Deploying to gh-pages from @ 408c6a7 🚀

Author: ecoisilva

llms.txt

@@ -101,17 +101,20 @@ citation("movedesign")
 
 ## All functions
 
+- [`fitting_models()`](https://ecoisilva.github.io/movedesign/reference/fitting_models.md)
+  : Fit continuous-time movement models
+
 - [`fixrates`](https://ecoisilva.github.io/movedesign/reference/fixrates.md)
   : Fix rates of animal tracking devices.
 
 - [`md_check()`](https://ecoisilva.github.io/movedesign/reference/md_check.md)
   : Assess output convergence in simulation outputs
 
 - [`md_compare()`](https://ecoisilva.github.io/movedesign/reference/md_compare.md)
-  : Visualize study design outputs
+  : Compare estimation error across study design workflows
 
 - [`md_compare_preview()`](https://ecoisilva.github.io/movedesign/reference/md_compare_preview.md)
-  : Preview plot for movedesign workflow outputs (single replicate)
+  : Compare estimation error across designs (single replicate)
 
 - [`md_configure()`](https://ecoisilva.github.io/movedesign/reference/md_configure.md)
   : Interactively configure movement design setup
@@ -120,7 +123,7 @@ citation("movedesign")
   : Merge multiple simulation outputs
 
 - [`md_optimize()`](https://ecoisilva.github.io/movedesign/reference/md_optimize.md)
-  : Optimize population sample size and sampling parameters
+  : Optimize sampling parameters and population sample size
 
 - [`md_plot()`](https://ecoisilva.github.io/movedesign/reference/md_plot.md)
   : Visualize study design outputs
@@ -129,26 +132,29 @@ citation("movedesign")
   : Preview plot for movedesign workflow outputs (single replicate)
 
 - [`md_plot_replicates()`](https://ecoisilva.github.io/movedesign/reference/md_plot_replicates.md)
-  : Plot replicate error estimates and confidence intervals
+  : Plot estimation error, replicates and confidence intervals
 
 - [`md_prepare()`](https://ecoisilva.github.io/movedesign/reference/md_prepare.md)
   : Prepare movement study design inputs
 
 - [`md_replicate()`](https://ecoisilva.github.io/movedesign/reference/md_replicate.md)
-  : Replicate study design and aggregate simulation outputs
+  : Replicate study design workflow and aggregate outputs
 
 - [`md_run()`](https://ecoisilva.github.io/movedesign/reference/md_run.md)
   : Run study design workflow
 
 - [`md_simulate()`](https://ecoisilva.github.io/movedesign/reference/md_simulate.md)
-  : Simulate movement data from species-level parameters
+  : Simulate movement data from species parameters
 
 - [`md_stack()`](https://ecoisilva.github.io/movedesign/reference/md_stack.md)
   : Stack simulation outputs as replicates
 
 - [`movmods`](https://ecoisilva.github.io/movedesign/reference/movmods.md)
   : Table of movement processes.
 
+- [`plot(`*`<movedesign_optimized>`*`)`](https://ecoisilva.github.io/movedesign/reference/plot.movedesign_optimized.md)
+  : Plot movedesign report outputs
+
 - [`print(`*`<movedesign_check>`*`)`](https://ecoisilva.github.io/movedesign/reference/print.movedesign_check.md)
   :
 
@@ -159,21 +165,31 @@ citation("movedesign")
 
   Print method for `movedesign_input`
 
+- [`print(`*`<movedesign_optimized>`*`)`](https://ecoisilva.github.io/movedesign/reference/print.movedesign_optimized.md)
+  :
+
+  Print method for `movedesign_optimized` objects
+
 - [`print(`*`<movedesign_output>`*`)`](https://ecoisilva.github.io/movedesign/reference/print.movedesign_output.md)
   :
 
   Print method for `movedesign_output`
 
-- [`print(`*`<movedesign_preprocess>`*`)`](https://ecoisilva.github.io/movedesign/reference/print.movedesign_preprocess.md)
+- [`print(`*`<movedesign_processed>`*`)`](https://ecoisilva.github.io/movedesign/reference/print.movedesign_processed.md)
   :
 
-  Print method for `movedesign_preprocess`
+  Print method for `movedesign_processed`
 
 - [`print(`*`<movedesign_report>`*`)`](https://ecoisilva.github.io/movedesign/reference/print.movedesign_report.md)
   :
 
   Print method for `movedesign_report` objects
 
+- [`read_md()`](https://ecoisilva.github.io/movedesign/reference/read_md.md)
+  :
+
+  Read a `movedesign` session file
+
 - [`run_app()`](https://ecoisilva.github.io/movedesign/reference/run_app.md)
   : Run movedesign R Shiny application
 
@@ -187,15 +203,16 @@ citation("movedesign")
 
   Summary method for `movedesign_input`
 
-- [`summary(`*`<movedesign_output>`*`)`](https://ecoisilva.github.io/movedesign/reference/summary.movedesign_output.md)
-  :
+- [`summary(`*`<movedesign_optimized>`*`)`](https://ecoisilva.github.io/movedesign/reference/summary.movedesign_optimized.md)
+  : Summarise a study design optimization
 
-  Summary method for `movedesign_output`
+- [`summary(`*`<movedesign_output>`*`)`](https://ecoisilva.github.io/movedesign/reference/summary.movedesign_output.md)
+  : Summarise a study design output
 
-- [`summary(`*`<movedesign_preprocess>`*`)`](https://ecoisilva.github.io/movedesign/reference/summary.movedesign_preprocess.md)
+- [`summary(`*`<movedesign_processed>`*`)`](https://ecoisilva.github.io/movedesign/reference/summary.movedesign_processed.md)
   :
 
-  Summary method for `movedesign_preprocess`
+  Summary method for `movedesign_processed`
 
 - [`summary(`*`<movedesign_report>`*`)`](https://ecoisilva.github.io/movedesign/reference/summary.movedesign_report.md)
   :

news/index.html

@@ -4,9 +4,11 @@
 
 ### New features
 
-- Added new core functions to compare `movedesign` scenarios.
-- Added `Download R script` button to Report tab which can replicate the
-  movedesign workflow.
+- Exported all internal functions, allowing workflows to run directly
+  from the command line.
+- Introduced new core functions to compare `movedesign` scenarios.  
+- Added a `Download R Script` button on the Report tab to replicate the
+  `movedesign` workflow.
 
 ### Minor improvements
 

news/index.md

@@ -6,7 +6,7 @@ articles:
   movedesign: movedesign.html
   tutorial_ind: tutorial_ind.html
   tutorial_pop: tutorial_pop.html
-last_built: 2026-03-31T14:34Z
+last_built: 2026-03-31T14:41Z
 urls:
   reference: https://ecoisilva.github.io/movedesign/reference
   article: https://ecoisilva.github.io/movedesign/articles

pkgdown.yml

@@ -9,7 +9,7 @@ required for each simulated individual.
 ## Usage
 
 ``` r
-estimate_speed(rv)
+estimate_speed(rv, stop_on_error = FALSE)
 ```
 
 ## Arguments