)
curveunsort <- curve[sample(1:50),]
## now the curve is scrambled
plot(curveunsort);lines(curveunsort,col=2)
curvesort <- sortCurve(curveunsort)
## after sorting lines are nice again
plot(curvesort$xsorted);lines(curvesort$xsorted,col=3)
symmetrize 165
symmetrize create a perfectly symmetric version of landmarks
Description
create a perfectly symmetric version of landmarks
Usage
symmetrize(x, pairedLM)
Arguments
x k x m matrix or k x m x n array, with rows containing landmark coordinates

pairedLM A X x 2 matrix containing the indices (rownumbers) of the paired LM. E.g. the
Details
the landmarks are reflected and relabled according to pairedLM and then rotated and translated onto
x. Both configurations are then averaged to obtain a perfectly symmetric one.
Value
a symmetrized version of x
References
Examples
data(boneData)
left <- c(4,6,8)
right <- c(3,5,7)
symx <- symmetrize(boneLM[,,2],pairedLM)
## Not run:
deformGrid3d(symx,boneLM[,,2])
## End(Not run)
166 tps3d
tps3d thin plate spline mapping (2D and 3D) for coordinates and triangular
meshes
Description
maps landmarks or a triangular mesh via thin plate spline based on a reference and a target config-
uration in 2D and 3D
Usage
tps3d(x, refmat, tarmat, lambda = 1e-08, threads = 0, ...)
tps2d(x, refmat, tarmat, lambda = 1e-08, threads = 0, ...)
Arguments
x matrix - e.g. the matrix information of vertices of a given surface or a triangular
mesh of class "mesh3d"
refmat reference matrix - e.g. landmark configuration on a surface
tarmat target matrix - e.g. landmark configuration on a target surface
lambda numeric: regularisation parameter of the TPS.
threads threads to be used for parallel execution in tps deformation.
... additional arguments, currently not used.
Value
returns the deformed input
Note
tps2d is simply an alias for tps3d that can handle both cases.
Author(s)
Stefan Schlager
References
Bookstein FL. 1989. Principal Warps: Thin-plate splines and the decomposition of deformations.
IEEE Transactions on pattern analysis and machine intelligence 11(6).
See Also
computeTransform, applyTransform
typprob 167
Examples
data(nose)
## define some landmarks
refind <- c(1:3,4,19:20)
## use a subset of shortnose.lm as anchor points for a TPS-deformation
reflm <- shortnose.lm[refind,]
tarlm <- reflm
##replace the landmark at the tip of the nose with that of longnose.lm
tarlm[4,] <- longnose.lm[4,]
## deform a set of semilandmarks by applying a TPS-deformation
## based on 5 reference points
deformed <- tps3d(shortnose.lm, reflm, tarlm,threads=1)
## Not run:
##visualize results by applying a deformation grid
deformGrid3d(shortnose.lm,deformed,ngrid = 5)
require(rgl)
shade3d(longnose.mesh,col=skin1)
## End(Not run)
data(boneData)
## deform mesh belonging to the first specimen
## onto the landmark configuration of the 10th specimen
## Not run:
warpskull <- tps3d(skull_0144_ch_fe.mesh,boneLM[,,1],
boneLM[,,10], threads=1)
## render deformed mesh and landmarks
shade3d(warpskull, col=2, specular=1)
## render original mesh
shade3d(skull_0144_ch_fe.mesh, col=3, specular=1)
## End(Not run)
typprob calculate typicality probabilities
Description
calculate typicality probabilities
168 typprob
Usage
typprob(
x,
data,
small = FALSE,
method = c("chisquare", "wilson"),
center = NULL,
cova = NULL,
...
)
typprobClass(
x,
data,
groups,
small = FALSE,
method = c("chisquare", "wilson"),
outlier = 0.01,
sep = FALSE,
cv = TRUE,
...
)
Arguments
x vector or matrix of data the probability is to be calculated.
data Reference data set. If missing x will be used.
small adjustion of Mahalanobis D^2 for small sample sizes as suggested by Wilson
(1981), only takes effect when method="wilson".
method select method for probability estimation. Available options are "chisquare" (or
any abbreviation) or "wilson". "chisquare" exploits simply the chisquare distri-
bution of the mahalanobisdistance, while "wilson" uses the methods suggested
by Wilson(1981). Results will be similar in general.
center vector: specify custom vector to calculate distance to. If not defined, group
mean will be used.
cova covariance matrix to calculate mahalanobis-distance: specify custom covariance
matrix to calculate distance.
robust character: determines covariance estimation methods, allowing for robust esti-
mations using MASS::cov.rob. Default is the standard product-moment covari-
ance matrix.
estimations.
groups vector containing grouping information.
outlier probability threshold below which a specimen will not be assigned to any group-
typprob 169
sep logical: if TRUE, probability will be calculated from the pooled within group
covariance matrix.
cv logical: if data is missing and cv=TRUE, the resulting classification will be vali-
dated by leaving-one-out crossvalidation.
Details
get the probability for an observation belonging to a given multivariate nromal distribution
Value
typprob: returns a vector of probabilities.
typprobClass:
probs matrix of probabilities for each group

