Usage
procSym(dataarray, scale=TRUE, reflect=TRUE, CSinit=TRUE, orp=TRUE, tol=1e-05,
pairedLM=NULL, sizeshape=FALSE, use.lm=NULL, center.part=FALSE,
distfun=c("angle", "riemann"),SMvector=NULL, outlines=NULL, deselect=FALSE,
recursive=TRUE,iterations=0, initproc=FALSE)Arguments
dataarray
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.
scale
logical: indicating if scaling is requested
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.
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 left column contains the lefthand landmarks,
while the right side contains the corresponding right hand landmarks.
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 registration.
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.
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
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 sli
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 sliding 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.