FIX: fix more missing package specification in function links in docstrings

Author: dfsp-spirit

R/brainview_magick.R

@@ -307,11 +307,11 @@ images.annotate <- function(images, annotations, do_extend = TRUE, background =
 #'
 #' @param view_angles list of strings. See \code{\link{get.view.angle.names}} for all valid strings.
 #'
-#' @param rgloptions option list passed to \code{\link{par3d}}. Example: \code{rgloptions = list("windowRect"=c(50,50,1000,1000))}.
+#' @param rgloptions option list passed to \code{\link[rgl]{par3d}}. Example: \code{rgloptions = list("windowRect"=c(50,50,1000,1000))}.
 #'
 #' @param rglactions named list. A list in which the names are from a set of pre-defined actions. The values can be used to specify parameters for the action.
 #'
-#' @param style character string, a rendering style, e.g., 'default', 'shiny' or 'semitransparent'. Alternatively, a named list of style parameters (see \code{\link{material3d}}), e.g., \code{list("shininess"=50, specular="black", alpha=0.5)}. Use the magic word 'from_mesh' to use the 'style' field of each coloredmesh instead of a single, global style. In that case, you will have to make sure your meshes have such a field, if not, the style 'default' is used as a fallback for those which don't.
+#' @param style character string, a rendering style, e.g., 'default', 'shiny' or 'semitransparent'. Alternatively, a named list of style parameters (see \code{\link[rgl]{material3d}}), e.g., \code{list("shininess"=50, specular="black", alpha=0.5)}. Use the magic word 'from_mesh' to use the 'style' field of each coloredmesh instead of a single, global style. In that case, you will have to make sure your meshes have such a field, if not, the style 'default' is used as a fallback for those which don't.
 #'
 #' @param output_img string, path to the output file. Defaults to "fsbrain_arranged.png"
 #'

R/cbar.R

@@ -2,7 +2,7 @@
 
 #' @title Draw colorbar into background of current plot.
 #'
-#' @description Requires a rgl 3d visualisation to be open that already contains a rendered object. Uses \code{\link{bgplot3d}} to add a colorbar in the background of the plot using \code{\link[fields]{image.plot}}. Experimental.
+#' @description Requires a rgl 3d visualisation to be open that already contains a rendered object. Uses \code{\link[rgl]{bgplot3d}} to add a colorbar in the background of the plot using \code{\link[fields]{image.plot}}. Experimental.
 #'
 #' @param coloredmeshes fs.coloredmesh as returned by the coloredmesh.from.* functions.
 #'

R/rglactions.R

@@ -314,7 +314,7 @@ perform.rglactions <- function(rglactions, at_index=NULL, silent=TRUE, ignore =
 
 #' @title Create rglactions list, suitable to be passed as parameter to vis functions.
 #'
-#' @note List of all available rglactions: (1) `snapshot_png=filepath` takes a screenshot in PNG format and saves it in at `filepath`. (2) `trans_fun=function` uses the transformation function trans_fun to the data before mapping data values to colors and plotting. Popular transformation functions are \code{\link{limit_fun}}, \code{\link{limit_fun_na}}, and \code{\link{clip_fun}}. (3) `text=arglist` calls \code{\link{text3d}} with the given args after plotting. (4) `snapshot_vec=filepath` takes a screenshot in vector format and saves it in at `filepath`. You also need to set the format via `snapshot_vec_format`, valid entries are one of "ps", "eps", "tex", "pdf", "svg", "pgf" (default is 'eps'). This is experimental and may take a while.
+#' @note List of all available rglactions: (1) `snapshot_png=filepath` takes a screenshot in PNG format and saves it in at `filepath`. (2) `trans_fun=function` uses the transformation function trans_fun to the data before mapping data values to colors and plotting. Popular transformation functions are \code{\link{limit_fun}}, \code{\link{limit_fun_na}}, and \code{\link{clip_fun}}. (3) `text=arglist` calls \code{\link[rgl]{text3d}} with the given args after plotting. (4) `snapshot_vec=filepath` takes a screenshot in vector format and saves it in at `filepath`. You also need to set the format via `snapshot_vec_format`, valid entries are one of "ps", "eps", "tex", "pdf", "svg", "pgf" (default is 'eps'). This is experimental and may take a while.
 #'
 #' @return named list, an example `rlgactions` instance that will save a screenshot of the plot produced by the vis function in the current working directory (see \code{getwd}), under the name 'fsbrain_out.png'.
 #'