groupaffin vector of groups each specimen has been assigned to. Outliers are classified
"none"
probsCV cross-validated matrix of probabilities for each group
groupaffinCV cross-validated vector of groups each specimen has been assigned to. Outliers
are classified "none"
self logical: if TRUE, the data has been classified by self-inference.
Author(s)
Stefan Schlager
References
Albrecht G. 1992. Assessing the affinities of fossils using canonical variates and generalized dis-
tances Human Evolution 7:49-69.
Wilson S. 1981. On comparing fossil specimens with population samples Journal of Human Evo-
lution 10:207 - 214.
Examples
data <- procSym(gorf.dat)$PCscores[,1:3]
probas <- typprob(data,data,small=TRUE)### get probability for each specimen
### now we check how this behaves compared to the mahalanobis distance
maha <- mahalanobis(data,colMeans(data),cov(data))
plot(probas,maha,xlab="Probability",ylab="Mahalanobis D^2")
data2 <- procSym(abind(gorf.dat,gorm.dat))$PCscores[,1:3]

fac <- as.factor(c(rep("female",dim(gorf.dat)[3]),rep("male",dim(gorm.dat)[3])))
typClass <- typprobClass(data2,groups=fac,method="w",small=TRUE,cv=TRUE)
## only 59 specimen is rather small.
typClass2 <- typprobClass(data2,groups=fac,method="c",cv=TRUE)## use default settings
170 unrefVertex
### check results for first method:

typClass
### check results for second method:

typClass2
}
unrefVertex some little helpers for vertex operations on triangular meshes
Description
some little helpers for vertex operations on triangular meshes
Usage
unrefVertex(mesh)
rmVertex(mesh, index, keep = FALSE)
vert2points(mesh)
rmUnrefVertex(mesh, silent = FALSE)
Arguments
mesh triangular mesh of class mesh3d.

