Merge pull request #244 from ices-tools-dev/dev

Fix discovered bugs after 2025 data call is submitted

Author: rix133

.Rbuildignore

@@ -8,9 +8,12 @@
 ^travis.yml$
 ^FishNCo$
 ^\.github$
+^\.vscode$
 ^.DS_Store$
 ^docs$
 ^doc$
 ^Meta$
 package_overview.Rmd
 ^.pptx$
+^_pkgdown\.yml$
+^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

@@ -47,3 +47,11 @@ FishNCo/testData/RegionalTestData/*
 
 /doc/
 /Meta/
+<<<<<<< Updated upstream
+.vscode/
+docs
+=======
+
+# Data to develop fun
+/NLdata/
+>>>>>>> Stashed changes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: RDBEScore
 Type: Package
 Title: Functions for the ICES Regional Database and Estimation System (RDBES)
-Version: 0.3.3
+Version: 0.3.4
 Author: c(
     person(given = "David", 
            family = "Currie", 
@@ -106,8 +106,7 @@ Maintainer: Colin Millar <colin.millar@ices.dk>
 Description: The RDBEScore package provides functions to import and work with  
     fisheries data downloaded from the ICES RDBES database. It also contains 
     functions to perform estimation analysis using the resulting objects. 
-URL: https://github.com/ices-tools-dev/RDBEScore,
-     https://rdbes.ices.dk
+URL: https://github.com/ices-tools-dev/RDBEScore, https://rdbes.ices.dk, https://ices-tools-dev.github.io/RDBEScore/
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 LazyData: true

NEWS.md

@@ -1,3 +1,14 @@
+# RDBEScore 0.3.4
+
+- Defaults: `createRDBESDataObject()`  now runs validation by default
+- Estimation object: added `incDesignVariables` to `createRDBESEstObject()` to optionally drop design variables; convert character columns to factors to reduce size.
+- SA sub-sampling: replaced recursive logic with a self-join + lookup (`prepareSubSampleLevelLookup`), with warnings for missing or non‑unique matches.
+- Memory: added frequent `gc()` calls across estimation/join steps for large data.
+- Joins: improved field selection for hierarchy 7 in `procRDBESEstObjUppHier()`; clarified logic for selecting `VDid` fields.
+- Docs/CI: added pkgdown GitHub Actions workflow; improved function docs (params/returns); updated `.Rbuildignore` and package URLs.
+- Vignettes: updated estimation workflow and sub-sampling sections; added memory tips, minimal examples, and brief benchmarking notes.
+- Performance: `filterRDBESDataObject()` now uses `data.table` for faster filtering.
+
 # RDBEScore 0.3.3 
 
 * Update to work with with the 2025 RDBES data call format

R/createRDBESDataObject.R

@@ -57,7 +57,7 @@
 #' @param verbose (Optional) Set to TRUE if you want informative text printed
 #'  out, or FALSE if you don't.  The default is FALSE.
 #' @param ... parameters passed to validateRDBESDataObject
-#' if input is list of data frames e.g.`strict=FALSE`
+#'  e.g.`strict=FALSE`
 #' @importFrom utils file_test
 #'
 #' @return A RDBESDataObject
@@ -106,7 +106,7 @@ createRDBESDataObject <- function(input = NULL,
 
   if(import.type == "csv") output <- importRDBESDataCSV(rdbesExtractPath = input,
                                                            listOfFileNames = listOfFileNames,
-                                                           castToCorrectDataTypes = castToCorrectDataTypes)
+                                                           castToCorrectDataTypes = castToCorrectDataTypes, ...)
 
 
   if(import.type == "list.of.dfs" || import.type == "list.of.dts") {
@@ -121,5 +121,6 @@ createRDBESDataObject <- function(input = NULL,
     output <- newRDBESDataObject()
   }
 
+
   return(output)
 }