R/vis.R

@@ -17,7 +17,7 @@
 #'
 #' @param views list of strings. Valid entries include: 'si': single interactive view. 't4': tiled view showing the brain from 4 angles. 't9': tiled view showing the brain from 9 angles.
 #'
-#' @param rgloptions option list passed to \code{\link{par3d}}. Example: \code{rgloptions = list("windowRect"=c(50,50,1000,1000))}.
+#' @param rgloptions option list passed to \code{\link[rgl]{par3d}}. Example: \code{rgloptions = list("windowRect"=c(50,50,1000,1000))}.
 #'
 #' @param rglactions named list. A list in which the names are from a set of pre-defined actions. The values can be used to specify parameters for the action. The following example clips outliers in the data before plotting and writes a screenshot in PNG format: \code{rglactions = list("snapshot_png"="~/fsbrain.png", "clip_data"=c(0.05, 0.95))}. See \code{\link{rglactions}}.
 #'
@@ -27,7 +27,7 @@
 #'
 #' @param style character string, a rendering style, e.g., 'default', 'shiny' or 'semitransparent'.
 #'
-#' @param makecmap_options named list of parameters to pass to \code{\link{makecmap}}. Must not include the unnamed first parameter, which is derived from 'measure'. Should include at least a colormap function as name 'colFn'.
+#' @param makecmap_options named list of parameters to pass to \code{\link[squash]{makecmap}}. Must not include the unnamed first parameter, which is derived from 'measure'. Should include at least a colormap function as name 'colFn'.
 #'
 #' @param bg a background definition. Can be a surface color layer or a character string like 'curv_light' to select a pre-defined layer, see \code{\link[fsbrain]{collayer.bg}} for valid strings.
 #'