index vector containing indices of vertices to be removed.
keep logical: if TRUE, the vertices specified by index are kept and the rest is removed.
silent logical: suppress output about info on removed vertices.
Details
extract vertex coordinates from meshes, find and/or remove (unreferenced) vertices from triangular
meshes
unrefVertex finds unreferenced vertices in triangular meshes of class mesh3d or tmesh3d.
rmVertex removes specified vertices from triangular meshes.
vert2points extacts vertex coordinates from triangular meshes.
rmUnrefVertex removes unreferenced vertices from triangular meshes.
updateIndices 171
Value
unrefVertex: vector with indices of unreferenced vertices.
rmVertex: returns mesh with specified vertices removed and faces and normals updated.
vert2points: k x 3 matrix containing vertex coordinates.
rmUnrefVertex: mesh with unreferenced vertices removed.
Author(s)
Stefan Schlager
See Also
ply2mesh, file2mesh
Examples
require(rgl)
data(nose)
testmesh <- rmVertex(shortnose.mesh,1:50) ## remove first 50 vertices
## Not run:
shade3d(testmesh,col=3)### view result
## End(Not run)
testmesh$vb <- cbind(testmesh$vb,shortnose.mesh$vb[,1:50]) ## add some unreferenced vertices
## Not run:
points3d(vert2points(testmesh),col=2)## see the vertices in the holes?
## End(Not run)
cleanmesh <- rmUnrefVertex(testmesh)## remove those lonely vertices!
## Not run:
pop3d()
points3d(vert2points(cleanmesh),col=2) ### now the holes are empty!!
## End(Not run)
updateIndices update a vector of indices after removal of some referenced items
Description
update a vector of indices after removal of some referenced items
Usage
updateIndices(x, ignore, indexrange)
172 updateNormals
Arguments
x vector containing indices (e.g. to matrix rows)
ignore integer vector: remove those items from the original structure
indexrange maximum range of the index in the referenced item structure
Examples
refItem <- matrix(1:10,5,2)
index <- c(1,3,5) # this indexes some rows of the matrix we are interested in
## now we want to ignore row 2 and 5 and want to update the index so it will still fit
indexNew <- updateIndices(index,c(2,5),indexrange=5)
## Here a more useful example:

data(boneData)
left <- c(4,6,8)
right <- c(3,5,7)
## now we want to remove some landmarks and need to updated the pairedLM indices
ignore <- c(5,6)
mynewboneLM <- boneLM[-ignore,,]
pairedLMnew <- apply(pairedLM,2,updateIndices,ignore=ignore,indexrange=dim(boneLM)[1])
updateNormals Compute face or vertex normals of a triangular mesh
Description
Compute face or vertex normals of a triangular mesh of class "mesh3d"
Usage
updateNormals(x, angle = TRUE)
facenormals(x)
Arguments
x triangular mesh of class "mesh3d"
angle logical: if TRUE, angle weighted normals are used.
Value
updateNormals returns mesh with updated vertex normals.
facenormals returns an object of class "mesh3d" with
vb faces’ barycenters
normals faces’ normals
vecx 173
Note
only supports triangular meshes
Author(s)
Stefan Schlager
References
Meshes. Informatics and Mathematical Modelling, .
See Also
ply2mesh
Examples
require(rgl)
require(Morpho)
data(nose)
### calculate vertex normals
shortnose.mesh$normals <- NULL ##remove normals
## Not run:
shade3d(shortnose.mesh,col=3)##render
## End(Not run)
shortnose.mesh <- updateNormals(shortnose.mesh)
## Not run:
clear3d()
shade3d(shortnose.mesh,col=3)##smoothly rendered now
## End(Not run)
## calculate facenormals
facemesh <- facenormals(shortnose.mesh)
## Not run:
plotNormals(facemesh,long=0.01)
points3d(vert2points(facemesh),col=2)
## End(Not run)
vecx convert an 3D array into a matrix and back
Description
converts a 3D-array (e.g. containing landmark coordinates) into a matrix, one row per specimen or
reverse this.
174 virtualMeshScan
Usage
vecx(x, byrow = FALSE, revert = FALSE, lmdim)
Arguments
x array or matrix
byrow logical: if TRUE, the resulting vector for each specimen will be x1,y1,z1,x2,y2,z2,...,
and x1,x2,...,y1,y2,...,z1,z2,... otherwise (default). The same is for re-
verting the process: if the matrix contains the coordinates as rows like: x1,y1,z1,x2,y2,z2,...
set byrow=TRUE
revert revert the process and convert a matrix with vectorized landmarks back into an
array.
lmdim number of columns for reverting
Value
returns a matrix with one row per specimen
Author(s)
Stefan Schlager
Examples
data <- vecx(gorf.dat)
#revert the procedure
gdat.restored <- vecx(data,revert=TRUE,lmdim=2)
range(gdat.restored-gorf.dat)
}
virtualMeshScan remove all parts of a triangular mesh, not visible from a set of view-
points
Description
remove all parts of a triangular mesh, not visible from a set of viewpoints
Usage
virtualMeshScan(x, viewpoints, offset = 0.001, cores = 1)

