Release v0.1.0: Complete hexsmoothR package with documentation

- Updated LICENSE with custom copyright for Max M. Lang
- Rebuilt package with proper license configuration
- Added comprehensive pkgdown documentation website
- Included favicons and proper branding
- Updated README and package metadata
- Added GitHub Actions workflow for automated documentation
- Complete vignette with examples and usage guide

Author: MaxMLang

.Rbuildignore

@@ -26,3 +26,6 @@ Thumbs.db
 ^Meta$
 ^cran-comments\.md$
 ^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -19,7 +19,6 @@ src/RcppExports.cpp
 src/RcppExports.R
 
 # Documentation build artifacts
-inst/doc/
 vignettes/*.html
 vignettes/*.pdf
 
@@ -80,3 +79,4 @@ output/
 
 # Version control
 /.git/
+docs

DESCRIPTION

@@ -11,7 +11,7 @@ Description: Creates hexagonal grids and applies spatial smoothing to satellite
     Gaussian-weighted spatial smoothing using C++ optimization. The package implements
     a two-step workflow for spatial analysis: (1) extract raster data into hexagonal grids,
     and (2) apply spatial smoothing with customizable neighborhood weights.
-License: MIT + file LICENSE
+License: file LICENSE
 Encoding: UTF-8
 Depends: R (>= 4.0.0)
 LinkingTo: Rcpp
@@ -29,4 +29,4 @@ Suggests:
 VignetteBuilder: knitr
 RoxygenNote: 7.3.2
 SystemRequirements: GDAL (>= 3.0), GEOS (>= 3.8), PROJ (>= 6.0)
- 
+URL: https://maxmlang.github.io/hexsmoothR/

LICENSE

@@ -1,21 +1,12 @@
-MIT License
+Copyright (c) 2024, hexsmoothR Max M. Lang
+All rights reserved.
 
-Copyright (c) 2024 hexsmoothR contributors
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+1.  Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+2.  Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE. 
+3.  Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT of THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 

README.md

@@ -1,7 +1,7 @@
 # hexsmoothR: Hexagonal Grid Smoothing for Satellite Data
 
 <div align="center">
-  <img src="inst/images/hexsmoothR_sticker.png" alt="hexsmoothR hex sticker" width="200">
+  <img src="man/figures/hexsmoothR_sticker.png" alt="hexsmoothR hex sticker" width="200">
 </div>
 
 <!-- badges: start -->
@@ -65,21 +65,20 @@ library(sf)
 library(terra)
 
 # Create hexagonal grid
-hex_grid <- create_grid(study_area, cell_size = 0.01, type = "hexagonal")
+hex_grid <- create_grid(study_area, cell_size = 20000, type = "hexagonal")
 
 # Compute spatial topology
 topology <- compute_topology(hex_grid)
 
 # Extract raster data
 raster_files <- c(ndvi = "path/to/ndvi.tif", elevation = "path/to/elevation.tif")
-extracted_data <- extract_raster_data(raster_files, study_area, cell_size = 10000)
+extracted_data <- extract_raster_data(raster_files, study_area, cell_size = 20000)
 
 # Apply spatial smoothing
 smoothed_results <- smooth_variables(
-  variable_values = list(ndvi = extracted_data$ndvi, elevation = extracted_data$elevation),
-  first_neighbors = topology$first_order_neighbors,
-  second_neighbors = topology$second_order_neighbors,
-  weights = c(1.0, 0.5, 0.25),
+  variable_values = list(ndvi = extracted_data$data$ndvi, elevation = extracted_data$data$elevation),
+  neighbors = topology$neighbors,
+  weights = topology$weights,
   var_names = c("ndvi", "elevation")
 )
 ```
@@ -120,37 +119,39 @@ grid <- st_sf(
 
 ## Output
 
-The result is an `sf` object with:
-- **Raw values**: `{variable}_raw` (extracted raster values)
-- **Neighbor averages**: `{variable}_neighbors_1st` (1st order neighbors), `{variable}_neighbors_2nd` (2nd order neighbors)
-- **Smoothed values**: `{variable}_smoothed_1st` (weighted 1st order), `{variable}_smoothed_all` (weighted all neighbors)
-- **Grid info**: `grid_id`, `grid_index`, `geometry`
-
-Ready for plotting with `ggplot2` or other spatial tools.
+The smoothing results contain:
+- `raw` - Weighted average of center cell and all neighbors
+- `neighbors_1st`, `neighbors_2nd`, etc. - Mean of neighbors at each order
+- `weighted_combined` - Final weighted average (recommended for analysis)
 
 ## Advanced Usage
 
 ### Multiple Variables
 ```r
 raster_files <- c(ndvi = "path/to/ndvi.tif", elevation = "path/to/elevation.tif")
-extracted_data <- extract_raster_data(raster_files, study_area, cell_size = 10000)
+extracted_data <- extract_raster_data(raster_files, study_area, cell_size = 20000)
 
