translate {ShapeRotator}

translate

Description

Translates array T to origin point.

Usage

translate(T, landmark, origin = c(0,0,0))

Arguments

T

an object of the class "array" that contains three-dimensional landmarks for 'n' specimens

landmark

an integer object that indicates the position of the three-dimensional landmark that will be used to translate each matrix of landmarks to the point of origin.

origin

a vector that contains three-dimensional coordinates (x, y, z) indicating where the origin point should be translanted to.

Details

Takes an array T and an index in the array landmark, and translates it to the origin. Each structure will be translated to the point of origin so that p0 =(0,0,0). We will be translating landmark A from structure 1 and landmark D from structure 2 for a single-point articulated rotation. And landmark A from structure 1 and landmark E from structure 2 for a double rotation (double-point articulated rotation). Thus, the distance from the coordinates of landmark A (Ax, Ay, Az) is substracted from all the landmarks in all specimens. For example (Nx - Ax, Ny - Ay, Nz - Az) for landmark N, for structure 1. For structure 2, the distance from the coordinates of landmark D or E depending on the type of rotation. For example, in a double rotation, (Ex, Ey, Ez) is substracted from all the landmarks in all specimens: (Nx - Ex, Ny - Ey, Nz - Ez). Landmarks A and E will equal (0,0,0), so that Ax=Ay=Az=Ex=Ey=Ez=0. The default is to set the origin to (0,0,0), but this can be specified to be something else. In order to use this function, the landmark data needs to be imported to the R environment using geomorph (Adams et al., 2018)

Value

This function returns a translated T array of dimensions (p, 3, n), in which p indicates the number of landmarks, and n the number of specimens included in the array. The translated array will keep the dimnames associated with each specimen (n).

Author(s)

Marta Vidal-Garcia

References

Adams, D. C., M. L. Collyer, and A. Kaliontzopoulou. 2018. Geomorph: Software for geometric morphometric analysis. R package version 3.0.6. Available at http://CRAN.R-project.org/package=geomorph.

M. Vidal-García, L. Bandara and J.S. Keogh. 2018. ShapeRotator: An R tool for standardized rigid rotations of articulated three-dimensional structures with application for geometric morphometrics. Ecology and Evolution. DOI: 10.1002/ece3.4018

Examples

#Data
data(double_data_1)
data(double_data_2)
data.1 <- double_data_1
data.2 <- double_data_2

#Landmarks
land.a=55
land.b=49
land.c=54
land.d=4

land.e=22
land.f=21
land.g=2
land.h=11

# Translate the data
data.1_t <- translate(data.1, land.a)
data.2_t <- translate(data.2, land.e)