#' A toolbox providing methods for data-acquisition, visualisation and
#' statistical methods related to Geometric Morphometrics and shape analysis
#'
#' A toolbox for Morphometric calculations. Including sliding operations for
#' Semilandmarks, importing, exporting and manipulating of 3D-surface meshes
#' and semi-automated placement of surface landmarks.
#'
#' \tabular{ll}{
#' Package: \tab Morpho\cr
#' Type: \tab Package\cr
#' Version: \tab 2.12\cr
#' Date: \tab 2023-12-04\cr
#' License: \tab GPL\cr
#' LazyLoad: \tab yes\cr
#' }
#'
#' @name Morpho-package
#' @aliases Morpho-package Morpho
#' @docType package
#' @author Stefan Schlager \email{zarquon42@@gmail.com}
#'
#' Maintainer: Stefan Schlager \email{zarquon42@@gmail.com}
#' @note
#' The pdf-version of Morpho-help can be obtained from CRAN on \url{https://cran.r-project.org/package=Morpho}
#'
#' For more advanced operations on triangular surface meshes, check out my package Rvcg: \url{https://cran.r-project.org/package=Rvcg} or the code repository on github \url{https://github.com/zarquon42b/Rvcg}
#'
#'
#'
#'
#' @references Schlager S. 2013. Soft-tissue reconstruction of the human nose:
#' population differences and sexual dimorphism. PhD thesis,
#' \enc{Universitätsbibliothek}{Universitaetsbibliothek} Freiburg. URL:
#' \url{http://www.freidok.uni-freiburg.de/volltexte/9181/}.
#' @encoding utf8
#' @keywords package
#' @useDynLib Morpho, .registration = TRUE
#' @import doParallel graphics grDevices methods stats utils
#' @importFrom foreach foreach '%dopar%' '%do%'
#' @importFrom Matrix sparseMatrix diag crossprod solve as.matrix t
#' @importFrom parallel mclapply detectCores
#' @importFrom rgl lines3d open3d points3d bg3d rgl.bringtotop clear3d close3d cur3d pop3d rgl.snapshot shade3d spheres3d text3d translate3d wire3d
#' @importFrom Rcpp evalCpp
#' @importFrom Rvcg vcgUpdateNormals
#' @importClassesFrom Matrix dgCMatrix dgeMatrix dsCMatrix dtCMatrix sparseMatrix
NULL
#' Landmarks and a triangular mesh
#'
#' Landmarks on the osseous human nose and a triangular mesh representing this
#' structure.
#'
#'
#' @name boneData
#' @aliases boneLM skull_0144_ch_fe.mesh
#' @docType data
#' @format \code{boneLM}: A 10x3x80 array containing 80 sets of 3D-landmarks
#' placed on the human osseous nose.
#'
#' \code{skull_0144_ch_fe.mesh}: The mesh representing the area of the first
#' individual of \code{boneLM}
#' @keywords datasets
NULL
#' predefined colors for bone and skin
#'
#' predefined colors for bone and skin
#'
#' available colors are:
#'
#' bone1
#'
#' bone2
#'
#' bone3
#'
#' skin1
#'
#' skin2
#'
#' skin3
#'
#' skin4
#'
#' @name colors
#' @export bone1 bone2 bone3 skin1 skin2 skin3 skin4
#' @aliases bone1 bone2 bone3 skin1 skin2 skin3 skin4
#' @docType data
#' @keywords datasets
NULL
#' landmarks and a triangular mesh representing a human nose
#'
#' triangular mesh representing a human nose and two matrices containing
#' landmark data
#'
#'
#' @name nose
#' @aliases shortnose.mesh shortnose.lm longnose.lm
#' @docType data
#' @format \code{shortnose.mesh}: A triangular mesh of class 'mesh3d'.
#'
#' \code{shortnose.lm}: matrix containing example landmark data placed on
#' \code{shortnose.mesh}.
#'
#' \code{longnose.lm}: matrix containing example landmark data representing a
#' caricaturesquely deformed human nose.
#' @keywords datasets
NULL
#' document deprecated functions
#'
#' @title deprecated functions of Morpho
#' @name deprecated
#' @rdname Morpho-deprecated
#' @keywords internal
NULL
#' @rdname Morpho-deprecated
#' @export deform.grid
deform.grid <- function (...)
{
.Deprecated("deformGrid3d", package="Morpho")
deformGrid3d(...)
}
#' @rdname Morpho-deprecated
#' @export deform.grid
showPC <- function (...)
{
.Deprecated("restoreShapes", package="Morpho")
restoreShapes(...)
}
#' @rdname Morpho-deprecated
#' @export
adnormals <- function (...)
{
.Deprecated("updateNormals", package="Morpho")
vcgUpdateNormals(...)
}
#' @rdname Morpho-deprecated
#' @export regdist.raw
regdist.raw <- function (...)
{
.Deprecated("regdist", package="Morpho")
regdist(...)
}
#' @rdname Morpho-deprecated
#' @export
crossp <- function (...)
{
.Deprecated("crossProduct", package="Morpho")
crossProduct(...)
}
#' @rdname Morpho-deprecated
#' @export
tanplan <- function (...)
{
.Deprecated("tangentPlane", package="Morpho")
tangentPlane(...)
}
#' @rdname Morpho-deprecated
#' @export
conv2backf <- function (...)
{
.Deprecated("invertFaces", package="Morpho")
invertFaces(...)
}
#' @rdname Morpho-deprecated
#' @export
warp.mesh <- function (mesh,matr,matt,lambda=1e-8,updateNormals=TRUE, silent=FALSE)
{
.Deprecated("tps3d", package="Morpho")
tps3d(x=mesh,refmat=matr,tarmat=matt,lambda=lambda,threads=1)
}
#' @rdname Morpho-deprecated
#' @export
showPC <- function(scores, PC, mshape) {
.Deprecated("restoreShapes", package="Morpho")
restoreShapes(scores = scores,PC=PC,mshape=mshape)
}
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