RaredonLab · RaredonLab · Apr 4, 2026 · Apr 4, 2026 · Apr 4, 2026
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -47,6 +47,7 @@ articles:
     contents:
       - getting-started
       - advanced-topology
+      - complete-reference
 
 news:
   releases:

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/advanced-topology.html b/docs/articles/advanced-topology.html
diff --git a/docs/articles/complete-reference.html b/docs/articles/complete-reference.html
diff --git a/docs/articles/complete-reference_files/figure-html/sec1-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec1-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec2-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec2-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec3-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec3-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec4-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec4-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec5-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec5-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec6-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec6-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec7a-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec7a-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec7b-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec7b-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec7c-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec7c-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec7d-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec7d-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec7e-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec7e-plot-1.png
diff --git a/docs/articles/complete-reference_files/figure-html/sec7f-plot-1.png b/docs/articles/complete-reference_files/figure-html/sec7f-plot-1.png
diff --git a/docs/articles/getting-started.html b/docs/articles/getting-started.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,8 +3,9 @@ pkgdown: 2.1.3
 pkgdown_sha: ~
 articles:
   advanced-topology: advanced-topology.html
+  complete-reference: complete-reference.html
   getting-started: getting-started.html
-last_built: 2026-04-04T14:33Z
+last_built: 2026-04-04T15:28Z
 urls:
   reference: https://raredonlab.github.io/TissueMask/reference
   article: https://raredonlab.github.io/TissueMask/articles
diff --git a/docs/reference/TissueMask-package.html b/docs/reference/TissueMask-package.html
diff --git a/docs/reference/fit_spatial_mask.html b/docs/reference/fit_spatial_mask.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
@@ -3,6 +3,7 @@
 <url><loc>https://raredonlab.github.io/TissueMask/LICENSE-text.html</loc></url>
 <url><loc>https://raredonlab.github.io/TissueMask/LICENSE.html</loc></url>
 <url><loc>https://raredonlab.github.io/TissueMask/articles/advanced-topology.html</loc></url>
+<url><loc>https://raredonlab.github.io/TissueMask/articles/complete-reference.html</loc></url>
 <url><loc>https://raredonlab.github.io/TissueMask/articles/getting-started.html</loc></url>
 <url><loc>https://raredonlab.github.io/TissueMask/articles/index.html</loc></url>
 <url><loc>https://raredonlab.github.io/TissueMask/authors.html</loc></url>

diff --git a/vignette_fit_spatial_mask.Rmd → ..._mask_files/vignette_fit_spatial_mask.Rmd b/vignette_fit_spatial_mask.Rmd → ..._mask_files/vignette_fit_spatial_mask.Rmd
diff --git a/vignette_fit_spatial_mask.html → ...mask_files/vignette_fit_spatial_mask.html b/vignette_fit_spatial_mask.html → ...mask_files/vignette_fit_spatial_mask.html