warpmovie3d 175
Arguments
x triangular mesh of class ’mesh3d’
viewpoints vector or k x 3 matrix containing a set of viewpoints
offset value to generate an offset at the meshes surface (see notes)
cores integer: number of cores to use (not working on windows)
Value
returns a list containing subsets of the original mesh
visible the parts visible from at least one of the viewpoints
invisible the parts not visible from the viewpoints
Note
The function tries to filter out all vertices where the line connecting each vertex with the viewpoints
intersects with the mesh itself. As, technically speaking this always occurs at a distance of value=0,
a mesh with a tiny offset is generated to avoid these false hits.
Examples
SCP1 <- file2mesh(system.file("extdata","SCP1.ply",package="Morpho"))
viewpoints <- read.fcsv(system.file("extdata","SCP1_Endo.fcsv",package="Morpho"))
## Create a quick endocast
quickEndo <- virtualMeshScan(SCP1,viewpoints)
## Not run:
rgl::shade3d(quickEndo$visible,col="orange")
rgl::shade3d(SCP1,col="white",alpha=0.5)
## End(Not run)
warpmovie3d Creates a sequence of images showing predefined steps of warping two

meshes or landmark configurations (2D and 3D) into each other
Description
Creates a sequence of images showing predefined steps of warping two meshes or landmark con-
figurations (2D and 3D) into each other
Usage
warpmovie3d(
x,
y,
n,
col = "green",
176 warpmovie3d
palindrome = FALSE,
folder = NULL,
movie = "warpmovie",
...
)

warpmovie3d(
x,
y,
n,
col = "green",
palindrome = FALSE,
folder = NULL,
add = FALSE,
close = TRUE,
countbegin = 0,
ask = TRUE,
radius = NULL,
links = NULL,
lwd = 1,
...
)
warpmovie2d(
x,
y,
n,
col = "green",
palindrome = FALSE,
folder = NULL,
links = NULL,
lwd = 1,
par = list(xaxt = "n", yaxt = "n", bty = "n"),
...
)

warpmovie3d(
x,
y,
n,
col = NULL,
palindrome = FALSE,
folder = NULL,
warpmovie3d 177
add = FALSE,
close = TRUE,
countbegin = 0,
ask = TRUE,
radius = NULL,
xland = NULL,
yland = NULL,
lmcol = "black",
...
)
Arguments
x mesh to start with (object of class mesh3d)

y resulting mesh (object of class mesh3d), having the same amount of vertices and
faces than the starting mesh
n integer: amount of intermediate steps.
col color of the mesh
palindrome logical: if TRUE, the procedure will go forth and back.
folder character: output folder for created images (optional)
movie character: name of the output files
... additional arguments passed to shade3d (3D) or points (2D).
add logical: if TRUE, the movie will be added to the focussed rgl-windows.
close logical: if TRUE, the rgl window will be closed when finished. width and 200
the height of the image.
countbegin integer: number to start image sequence.
ask logical: if TRUE, the viewpoint can be selected manually.
radius numeric: define size of spheres (overides atuomatic size estimation).
links vector or list of vectors containing wireframe information to connect landmarks
(optional).
lwd numeric: controls width of lines defined by "links".
imagedim character of pattern "100x200" where 100 determines the width and 200 the
height of the image.
par list of graphial parameters: details can be found here: par.
xland optional argument: add landmarks on mesh x
yland optional argument: add landmarks on mesh y
lmcol optional argument: color of landmarks xland and yland
178 warpmovie3d
Details
given two landmark configurations or two meshes with the same amount of vertices and faces (e.g a
mesh and its warped counterpart), the starting configuration/mesh will be subsequently transformed
into the final configuration/mesh by splitting the differences into a predefined set of steps.
A series of png files will be saved to disk. These can be joined to animated gifs by external pro-
grams such as imagemagick or used to create animations in PDFs in a latex environment (e.g. latex
package: aninmate).
Author(s)
Stefan Schlager
See Also
ply2mesh,file2mesh,mesh2ply,tps3d
Examples
###3D example
if (interactive()){
warpmovie3d(shortnose.mesh,longnose.mesh,n=15)## create 15 images.
### ad some landmarks

