Merge pull request #11 from egouldo/pkgdown-edits

setup pkgdown:: usethis gh actions workflow

.Rbuildignore

@@ -8,3 +8,4 @@ _targets.R
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+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@v3
+
+      - 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@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -68,5 +68,6 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-URL: https://github.com/egouldo/ManyEcoEvo
+URL: https://github.com/egouldo/ManyEcoEvo,
+    https://egouldo.github.io/ManyEcoEvo/
 BugReports: https://github.com/egouldo/ManyEcoEvo/issues

_pkgdown.yml

@@ -1,82 +1,82 @@
-url: ~
+url: https://egouldo.github.io/ManyEcoEvo/
 template:
   bootstrap: 5
 reference:
-- title: "Unprocessed data cleaning and checking"
-  desc: "Functions for cleaning and QA checking unprocessed analyst data"
-- subtitle: "Miscellaneous cleaning functions"
+- title: Unprocessed data cleaning and checking
+  desc: Functions for cleaning and QA checking unprocessed analyst data
+- subtitle: Miscellaneous cleaning functions
   contents:
-    - rm_inf_na
-    - anonymise_teams
-    - clean_response_transformation
-    - assign_transformation_type
-- subtitle: "Working with analyst-provided out-of-sample predictions"
-  desc:
+  - rm_inf_na
+  - anonymise_teams
+  - clean_response_transformation
+  - assign_transformation_type
+- subtitle: Working with analyst-provided out-of-sample predictions
+  desc: ~
   contents:
-    - augment_prediction_data
-    - preprocess_prediction_files
-    - preprocess_updated_prediction_files
-    - read_submission_data
-    - starts_with("validate_predictions")
-- title: "Data Processing for Meta-analysis and Modelling"
-  desc: "Calculating and standardising variables for analysis"
+  - augment_prediction_data
+  - preprocess_prediction_files
+  - preprocess_updated_prediction_files
+  - read_submission_data
+  - starts_with("validate_predictions")
+- title: Data Processing for Meta-analysis and Modelling
+  desc: Calculating and standardising variables for analysis
   contents:
-    - est_to_zr
-    - Z_VZ_preds
-    - pred_to_Z
-    - apply_VZ_exclusions
-    - box_cox_transform
-    - log_transform
-    - calculate_deviation_score
-    - calculate_sorensen_diversity_index
-    - apply_sorensen_calc
-    - conversion
-    - conversion_2
-    - convert_predictions
-    - ends_with("_back")
-    - back_transform_response_vars_yi
-    - starts_with("exclude_")
-    - starts_with("subset_fns")
-    - standardise_response
-- title: "Process and create datasets for analysis"
-  desc: "Functions for creating datasets ready for meta-analysis or other analyses"
+  - est_to_zr
+  - Z_VZ_preds
+  - pred_to_Z
+  - apply_VZ_exclusions
+  - box_cox_transform
+  - log_transform
+  - calculate_deviation_score
+  - calculate_sorensen_diversity_index
+  - apply_sorensen_calc
+  - conversion
+  - conversion_2
+  - convert_predictions
+  - ends_with("_back")
+  - back_transform_response_vars_yi
+  - starts_with("exclude_")
+  - starts_with("subset_fns")
+  - standardise_response
+- title: Process and create datasets for analysis
+  desc: Functions for creating datasets ready for meta-analysis or other analyses
   contents:
-    - make_param_table
-    - compute_MA_inputs
-    - compute_metaanalysis_inputs
-    - get_diversity_data
-    - starts_with("prepare_")
-- title: "Model Fitting & Meta-analysis"
-  desc: "Functions for fitting meta-analysis and other models described ion *Gould et al. (2023)*"
+  - make_param_table
+  - compute_MA_inputs
+  - compute_metaanalysis_inputs
+  - get_diversity_data
+  - starts_with("prepare_")
+- title: Model Fitting & Meta-analysis
+  desc: Functions for fitting meta-analysis and other models described ion *Gould
+    et al. (2023)*
+  contents: starts_with("fit_")
+- title: Extracting Analysis Outputs & Visualisation
+  desc: Functions for extracting model outputs, and visualising analysis results
   contents:
-    - starts_with("fit_")
-- title: "Extracting Analysis Outputs & Visualisation"
-  desc: "Functions for extracting model outputs, and visualising analysis results"
-  contents:
-    - gg_forest
-    - starts_with("plot_")
-    - i2_ml
-    - calc_I2_ml
-    - apportion_heterogeneity_ml
-    - compare_ml_MA
-    - get_MA_fit_stats
-    - run_model_checks
-- title: "Scaling Up: Working with data subsets or multiple datasets"
-  desc: >
+  - gg_forest
+  - starts_with("plot_")
+  - i2_ml
+  - calc_I2_ml
+  - apportion_heterogeneity_ml
+  - compare_ml_MA
+  - get_MA_fit_stats
+  - run_model_checks
+- title: 'Scaling Up: Working with data subsets or multiple datasets'
+  desc: |
     Functions for working with multiple datasets or data subsets within a tidyverse list-column framework.
-- subtitle: "Wrapper Functions"
-  desc: ""
+- subtitle: Wrapper Functions
+  desc: ''
   contents:
-    - compute_metaanalysis_inputs
-    - meta_analyse_datasets
-    - make_viz
-- subtitle: "Generate data subsets of full ManyEcoEvo or ManyAnalyst dataset"
-  desc: ""
+  - compute_metaanalysis_inputs
+  - meta_analyse_datasets
+  - make_viz
+- subtitle: Generate data subsets of full ManyEcoEvo or ManyAnalyst dataset
+  desc: ''
+  contents: starts_with("generate_")
+- title: Utility Functions
+  desc: Miscelaneous utility functions
   contents:
-    - starts_with("generate_")
-- title: "Utility Functions"
-  desc: "Miscelaneous utility functions"
-  contents: 
-    - capwords
-    - hex_key
-    - named_group_split
+  - capwords
+  - hex_key
+  - named_group_split
+