R/vis_meshes.R

@@ -11,7 +11,7 @@
 #'
 #' @param style a named list of style parameters or a string specifying an available style by name (e.g., 'shiny'). Defaults to 'default', the default style.
 #'
-#' @param rgloptions option list passed to \code{\link{par3d}}. Example: \code{rgloptions = list("windowRect"=c(50,50,1000,1000))};
+#' @param rgloptions option list passed to \code{\link[rgl]{par3d}}. Example: \code{rgloptions = list("windowRect"=c(50,50,1000,1000))};
 #'
 #' @param rglactions named list. A list in which the names are from a set of pre-defined actions. Defaults to the empty list.
 #'
@@ -172,17 +172,17 @@ vis.renderable <- function(cmesh, skip_all_na=TRUE, style="default") {
 #'
 #' @param style a named list of style parameters or a string specifying an available style by name (e.g., 'shiny'). Defaults to 'default', the default style.
 #'
-#' @param x rotation x axis value, passed to \code{\link{spin3d}}. Defaults to 0.
+#' @param x rotation x axis value, passed to \code{\link[rgl]{spin3d}}. Defaults to 0.
 #'
-#' @param y rotation y axis value, passed to \code{\link{spin3d}}. Defaults to 1.
+#' @param y rotation y axis value, passed to \code{\link[rgl]{spin3d}}. Defaults to 1.
 #'
-#' @param z rotation z axis value, passed to \code{\link{spin3d}}. Defaults to 0.
+#' @param z rotation z axis value, passed to \code{\link[rgl]{spin3d}}. Defaults to 0.
 #'
-#' @param rpm rotation rpm value, passed to \code{\link{spin3d}}. Defaults to 15.
+#' @param rpm rotation rpm value, passed to \code{\link[rgl]{spin3d}}. Defaults to 15.
 #'
-#' @param duration rotation duration value, passed to \code{\link{spin3d}}. Defaults to 20.
+#' @param duration rotation duration value, passed to \code{\link[rgl]{spin3d}}. Defaults to 20.
 #'
-#' @param rgloptions option list passed to \code{\link{par3d}}. Example: rgloptions = list("windowRect"=c(50,50,1000,1000));
+#' @param rgloptions option list passed to \code{\link[rgl]{par3d}}. Example: rgloptions = list("windowRect"=c(50,50,1000,1000));
 #'
 #' @param rglactions named list. A list in which the names are from a set of pre-defined actions. Defaults to the empty list.
 #'
@@ -228,13 +228,13 @@ vis.coloredmeshes.rotating <- function(coloredmeshes, background="white", skip_a
 #'
 #' @param coloredmeshes list of renderables. A coloredmesh is a named list as returned by the coloredmesh.from.* functions. It has the entries 'mesh' of type tmesh3d, a 'col', which is a color specification for such a mesh.
 #'
-#' @param rotation_angle angle in radians. Passed to \code{\link{rotate3d}}.
+#' @param rotation_angle angle in radians. Passed to \code{\link[rgl]{rotate3d}}.
 #'
-#' @param x x value passed to \code{\link{rotate3d}}.
+#' @param x x value passed to \code{\link[rgl]{rotate3d}}.
 #'
-#' @param y y value passed to \code{\link{rotate3d}}.
+#' @param y y value passed to \code{\link[rgl]{rotate3d}}.
 #'
-#' @param z z value passed to \code{\link{rotate3d}}.
+#' @param z z value passed to \code{\link[rgl]{rotate3d}}.
 #'
 #' @param style a named list of style parameters or a string specifying an available style by name (e.g., 'shiny'). Defaults to 'default', the default style.
 #'
@@ -309,7 +309,7 @@ vis.coloredmesh <- function(cmesh, style="default") {
 #'
 #' @param style A style definition. Can be a character string like 'shiny' or 'from_mesh', or already a named list of material properties (which will be returned as-is).
 #'
-#' @return a style, resolved to a parameter list compatible with \code{\link{material3d}}.
+#' @return a style, resolved to a parameter list compatible with \code{\link[rgl]{material3d}}.
 #'
 #' @keywords internal
 get.rglstyle.parameters <- function(renderable, style) {
@@ -334,13 +334,13 @@ get.rglstyle.parameters <- function(renderable, style) {
 
 #' @title Get the default visualization style parameters as a named list.
 #'
-#' @description Run \code{\link{material3d}} without arguments to see valid style keywords to create new styles.
+#' @description Run \code{\link[rgl]{material3d}} without arguments to see valid style keywords to create new styles.
 #'
 #' @param style string. A style name. Available styles are one of: "default", "shiny", "semitransparent", "glass", "edges".
 #'
-#' @return a style, resolved to a parameter list compatible with \code{\link{material3d}}.
+#' @return a style, resolved to a parameter list compatible with \code{\link[rgl]{material3d}}.
 #'
-#' @seealso \code{\link{shade3d}} can use the returned style
+#' @seealso \code{\link[rgl]{shade3d}} can use the returned style
 #'
 #' @export
 get.rglstyle <- function(style) {
@@ -364,9 +364,9 @@ get.rglstyle <- function(style) {
 
