R/Morpho-package.R

In Morpho: Calculations and Visualisations Related to Geometric Morphometrics

#' 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 2.11\cr
#' Date: \tab 2023-01-26\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)
}