warpmovie3d(shortnose.mesh,longnose.mesh,n=15,xland=shortnose.lm,
yland=longnose.lm)## create 15 images.
### restrict to landmarks

warpmovie3d(shortnose.lm,longnose.lm,n=15,movie="matrixmovie")## create 15 images.
### the images are now stored in your current working directory and can
### be concatenated to a gif using an external program such as
### imagemagick.
}
### 2D example
bb <- procSym(gorf.dat)
### morph superimposed first specimen onto sample mean
warpmovie2d(bb$rotated[,,1],bb$mshape,n=20,links=c(1,5,4:2,8:6,1),imagedim="600x400")
## remove files
unlink("warpmovie00*")
}
write.fcsv 179
write.fcsv write fiducials in slicer4 format
Description
write fiducials in slicer4 format
Usage
write.fcsv(x, filename = dataname, description = NULL, slicer4.11 = FALSE)
Arguments
x matrix with row containing 2D or 3D coordinates
filename will be substituted with ".fcsv"
description optional: character vector containing a description for each landmark
slicer4.11 logical: Slicer changed their fiducial format in version >= 4.11. Set TRUE if
you use the latest Slicer version
Examples
require(Rvcg)
data(dummyhead)
write.fcsv(dummyhead.lm)
## remove file
unlink("dummyhead.lm.fcsv")
write.pts exports a matrix containing landmarks into .pts format
Description
exports a matrix containing landmarks into .pts format that can be read by IDAV Landmark.
Usage
write.pts(x, filename = dataname, rownames = NULL, NA.string = 9999)
Arguments
x k x m matrix containing landmark configuration
filename character: Path/name of the requested output - extension will be added atuomat-
ically. If not specified, the file will be named as the exported object.
rownames provide an optional character vector with rownames
NA.string specify the string to use for encoding missing values
180 write.slicerjson
Details
you can import the information into the program landmarks available at http://graphics.idav.ucdavis.edu/research/EvoMorph
Author(s)
Stefan Schlager
See Also
read.pts
Examples
data(nose)
write.pts(shortnose.lm, filename="shortnose")
unlink("shortnose.pts")
write.slicerjson Export landmarks (or any 3D coordinates) to the new slicer json for-
mat
Description
Export landmarks (or any 3D coordinates) to the new slicer json format
Usage
write.slicerjson(
x,
filename = dataname,
type = c("Fiducial", "Curve", "ClosedCurve"),
coordinateSystem = c("LPS", "RAS"),
labels = dataname
)
Arguments
x k x 3 matrix containing 3D coordinates
filename will be substituted with ".mrk.json"
type character: specify type of coordinates. Can be any of "Fiducial", "Curve",
"ClosedCurve".
coordinateSystem
character: specify coordinate system the data are in. Can be "LPS" or "RAS".
labels character or character vector containing landmark labels.
Index
∗ datasets covPCA (covDist), 26

boneData, 16 covW, 28
colors, 23 createAtlas, 19, 29, 97, 99, 101, 102
nose, 90 CreateL, 30
∗ package createMissingList, 32, 161
Morpho-package, 5 crossProduct, 33
cSize, 34
align2procSym, 6, 58 cutMeshPlane, 35
angle.calc, 7 cutSpace, 35, 35
angleTest, 7, 13 CVA, 21, 36, 66, 110
anonymize, 8
applyTransform, 9, 64, 166 data2platonic, 40
areaSphere, 10 deformGrid2d, 41
areaSpherePart, 11 deformGrid3d, 43
armaGinv, 11
array, 15 equidistantCurve, 45
array2list, 12 export (render), 142
arrMean3, 12 export.meshDist, 82
asymPermute, 13 exVar, 46
barycenter, 14 facenormals (updateNormals), 172