 #' @title Get the default visualization style parameters as a named list.
 #'
-#' @description The default rendering style, which is is rather plain. Does not look super fancy, but allows for clear data visualization without distractions. Hint: Run \code{\link{material3d}} without arguments to see valid style keywords to create new styles.
+#' @description The default rendering style, which is is rather plain. Does not look super fancy, but allows for clear data visualization without distractions. Hint: Run \code{\link[rgl]{material3d}} without arguments to see valid style keywords to create new styles.
 #'
-#' @return named list, style parameters that can be passed to \code{\link{shade3d}} via \code{\link{do.call}}.
+#' @return named list, style parameters that can be passed to \code{\link[rgl]{shade3d}} via \code{\link{do.call}}.
 #'
 #' @keywords internal
 get.rglstyle.default <- function() {
@@ -376,9 +376,9 @@ get.rglstyle.default <- function() {
 
 #' @title Get the semi-transparent visualization style parameters as a named list.
 #'
-#' @description Semitransparent rendering style. This style has a very negative impact on rendering performance (in interactive mode). Hint: Run \code{\link{material3d}} without arguments to see valid style keywords to create new styles.
+#' @description Semitransparent rendering style. This style has a very negative impact on rendering performance (in interactive mode). Hint: Run \code{\link[rgl]{material3d}} without arguments to see valid style keywords to create new styles.
 #'
-#' @return named list, style parameters that can be passed to \code{\link{shade3d}} via \code{\link{do.call}}.
+#' @return named list, style parameters that can be passed to \code{\link[rgl]{shade3d}} via \code{\link{do.call}}.
 #'
 #' @keywords internal
 get.rglstyle.semitransparent <- function() {
@@ -390,7 +390,7 @@ get.rglstyle.semitransparent <- function() {
 #'
 #' @description Mesh edges rendering style. Zoom in enough to see them.
 #'
-#' @return named list, style parameters that can be passed to \code{\link{shade3d}} via \code{\link{do.call}}.
+#' @return named list, style parameters that can be passed to \code{\link[rgl]{shade3d}} via \code{\link{do.call}}.
 #'
 #' @keywords internal
 get.rglstyle.edges <- function() {
@@ -400,9 +400,9 @@ get.rglstyle.edges <- function() {
 
 #' @title Get the glass visualization style parameters as a named list.
 #'
-#' @description Glass-brain rendering style. This style has a very negative impact on rendering performance (especially in interactive mode). Hint: Run \code{\link{material3d}} without arguments to see valid style keywords to create new styles.
+#' @description Glass-brain rendering style. This style has a very negative impact on rendering performance (especially in interactive mode). Hint: Run \code{\link[rgl]{material3d}} without arguments to see valid style keywords to create new styles.
 #'
-#' @return named list, style parameters that can be passed to \code{\link{shade3d}} via \code{\link{do.call}}.
+#' @return named list, style parameters that can be passed to \code{\link[rgl]{shade3d}} via \code{\link{do.call}}.
 #'
 #' @keywords internal
 get.rglstyle.glass <- function() {
@@ -412,9 +412,9 @@ get.rglstyle.glass <- function() {
 
 #' @title Get the glass2 visualization style parameters as a named list.
 #'
-#' @description Glass-brain rendering style. This style has a very negative impact on rendering performance (especially in interactive mode). Hint: Run \code{\link{material3d}} without arguments to see valid style keywords to create new styles.
+#' @description Glass-brain rendering style. This style has a very negative impact on rendering performance (especially in interactive mode). Hint: Run \code{\link[rgl]{material3d}} without arguments to see valid style keywords to create new styles.
 #'
-#' @return named list, style parameters that can be passed to \code{\link{shade3d}} via \code{\link{do.call}}.
+#' @return named list, style parameters that can be passed to \code{\link[rgl]{shade3d}} via \code{\link{do.call}}.
 #'
 #' @keywords internal
 get.rglstyle.glass2 <- function() {
@@ -424,9 +424,9 @@ get.rglstyle.glass2 <- function() {
 
