From 67131037ad73ba42a9f1f124c795abb8a8dc9603 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: Fri, 8 Nov 2024 14:46:52 +0100
Subject: [PATCH] Update axis1 and axis2 according to the changes

---
 R/jnd2xyz.R    | 20 ++++++++++++--------
 man/jnd2xyz.Rd | 20 ++++++++++++--------
 man/jndrot.Rd  | 22 +++++++++++++---------
 3 files changed, 37 insertions(+), 25 deletions(-)

diff --git a/R/jnd2xyz.R b/R/jnd2xyz.R
index 06c39d7b..60889e98 100644
--- a/R/jnd2xyz.R
+++ b/R/jnd2xyz.R
@@ -17,14 +17,18 @@
 #' (for no first rotation in the 3-dimensional case) or must match name
 #' in the original data that was used for [coldist()]. Defaults to 'u'.
 #' (only used if data has 3 dimensions).
-#' @param 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 `ref1` is `NULL` (in 3-dimensional case only)
-#' @param 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 `ref2` is `NULL` (in 3-dimensional case only)
+#' @param axis1 A vector of length number of cones minus 1 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) in 3 dimensions, such that the rotation aligns with the xy plane,
+#' and c(1, 0) in 2 dimentions, such that the rotation is centered on the x
+#' axis. Ignored if `ref1` is `NULL` (in 3-dimensional case only). Ignored for
+#' dichromats.
+#' @param axis2 A vector of length number of cones minus 1 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) in 3 dimensions, such that the rotation aligns with the z axis,
+#' and c(0, 1) in 2 dimentions, such that the rotation is centered on the y
+#' axis. Ignored if `ref1` is `NULL` (in 3-dimensional case only). Ignored for
+#' dichromats.
 #'
 #' @examples
 #' # Load floral reflectance spectra
diff --git a/man/jnd2xyz.Rd b/man/jnd2xyz.Rd
index 4b39a1aa..f3a425f2 100644
--- a/man/jnd2xyz.Rd
+++ b/man/jnd2xyz.Rd
@@ -35,15 +35,19 @@ in the original data that was used for \code{\link[=coldist]{coldist()}}. Defaul
 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{axis1}{A vector of length number of cones minus 1 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) in 3 dimensions, such that the rotation aligns with the xy plane,
+and c(1, 0) in 2 dimentions, such that the rotation is centered on the x
+axis. Ignored if \code{ref1} is \code{NULL} (in 3-dimensional case only). Ignored for
+dichromats.}
 
-\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)}
+\item{axis2}{A vector of length number of cones minus 1 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) in 3 dimensions, such that the rotation aligns with the z axis,
+and c(0, 1) in 2 dimentions, such that the rotation is centered on the y
+axis. Ignored if \code{ref1} is \code{NULL} (in 3-dimensional case only). Ignored for
+dichromats.}
 }
 \description{
 Converts a \code{\link[=coldist]{coldist()}} output into Cartesian coordinates that are
diff --git a/man/jndrot.Rd b/man/jndrot.Rd
index af150b1e..3fa338a6 100644
--- a/man/jndrot.Rd
+++ b/man/jndrot.Rd
@@ -28,15 +28,19 @@ in the original data that was used for \code{\link[=coldist]{coldist()}}. Defaul
 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)}
+\item{axis1}{A vector of length number of cones minus 1 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) in 3 dimensions, such that the rotation aligns with the xy plane,
+and c(1, 0) in 2 dimentions, such that the rotation is centered on the x
+axis. Ignored if \code{ref1} is \code{NULL} (in 3-dimensional case only). Ignored for
+dichromats.}
+
+\item{axis2}{A vector of length number of cones minus 1 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) in 3 dimensions, such that the rotation aligns with the z axis,
+and c(0, 1) in 2 dimentions, such that the rotation is centered on the y
+axis. Ignored if \code{ref1} is \code{NULL} (in 3-dimensional case only). Ignored for
+dichromats.}
 }
 \description{
 Rotate Cartesian coordinates obtained from \code{\link[=jnd2xyz]{jnd2xyz()}}