 smoothed_results <- smooth_variables(
-  variable_values = list(ndvi = extracted_data$ndvi, elevation = extracted_data$elevation),
-  first_neighbors = topology$first_order_neighbors,
-  second_neighbors = topology$second_order_neighbors,
-  weights = c(1.0, 0.5, 0.25),
+  variable_values = list(ndvi = extracted_data$data$ndvi, elevation = extracted_data$data$elevation),
+  neighbors = topology$neighbors,
+  weights = topology$weights,
   var_names = c("ndvi", "elevation")
 )
 ```
 
 ### Custom Weights
 ```r
-topology <- compute_topology(hex_grid, sigma = 1000, center_weight = 1.0, first_order_weight = 0.5, second_order_weight = 0.25)
+topology <- compute_topology(hex_grid, neighbor_orders = 3, center_weight = 1.0)
 ```
 
 ## Grid Requirements
 
+hexsmoothR works with any hexagonal grid that follows the required structure. You can use grids created with:
+
+- **Uber H3 grids** from Python, R, or any programming language
+- **Custom hexagonal grids** created with any GIS software
+- **Grids from other packages** (as long as they follow the structure below)
+
 **Required grid structure:**
 ```r
 grid <- st_sf(
@@ -160,10 +161,22 @@ grid <- st_sf(
 )
 ```
 
-**Compatible with:**
-- Uber H3 grids from Python/R
-- Custom hexagonal grids
-- Square grids (for comparison)
+**Example with H3 grids from Python:**
+```python
+import h3
+import geopandas as gpd
+from shapely.geometry import Polygon
+
+# Create H3 hexagons in Python
+h3_hexes = h3.polygon_to_cells(polygon, resolution=8)
+geometries = [Polygon(h3.cell_to_boundary(hex_id)) for hex_id in h3_hexes]
+
+# Convert to GeoDataFrame with required structure
+gdf = gpd.GeoDataFrame({
+    'grid_id': h3_hexes,
+    'grid_index': range(len(h3_hexes))
+}, geometry=geometries, crs='EPSG:4326')
+```
 
 **Tip:** Use projected CRS (UTM) for real-world analysis with cell sizes in meters.
 
@@ -175,12 +188,7 @@ grid <- st_sf(
 
 ## Implementation Details
 
-hexsmoothR uses Rcpp for high-performance spatial smoothing algorithms with automatic fallback to R implementation if needed. The package provides:
-
-- **C++ optimization**: Multi-variable processing in single pass
-- **Memory efficiency**: Contiguous array operations for large datasets
-- **Automatic fallback**: R implementation when C++ is unavailable
-- **Progress reporting**: For long-running operations
+hexsmoothR uses Rcpp for high-performance spatial smoothing algorithms with automatic fallback to R implementation if needed.
 
 ## Dependencies
 
@@ -198,14 +206,6 @@ hexsmoothR uses Rcpp for high-performance spatial smoothing algorithms with auto
 2. **Restart R/RStudio** after installing Rtools
 3. **Verify installation**: Run `Sys.which("make")` - it should return a path, not `""`
 
-**Alternative for Windows users who can't compile:**
-- Use the package on systems with build tools available
-- Consider using RStudio Cloud or similar cloud-based R environments
-- Contact the maintainer for pre-compiled binaries if available
-
-**Windows Diagnostic Tool:**
-Run `source("windows_check.R")` to diagnose your build environment setup.
-
 ## Contributing
 
 1. Fork the repository

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://maxmlang.github.io/hexsmoothR/
+template:
+  bootstrap: 5
+