- 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 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 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.
- 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.
- pcAlign
logical: if TRUE, the shapes are aligned by the principal axis of the first specimen
- 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 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 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.
- 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
.