From 8c761fda6d69a1377997b18f65dbcc6ff2493ab5 Mon Sep 17 00:00:00 2001
From: Ken Kellner <ken@kenkellner.com>
Date: Thu, 18 Jan 2024 14:54:28 -0500
Subject: Update pkgdown settings

---
 NEWS.md      | 22 +++++++++++-----------
 _pkgdown.yml | 23 ++++++++++++++++++++++-
 2 files changed, 33 insertions(+), 12 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index ff2a91b..a9a24dc 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,24 +1,24 @@
-# ubms v.1.2.6
+# ubms 1.2.6
 
 * Fix deprecated Stan code
 
-# ubms v.1.2.5
+# ubms 1.2.5
 
 * Fix issue with version number not being a string
 * Adding missing roxygen tag
 
-# ubms v.1.2.4
+# ubms 1.2.4
 
 * Adjust Makevars to fix problems with clang 16
 
-# ubms v1.2.3
+# ubms 1.2.3
 
 * Fix bug in Stan code revealed by new StanHeaders
 * Drop C++ specification per CRAN instructions
 * Remove deprecated ggplot2 functions
 * Small updates to overview vignette
 
-# ubms v1.2.2
+# ubms 1.2.2
 
 * Fix broken URLs in vignettes
 * New kfold function
@@ -28,7 +28,7 @@
 * Fix CRAN clang warnings
 * Misc. bugfixes
 
-# ubms v1.1.0
+# ubms 1.1.0
 
 * Support for restricted spatial regression (RSR)
 * Add vignette for RSR
@@ -36,32 +36,32 @@
 * Support for offsets
 * New utility functions and bugfixes
 
-# ubms v1.0.2
+# ubms 1.0.2
 
 * Make default priors less informative
 * Fix issues in `sim_z` C++ code that triggered clang-UBSAN errors
 * Fix various minor issues with checks/tests on R-oldrel 
 
-# ubms v1.0.1
+# ubms 1.0.1
 
 * Added vignette comparing ubms and JAGS output
 * Added configuration for pkgdown site
 * Small adjustments to wording in DESCRIPTION and docs for CRAN submission
 
-# ubms v0.1.9
+# ubms 0.1.9
 
 * Add time-to-detection occupancy model (`stan_occuTTD`)
 * Wrote examples for all fitting functions
 * Many new tests added
 * Wrote a vignette demonstrating random effects
 
-# ubms v0.1.8
+# ubms 0.1.8
 
 * Added distance-sampling model (`stan_distsamp`)
 * Added multinomial-Poisson mixture model (`stan_multinomPois`)
 * Wrote overview vignette
 
-# ubms v0.1.4
+# ubms 0.1.4
 
 * Added dynamic occupancy model (`stan_colext`)
 * Consolidated single-season models into one Stan file to speed up compilation
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 1625f2d..e7b91cc 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -7,11 +7,13 @@ reference:
     contents:
       - starts_with("stan_")
       - priors
+      - RSR
 
   - title: Model diagnostics
     contents:
       - fitted,ubmsFit-method
       - gof
+      - plot,ubmsFit,ANY-method
       - plot_residuals
       - plot_posteriors,ubmsFit-method
       - residuals,ubmsFit-method
@@ -19,14 +21,16 @@ reference:
 
   - title: Model selection
     contents:
+      - extract_log_lik
       - fitList
       - kfold,ubmsFit-method
       - loo,ubmsFit-method
       - modSel,ubmsFitList-method
       - waic,ubmsFit-method
-  
+
   - title: Inference
     contents:
+      - coef,ubmsFit-method
       - extract,ubmsFit-method
       - plot_marginal
       - plot_spatial
@@ -35,4 +39,21 @@ reference:
       - predict
       - projected
       - ranef
+      - summary,ubmsFit-method 
       - turnover
+
+  - title: Utility
+    contents:
+      - get_elapsed_time,ubmsFit-method
+      - get_stancode,ubmsFit-method
+
+  - title: internal
+    contents:
+      - "[,ubmsFit,character,missing,missing-method"
+      - "[,ubmsSubmodelList,character,missing,missing-method"
+      - getY,ubmsFit-method
+      - names,ubmsFit-method
+      - names,ubmsFitList-method
+      - nsamples,ubmsFit-method
+      - ubms
+      - ubmsFitList-extractors 
-- 
cgit v1.2.3