 #' @title Get a shiny visualization style.
 #'
-#' @description A shiny or glossy rendering style. Looks a bit more modern, but the resulting highlights may make the interpretation of the plotted data a bit harder in some areas. Hint: Run \code{\link{material3d}} without arguments to see valid style keywords to create new styles.
+#' @description A shiny or glossy rendering style. Looks a bit more modern, but the resulting highlights may make the interpretation of the plotted data a bit harder in some areas. Hint: Run \code{\link[rgl]{material3d}} without arguments to see valid style keywords to create new styles.
 #'
-#' @return named list, style parameters that can be passed to to \code{\link{shade3d}} via \code{\link{do.call}}.
+#' @return named list, style parameters that can be passed to to \code{\link[rgl]{shade3d}} via \code{\link{do.call}}.
 #'
 #' @keywords internal
 get.rglstyle.shiny <- function() {

R/vis_volume.R

@@ -723,7 +723,7 @@ normalize <- function(x) {
 
 #' @title Return triangles for a 3D cube or cuboid.
 #'
-#' @description Each row of the returned matrix encodes a point (the x, y, and z coordinates), and 3 consecutive rows encode a triangle. Obvisouly, a point will occur several times (as part of several triangles). The result can be passed to \code{\link{triangles3d}} to render a 3D box. The defaults for the parameters will create a cube with edge length 1 centered at (0, 0, 0).
+#' @description Each row of the returned matrix encodes a point (the x, y, and z coordinates), and 3 consecutive rows encode a triangle. Obvisouly, a point will occur several times (as part of several triangles). The result can be passed to \code{\link[rgl]{triangles3d}} to render a 3D box. The defaults for the parameters will create a cube with edge length 1 centered at (0, 0, 0).
 #'
 #' @param xmin numeric, minimal x coordinate
 #'

R/vis_volume_3d.R

@@ -11,7 +11,7 @@
 #'
 #' @param voxelcol character string or a *voxel coloring*. A *voxel coloring* can be specified in three ways: 1) the string 'from_intensity' will compute colors based on the intensity values of the foreground voxels in the volume, applying normalization of the intensity values if needed. 2) an array of RGB color strings: will be used to retrieve the colors for all foreground vertices, at their CRS indices. 3) A vector with length identical to the number of foreground voxels in the volume: will be applied directly.  Obvisouly, you should not pass a color material parameter (see `...`) when using this.
 #'
-#' @param ... material properties, passed to \code{\link{triangles3d}}. Example: \code{color = "#0000ff", lit=FALSE}.
+#' @param ... material properties, passed to \code{\link[rgl]{triangles3d}}. Example: \code{color = "#0000ff", lit=FALSE}.
 #'
 #' @examples
 #' \dontrun{
@@ -339,15 +339,15 @@ apply.transform <- function(object, matrix_fun) {
 
 #' @title Draw 3D boxes at locations using rgl.
 #'
-#' @description Draw 3D boxes at all given coordinates using rgl, analogous to \code{\link{spheres3d}}. Constructs the coordinates for triangles making up the boxes, then uses \code{\link{triangles3d}} to render them.
+#' @description Draw 3D boxes at all given coordinates using rgl, analogous to \code{\link[rgl]{spheres3d}}. Constructs the coordinates for triangles making up the boxes, then uses \code{\link[rgl]{triangles3d}} to render them.
 #'
 #' @param centers numerical matrix with 3 columns. Each column represents the x, y, z coordinates of a center at which to create a cube.
 #'
 #' @param r numerical vector or scalar, the cube edge length. This is the length of the axis-parallel edges of the cube. The vector must have length 1 (same edge length for all cubes), or the length must be identical to the number of rows in parameter `centers`.
 #'
 #' @param voxelcol vector of rgb color strings for the individual voxels. Its length must be identical to \code{nrow(centers)} if given.
 #'
-#' @param ... material properties, passed to \code{\link{triangles3d}}. Example: \code{color = "#0000ff", lit=FALSE}.
+#' @param ... material properties, passed to \code{\link[rgl]{triangles3d}}. Example: \code{color = "#0000ff", lit=FALSE}.
 #'
 #' @param do_show logical, whether to visualize the result in the current rgl scene
 #'