From 3c9e3df0b44a7f6e31e8e0af5d04d398b2b1f004 Mon Sep 17 00:00:00 2001
From: Paul Hoffman <mojaveazure@users.noreply.github.com>
Date: Thu, 10 Nov 2022 15:37:06 -0500
Subject: [PATCH] pkgdown fixes

---
 R/generics.R                 |  4 ++--
 R/neighbor.R                 |  4 ++--
 _pkgdown.yml                 | 25 +++++++++++++++++++++++++
 man/{Index.Rd => NNIndex.Rd} |  0
 4 files changed, 29 insertions(+), 4 deletions(-)
 rename man/{Index.Rd => NNIndex.Rd} (100%)

diff --git a/R/generics.R b/R/generics.R
index fe8873d2..780169d8 100644
--- a/R/generics.R
+++ b/R/generics.R
@@ -669,7 +669,7 @@ Idents <- function(object, ... ) {
 #'
 #' @return Returns the value in the alg.idx slot of the Neighbor object
 #'
-#' @rdname Index
+#' @rdname NNIndex
 #' @export Index
 #'
 #' @concept data-access
@@ -682,7 +682,7 @@ Index <- function(object, ...) {
 #'
 #' @return \code{Idents<-}: A Neighbor object with the index stored
 #'
-#' @rdname Index
+#' @rdname NNIndex
 #' @export Index<-
 #'
 "Index<-" <- function(object, ..., value) {
diff --git a/R/neighbor.R b/R/neighbor.R
index 8bf748da..4669017f 100644
--- a/R/neighbor.R
+++ b/R/neighbor.R
@@ -78,7 +78,7 @@ Distances.Neighbor <- function(object, ...) {
   return(distances)
 }
 
-#' @rdname Index
+#' @rdname NNIndex
 #' @export
 #' @method Index Neighbor
 #'
@@ -93,7 +93,7 @@ Index.Neighbor <- function(object, ...) {
   return(index)
 }
 
-#' @rdname Index
+#' @rdname NNIndex
 #' @export
 #' @method Index<- Neighbor
 #'
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 560cd7a2..d774ee47 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -51,4 +51,29 @@ reference:
   - SeuratObject-package
   - pbmc_small
   - reexports
+- title: internal
+  contents:
+    - aggregate
+    - as.Centroids
+    - Boundaries
+    - Centroids-class
+    - Centroids-methods
+    - CreateCentroids
+    - CreateFOV
+    - CreateMolecules
+    - CreateSegmentation
+    - Crop
+    - DefaultFOV
+    - FOV-class
+    - FOV-methods
+    - IsNamedList
+    - LogMap-class
+    - MatchCells
+    - Molecules-class
+    - Molecules-methods
+    - Overlay
+    - Segmentation-class
+    - Segmentation-methods
+    - Simplify
+    - Theta
 
diff --git a/man/Index.Rd b/man/NNIndex.Rd
similarity index 100%
rename from man/Index.Rd
rename to man/NNIndex.Rd