Morpho: createAtlas – R documentation

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createAtlas

Create an atlas needed in placePatch

Create an atlas needed in placePatch

createAtlas(mesh, landmarks, patch, corrCurves = NULL,
  patchCurves = NULL, keep.fix = NULL)

`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 landmarks 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`)

Returns a list of class "atlas". Its content is corresponding to argument names.

This is a helper function of placePatch.

data(nose)
atlas <- createAtlas(shortnose.mesh, landmarks =
            shortnose.lm[c(1:5,20:21),], patch=shortnose.lm[-c(1:5,20:21),])

Calculations and Visualisations Related to Geometric Morphometrics

v2.8

GPL-2

Authors

Stefan Schlager [aut, cre, cph], Gregory Jefferis [ctb], Dryden Ian [cph]

Initial release

2020-02-26