bindArr, 15 fastKmeans, 48
bone1 (colors), 23 file2mesh, 19, 49, 76, 77, 152, 160, 171, 178
bone2 (colors), 23 find.outliers, 50
bone3 (colors), 23 fixLMmirror, 32, 52
boneData, 16 fixLMtps, 32, 53, 90
boneLM (boneData), 16 formula, 114
CAC, 16 getFaces, 55
cbind, 15 getMeaningfulPCs, 55, 59
cExtract, 17 getOuterViewpoints, 56
checkLM, 18, 99 getPCscores, 57, 147
checkNA, 20 getPCtol, 56, 58
classify, 20 getPLSCommonShape, 59, 104, 107
closemeshKD, 14, 21, 75, 124, 128 getPLSfromScores, 60, 104, 106, 107
colors, 23 getPLSscores, 61, 104, 106, 107, 111, 112
computeArea, 23 getPointAlongOutline, 62
computeTransform, 10, 24, 166 getSides, 62
cov, 29 getTrafo4x4, 63
covDist, 26 getTrafoRotaxis, 64
181
182 INDEX
getVisibleVertices, 64 plot.slider3d, 100

groupPCA, 21, 38, 65, 110 plotAtlas, 19, 30, 101
plotNormals, 102
hist, 69 pls2B, 61, 103, 106, 107, 111, 112
histGroup, 67 plsCoVar, 104, 105, 107
plsCoVarCommonShape, 60, 104, 106, 106
icpmat, 69 ply2mesh, 22, 76–78, 128, 171, 173, 178
invertFaces, 70 ply2mesh (file2mesh), 49
points, 68, 177
kendalldist, 71
points2plane, 24, 107
line2plane, 72 prcomp, 27, 147
lineplot, 42, 73 prcompfast, 108
list2array, 74 predict.bgPCA, 109
lm, 114 predict.CVA, 110
longnose.lm (nose), 90 predictPLSfromData, 61, 104, 106, 107, 111,
LPS2RAS, 74, 129, 132 112
predictPLSfromScores, 61, 104, 106, 107,
material3d, 81, 143 111, 112
mcNNindex, 75 predictRelWarps, 112
mergeMeshes, 76 predictShape.lm, 113
mesh2grey, 77 proc.weight, 53, 54, 90, 115
mesh2obj, 77 procAOVsym, 116
mesh2ply, 76, 152, 160, 178 ProcGPA, 103, 118
mesh2ply (mesh2obj), 77 procSym, 13, 14, 93, 117, 119, 119, 127, 147
meshcube, 79 projRead, 123
meshDist, 79, 144
meshPlaneIntersect, 83 qqmat, 125
meshres, 84 qqplot, 125
mirror, 62, 85 quad2trimesh, 78, 126
mirror2plane, 87
r2morphoj, 126
model.matrix, 114
r2morphologika (r2morphoj), 126
Morpho (Morpho-package), 5
ray2mesh, 127
Morpho-package, 5
rbind, 15
name2factor, 88 read.csv.folder, 128
name2num (name2factor), 88 read.fcsv, 129
NNshapeReg, 89 read.lmdta, 17, 130, 133
nose, 90 read.mpp, 130
read.pts, 17, 131, 131, 133, 180
obj2mesh (file2mesh), 49 read.slicerjson, 132
read.table, 129, 134
p.adjust.methods, 37, 94 readallTPS, 132
par, 177 readLandmarks.csv, 133
pcAlign, 90 regdist, 134, 135
pcaplot3d, 73, 92 RegScore, 135
PCdist, 93 relaxLM, 31, 99, 136, 158, 161
permudist, 94 relWarps, 140
permuvec, 95 render, 142
placePatch, 19, 30, 97, 102 render.meshDist, 82
INDEX 183
resampleCurve, 144 write.fcsv, 179

