% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/jndrot.R
\name{jndrot}
\alias{jndrot}
\title{Rotate Cartesian coordinates obtained from \code{\link[=jnd2xyz]{jnd2xyz()}}}
\usage{
jndrot(
  jnd2xyzres,
  center = c("mean", "achro"),
  ref1 = "l",
  ref2 = "u",
  axis1 = c(1, 1, 0),
  axis2 = c(0, 0, 1)
)
}
\arguments{
\item{jnd2xyzres}{(required) the output from a \code{\link[=jnd2xyz]{jnd2xyz()}} call.}

\item{center}{should the vectors for rotation be centered in the achromatic
center ("achro") or the data centroid ("mean", the default)?}

\item{ref1}{the cone to be used as a the first reference. May be \code{NULL}
(for no first rotation in the 3-dimensional case) or must match name
in the original data that was used for \code{\link[=coldist]{coldist()}}. Defaults to 'l'.}

\item{ref2}{the cone to be used as a the second reference. May be \code{NULL}
(for no first rotation in the 3-dimensional case) or must match name
in the original data that was used for \code{\link[=coldist]{coldist()}}. Defaults to 'u'.
(only used if data has 3 dimensions).}

\item{axis1}{A vector of length 3 composed of 0's and 1's, with
1's representing the axes (x, y, z) to rotate around. Defaults to c(1, 1, 0), such
that the rotation aligns with the xy plane (only used if data has 2 or 3 dimensions).
Ignored if \code{ref1} is \code{NULL} (in 3-dimensional case only)}

\item{axis2}{A vector of length 3 composed of 0's and 1's, with
1's representing the axes (x, y, z) to rotate around. Defaults to c(0, 0, 1), such
that the rotation aligns with the z axis (only used if data has 3 dimensions).
Ignored if \code{ref2} is \code{NULL} (in 3-dimensional case only)}
}
\description{
Rotate Cartesian coordinates obtained from \code{\link[=jnd2xyz]{jnd2xyz()}}
}
\examples{
# Load floral reflectance spectra
data(flowers)

# Estimate quantum catches visual phenotype of a Blue Tit
vis.flowers <- vismodel(flowers, visual = "bluetit")

# Estimate noise-weighted colour distances between all flowers
cd.flowers <- coldist(vis.flowers)

# Convert points to Cartesian coordinates in which Euclidean distances are
# noise-weighted, before rotating them about the data centroid
jndrot(jnd2xyz(cd.flowers))

}
\author{
Rafael Maia \email{rm72@zips.uakron.edu}
}
\keyword{internal}
