update the vignette

Merge branch 'main' of https://github.com/haganjam/FW_invert_biomass_allometry into main

# Conflicts:
#	vignettes/InvTraitR_vignette.Rmd

.Rbuildignore

@@ -11,4 +11,4 @@
 .github
 database
 companion_scripts
-cran-comments.md
+cran-comments.md

.devcontainer/Dockerfile

@@ -7,6 +7,7 @@ RUN apt update \
         libgdal-dev \
         libudunits2-dev \
         cmake \
+        pandoc \
     && :
 
 # install dev dependencies

.github/workflows/R-CMD-check.yaml

@@ -44,32 +44,7 @@ jobs:
                     exit 1
               fi
         shell: bash
-      - name: Set RENV_PATHS_ROOT
-        shell: bash
-        run: |
-          echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV
-      - name: Install and activate renv
-        run: |
-          install.packages("renv")
-          renv::activate()
-        shell: Rscript {0}
-      - name: Get R and OS version
-        id: get-version
-        run: |
-          cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "")
-          cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "")
-        shell: Rscript {0}
-      - name: Restore Renv package cache
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }}
-          restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-
-      - name: Restore packages
-        shell: Rscript {0}
-        run: |
-          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
-          renv::restore()
+      - uses: r-lib/actions/setup-renv@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

.github/workflows/test-coverage.yaml

@@ -21,32 +21,7 @@ jobs:
       - name: Install OS packages
         run:   |
           sudo apt install -y libgdal-dev libudunits2-dev
-      - name: Set RENV_PATHS_ROOT
-        shell: bash
-        run: |
-          echo "RENV_PATHS_ROOT=${{ runner.temp }}/renv" >> $GITHUB_ENV
-      - name: Install and activate renv
-        run: |
-          install.packages("renv")
-          renv::activate()
-        shell: Rscript {0}
-      - name: Get R and OS version
-        id: get-version
-        run: |
-          cat("##[set-output name=os-version;]", sessionInfo()$running, "\n", sep = "")
-          cat("##[set-output name=r-version;]", R.Version()$version.string, sep = "")
-        shell: Rscript {0}
-      - name: Restore Renv package cache
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ inputs.cache-version }}-${{ hashFiles('renv.lock') }}
-          restore-keys: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{inputs.cache-version }}-
-      - name: Restore packages
-        shell: Rscript {0}
-        run: |
-          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
-          renv::restore()
+      - uses: r-lib/actions/setup-renv@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::covr

.gitignore

@@ -43,3 +43,4 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+inst/doc

DESCRIPTION

@@ -30,5 +30,8 @@ Imports:
     rappdirs,
     doParallel
 Suggests: 
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+VignetteBuilder: knitr

NEWS.md

@@ -1,3 +1,3 @@
-# InvertR 
+# InvTraitR (0.0.0.1)
 
 * Added a `NEWS.md` file to track changes to the package.

cran-comments.md

@@ -1,7 +1,7 @@
 ## R CMD check results
 
 * Namespace in Imports field not imported from: ‘doParallel’
-* * Some package seems to depend on it without declaring it; tests fail without having it installed
+* * bdc 1.1.4 depends on it without declaring it; tests fail without having it installed - fix will come with 1.1.5
 * Regarding `no visible binding for global varible X` for column names:
 * * Should we really just define a local variable with the same name to silence the linter?
 That seems odd.

renv.lock

@@ -1295,13 +1295,11 @@
     },
     "renv": {
       "Package": "renv",
-      "Version": "0.17.3",
-      "Source": "Repository",
+      "Version": "1.0.0",
+      "OS_type": null,
+      "NeedsCompilation": "no",
       "Repository": "CRAN",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "4543b8cd233ae25c6aba8548be9e747e"
+      "Source": "Repository"
     },
     "rgbif": {
       "Package": "rgbif",