restoreFromPCA, 145 write.pts, 179
restoreShapes, 58, 146 write.slicerjson, 180
retroDeform3d, 147, 149
retroDeformMesh, 148
rmUnrefVertex (unrefVertex), 170
rmVertex (unrefVertex), 170
rotaxis3d, 149, 151
rotaxisMat, 150
rotmesh.onto, 150, 151, 153, 155, 156
rotonmat, 152
rotonto, 10, 25, 44, 119, 150–153, 154
rotreverse (rotonto), 154
scalemesh, 156
shade3d, 81, 82, 143, 144, 177
shortnose.lm (nose), 90
shortnose.mesh (nose), 90
skin1 (colors), 23
skin2 (colors), 23
skin3 (colors), 23
skin4 (colors), 23
skull_0144_ch_fe.mesh (boneData), 16
slider2d, 157
slider3d, 31, 32, 99, 122, 138, 158, 158
solutionSpace, 163
sortCurve, 164
svd, 104, 106, 107
symmetrize, 165
tangentPlane (crossProduct), 33
tps2d (tps3d), 166
tps3d, 10, 25, 31, 43, 45, 54, 99, 148, 149,
152, 166, 178
typprob, 51, 167
typprobClass, 21, 29, 51
typprobClass (typprob), 167
unrefVertex, 170
updateIndices, 171
updateNormals, 71, 172
vcgSphere, 57
vecx, 104, 173
vert2points (unrefVertex), 170
virtualMeshScan, 174
warpmovie2d (warpmovie3d), 175

warpmovie3d, 175

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Package ‘Morpho’

January 27, 2023

Morpho-package A toolbox providing methods for data-acquisition, visualisation and

The pdf-version of Morpho-help can be obtained from CRAN on https://cran.r-project.org/

Stefan Schlager <zarquon42@gmail.com>

align2procSym align new data to an existing Procrustes registration

angle.calc calculate angle between two vectors

#calculate angle between two centered and

angleTest Test whether the direction of two vectors is similar

angle angle between vectors

anonymize Replace ID-strings of data and associated files.

applyTransform apply affine transformation to data

## S3 method for class 'matrix'

## S3 method for class 'mesh3d'

areaSphere compute the area of an n-dimensional hypersphere

areaSpherePart compute the area of an n-dimensional hypersphere cap

armaGinv calculate Pseudo-inverse of a Matrix using RcppArmadillo

array2list reverts list2array, converting an array to a list of matrices

arrMean3 calculate mean of an array

asymPermute Assess differences in amount and direction of asymmetric variation

barycenter calculates the barycenters for all faces of a triangular mesh

calculates the barycenters for all faces of a triangular mesh

mesh triangular mesh of class ’mesh3d’

k x 3 matrix of barycenters for all k faces of input mesh.

bindArr concatenate multiple arrays/matrices

boneData Landmarks and a triangular mesh

CAC calculate common allometric component

point how to render landmarks. "s"=spheres, "p"=points.

## create landmark array

## now visualize by using an atlas:

checkNA check for NA values in a matrix (of landmarks)

check for NA values in a matrix (of landmarks)

x matrix containing landmarks

classify classify specimen based on between-group PCA or CVA or typprob-

classify specimen based on between-group PCA, CVA or typprobClass

classify(x, cv = TRUE, ...)

## S3 method for class 'bgPCA'

## S3 method for class 'CVA'

## S3 method for class 'typprob'

x result of groupPCA, CVA or typprobClass

class classification result

closemeshKD Project coordinates onto a target triangular surface mesh.

vb 4xn matrix containing n vertices as homolougous coordinates

colors predefined colors for bone and skin

computeArea Compute area enclosed within an irregular polygon

returns a list containing

area size of the enclosed area

computeTransform calculate an affine transformation matrix

calculate an affine transformation matrix

x fix landmarks. Can be a k x m matrix or mesh3d.

x and y can also be a pair of meshes with corresponding vertices.

rotonto, link{rotmesh.onto}, tps3d

covDist calculates distances and PC-coordinates of covariance matrices

dist distance matrix

cpca <- covPCA(iris[,1:4],iris[,5])

#do some bootstrapping 1000 rounds

covW calculate the pooled within groups covariance matrix

calculate the pooled within groups covariance matrix

covW(data, groups, robust = c("classical", "mve", "mcd"), ...)

createAtlas Create an atlas needed in placePatch