Update pkgdown settings

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
@@ -28,40 +28,40 @@
 * Fix CRAN clang warnings
 * Misc. bugfixes
 
-# ubms v1.1.0
+# ubms 1.1.0
 
 * Support for restricted spatial regression (RSR)
 * Add vignette for RSR
 * Update default priors and allow setting custom priors
 * 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

_pkgdown.yml

@@ -7,26 +7,30 @@ 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
       - traceplot,ubmsFit-method
 
   - 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