Update readme

Author: jaseeverett

README.Rmd

@@ -17,12 +17,17 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![Windows](https://github.com/SpatialPlanning/minpatch/actions/workflows/Windows.yaml/badge.svg)](https://github.com/SpatialPlanning/minpatch/actions/workflows/Windows.yaml)
-[![Linux](https://github.com/SpatialPlanning/minpatch/actions/workflows/Linux.yaml/badge.svg)](https://github.com/SpatialPlanning/minpatch/actions/workflows/Linux.yaml)
+[![Ubuntu](https://github.com/SpatialPlanning/minpatch/actions/workflows/Ubuntu.yaml/badge.svg)](https://github.com/SpatialPlanning/minpatch/actions/workflows/Ubuntu.yaml)
 [![MacOS](https://github.com/SpatialPlanning/minpatch/actions/workflows/MacOS.yaml/badge.svg)](https://github.com/SpatialPlanning/minpatch/actions/workflows/MacOS.yaml)
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 [![Codecov test coverage](https://codecov.io/gh/SpatialPlanning/minpatch/graph/badge.svg)](https://app.codecov.io/gh/SpatialPlanning/minpatch)
 <!-- badges: end -->
 
+
+** Note: This is still a work in progress and significant bugs may be present. Use with caution **
+
+More information on the original implemention of MinPatch for Marxan and QGIS is available here:  https://cluz-systematic-conservation-planning.github.io
+
 ## Overview
 
 An R implementation of the MinPatch algorithm for post-processing conservation planning solutions to ensure minimum protected area sizes.
@@ -50,7 +55,7 @@ MinPatch addresses this by post-processing conservation solutions through three
 
 ```{r, eval=FALSE}
 # Install from GitHub
-devtools::install_github("SpatialPlanning/minpatch")
+pak::pak("SpatialPlanning/minpatch")
 ```
 
 
@@ -96,21 +101,6 @@ Removes unnecessary planning units through an iterative process:
    - Must not increase total cost (if boundary penalty > 0)
    - Must not split patches into non-viable pieces
 
-## Parameters
-
-- `min_patch_size`: Minimum area threshold for patches
-- `patch_radius`: Radius for adding new patches (allows elongated shapes)
-- `boundary_penalty`: Boundary penalty value for cost calculations
-- `remove_small_patches`: Enable/disable Stage 1
-- `add_patches`: Enable/disable Stage 2  
-- `whittle_patches`: Enable/disable Stage 3
-
-## Performance Considerations
-
-- Boundary matrix calculation can be slow for large datasets
-- Consider using simpler geometries or pre-computed adjacency matrices for very large problems
-- The algorithm scales roughly O(n²) with the number of planning units
-
 ## Citation
 
 If you use this package, please cite both the original paper and this implementation:
@@ -120,7 +110,8 @@ Smith, R.J., Di Minin, E., Linke, S., Segan, D.B., Possingham, H.P. (2010).
 An approach for ensuring minimum protected area size in systematic conservation planning. 
 Biological Conservation, 143(10), 2525-2531.
 
-[Your citation for this R package]
+Everett J.D., Richardson A.J., Smith R.J. (2025). _minpatch: Post-Processing for Conservation Planning Solutions to Ensure Minimum Patch
+  Sizes_. R package version 0.1.0, <https://github.com/SpatialPlanning/minpatch>.
 ```
 
 ## License

README.md

@@ -8,14 +8,21 @@
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![Windows](https://github.com/SpatialPlanning/minpatch/actions/workflows/Windows.yaml/badge.svg)](https://github.com/SpatialPlanning/minpatch/actions/workflows/Windows.yaml)
-[![Linux](https://github.com/SpatialPlanning/minpatch/actions/workflows/Linux.yaml/badge.svg)](https://github.com/SpatialPlanning/minpatch/actions/workflows/Linux.yaml)
+[![Ubuntu](https://github.com/SpatialPlanning/minpatch/actions/workflows/Ubuntu.yaml/badge.svg)](https://github.com/SpatialPlanning/minpatch/actions/workflows/Ubuntu.yaml)
 [![MacOS](https://github.com/SpatialPlanning/minpatch/actions/workflows/MacOS.yaml/badge.svg)](https://github.com/SpatialPlanning/minpatch/actions/workflows/MacOS.yaml)
 [![issues -
 zoomss](https://img.shields.io/github/issues/SpatialPlanning/minpatch)](https://github.com/SpatialPlanning/minpatch/issues)
 [![Codecov test
 coverage](https://codecov.io/gh/SpatialPlanning/minpatch/graph/badge.svg)](https://app.codecov.io/gh/SpatialPlanning/minpatch)
 <!-- badges: end -->
 
+\*\* Note: This is still a work in progress and significant bugs may be
+present. Use with caution \*\*
+
+More information on the original implemention of MinPatch for Marxan and
+QGIS is available here:
+<https://cluz-systematic-conservation-planning.github.io>
+
 ## Overview
 
 An R implementation of the MinPatch algorithm for post-processing
@@ -56,7 +63,7 @@ through three stages:
 
 ``` r
 # Install from GitHub
-devtools::install_github("SpatialPlanning/minpatch")
+pak::pak("SpatialPlanning/minpatch")
 ```
 
 ## Key Features
@@ -105,23 +112,6 @@ Removes unnecessary planning units through an iterative process:
     - Must not increase total cost (if boundary penalty \> 0)
     - Must not split patches into non-viable pieces
 
-## Parameters
-
-- `min_patch_size`: Minimum area threshold for patches
-- `patch_radius`: Radius for adding new patches (allows elongated
-  shapes)
-- `boundary_penalty`: Boundary penalty value for cost calculations
-- `remove_small_patches`: Enable/disable Stage 1
-- `add_patches`: Enable/disable Stage 2  
-- `whittle_patches`: Enable/disable Stage 3
-
-## Performance Considerations
-
-- Boundary matrix calculation can be slow for large datasets
-- Consider using simpler geometries or pre-computed adjacency matrices
-  for very large problems
-- The algorithm scales roughly O(n²) with the number of planning units
-
 ## Citation
 
 If you use this package, please cite both the original paper and this
@@ -131,7 +121,8 @@ implementation:
     An approach for ensuring minimum protected area size in systematic conservation planning. 
     Biological Conservation, 143(10), 2525-2531.
 
-    [Your citation for this R package]
+    Everett J.D., Richardson A.J., Smith R.J. (2025). _minpatch: Post-Processing for Conservation Planning Solutions to Ensure Minimum Patch
+      Sizes_. R package version 0.1.0, <https://github.com/SpatialPlanning/minpatch>.
 
 ## License