Merge pull request #193 from remlapmot/devel

Add medflex R package to v2 image and 2 other minor updates

Author: bloodearnest

.github/workflows/main.yaml

@@ -13,7 +13,7 @@ jobs:
     outputs:
       versions: ${{ steps.versions.outputs.versions }}
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Set matrix
         id: versions
         run: |
@@ -35,7 +35,7 @@ jobs:
 
     steps:
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - uses: "opensafely-core/setup-action@v1"
       with:
           install-just: true

v2/env

@@ -1,6 +1,6 @@
 MAJOR_VERSION=v2
 BASE=22.04
 RSTUDIO_BASE_URL=https://download2.rstudio.org/server/jammy/amd64/
-RSTUDIO_DEB=rstudio-server-2025.09.0-387-amd64.deb
+RSTUDIO_DEB=rstudio-server-2026.01.0-392-amd64.deb
 CRAN_DATE=2025-03-05
 REPOS=https://packagemanager.posit.co/cran/__linux__/jammy/${CRAN_DATE}

v2/packages.md

@@ -283,6 +283,7 @@ tcltk, tools, and utils) for the respective version of R.
 | matrixStats           | 1.5.0         | <https://cran.r-project.org/package=matrixStats>           |
 | maxstat               | 0.7-25        | <https://cran.r-project.org/package=maxstat>               |
 | mclust                | 6.1.1         | <https://cran.r-project.org/package=mclust>                |
+| medflex               | 0.6-10        | <https://cran.r-project.org/package=medflex>               |
 | memoise               | 2.0.1         | <https://cran.r-project.org/package=memoise>               |
 | metadat               | 1.4-0         | <https://cran.r-project.org/package=metadat>               |
 | metafor               | 4.8-0         | <https://cran.r-project.org/package=metafor>               |

v2/packages.toml

@@ -206,3 +206,7 @@ comment = "Requested by Will. This is a soft (Suggests list) dependency of gtsum
 [marginaleffects]
 packages = "marginaleffects"
 comment = "Requested by Will. This is a package to compute and plot marginal effects for fitted statistical models."
+
+[mediation-package]
+packages = "medflex"
+comment = "Requested by Ruth Costello. This is a package to for flexible mediation analysis using natural effect models"