Merge pull request #153 from shwilks/master

Update to v1.2.5

.Rbuildignore

@@ -1,4 +1,5 @@
 ^.*\.Rproj$
+^.*\.code-workspace$
 ^\.Rproj\.user$
 ^doc$
 ^Meta$
@@ -13,3 +14,7 @@
 ^\.lintr$
 ^tests/testoutput$
 ^builds$
+^CRAN-SUBMISSION$
+^cran-comments\.md$
+^vignettes/figures$
+^vignettes/intro-to-antigenic-cartography\.Rmd$

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

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,30 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -12,24 +14,33 @@ 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 }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - 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

.gitignore

@@ -9,9 +9,12 @@
 *.sublime-workspace
 *.o
 *.o.tmp
-src/.vscode/*
+*.code-workspace
+.vscode*
 doc
 inst/doc
 Meta
 tests/testoutput/*
 docs
+/doc/
+/Meta/

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.2.7
+Date: 2023-09-01 05:06:17 UTC
+SHA: 427a0fcec70ce202358ed9f72e4a207d150cfb85

DESCRIPTION

@@ -1,56 +1,69 @@
 Package: Racmacs
 Type: Package
-Title: R Antigenic Cartography Macros
-Version: 1.1.35
-Date: 2022-02-23
-Author: Sam Wilks
-Maintainer: Sam Wilks <sw463@cam.ac.uk>
-Description: A toolkit for making antigenic maps from assay data such as HI assays.
+Title: Antigenic Cartography Macros
+Version: 1.2.7
+Date: 2023-09-01
+Authors@R: 
+  c(person(given = "Sam",
+           family = "Wilks",
+           role = c("aut", "cre"),
+           email = "sw463@cam.ac.uk"))
+Description: A toolkit for making antigenic maps from immunological assay data,
+    in order to quantify and visualize antigenic differences between different
+    pathogen strains as described in
+    Smith et al. (2004) <doi:10.1126/science.1097211> and used in the World
+    Health Organization influenza vaccine strain selection process. Additional
+    functions allow for the diagnostic evaluation of antigenic maps and an
+    interactive viewer is provided to explore antigenic relationships amongst
+    several strains and incorporate the visualization of associated genetic
+    information.
 Depends: R (>= 4.0)
 Imports: 
     Rcpp,
-    parallel,
     jsonlite,
     ks,
+    brotli,
     shiny,
     shinyFiles,
     shinyjs,
     htmlwidgets,
-    crayon,
-    ggplot2,
+    ggplot2 (>= 3.0.0),
     htmltools,
     rmarchingcubes,
     shape,
     ellipsis,
     MASS,
-    lifecycle,
+    magrittr,
     igraph,
-    brotli
+    dplyr,
+    vctrs,
+    rlang
 LazyData: TRUE
 Suggests: 
     testthat,
+    r3js,
     knitr,
     rmarkdown,
     rstudioapi,
     plotly,
     geometry,
     gdata,
     stringr,
-    r3js,
     tibble,
+    tidyr,
     base64enc,
+    lifecycle,
     MCMCpack
-RoxygenNote: 7.1.2.9000
-Roxygen: list(markdown = TRUE)
 LinkingTo: 
     Rcpp, 
     RcppArmadillo, 
     RcppProgress, 
     RcppEnsmallen, 
     rapidjsonr
-Remotes: 
-    shwilks/r3js
+Encoding: UTF-8
+RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
-URL: https://acorg.github.io/Racmacs, https://github.com/acorg/Racmacs
+URL: https://acorg.github.io/Racmacs/, https://github.com/acorg/Racmacs/
 BugReports: https://github.com/acorg/Racmacs/issues
 License: AGPL-3

NAMESPACE

@@ -1,6 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(drawDetails,acpoint)
+S3method(ggplot,acmap)
 S3method(plot,acmap)
+S3method(postDrawDetails,acpoint)
+S3method(preDrawDetails,acpoint)
 S3method(print,Rac_html_merge_report)
 S3method(print,acmap)
 S3method(view,acmap)
@@ -85,6 +89,7 @@ export(agAnnotations)
 export(agAspect)
 export(agBaseCoords)
 export(agBootstrapBlob)
+export(agBootstrapBlobs)
 export(agBootstrapCoords)
 export(agClades)
 export(agCohesion)
@@ -94,6 +99,7 @@ export(agDates)
 export(agExtra)
 export(agFill)
 export(agGroups)
+export(agHomologousSr)
 export(agIDs)
 export(agLabIDs)
 export(agLeverage)
@@ -112,16 +118,17 @@ export(agShape)
 export(agShown)
 export(agSize)
 export(agStress)
-export(agStressBlobSize)
 export(agStressPerTiter)
 export(agStrings)
-export(agTriangulationBlobSize)
+export(agTriangulationBlob)
+export(agTriangulationBlobs)
 export(allMapDimensions)
 export(allMapStresses)
 export(applyMapTransform)
 export(applyPlotspec)
 export(as.json)
 export(blob)
+export(blobsize)
 export(bootstrapBlobs)
 export(bootstrapMap)
 export(checkHemisphering)
@@ -133,7 +140,6 @@ export(edit_srNames)
 export(export_viewer)
 export(fixedColBases)
 export(getOptimization)
-export(grid.plot.acmap)
 export(htmlAdjustedTiterTable)
 export(htmlMergeReport)
 export(htmlTiterTable)
@@ -143,6 +149,7 @@ export(keepSingleOptimization)
 export(layerNames)
 export(listOptimizations)
 export(logtiterTable)
+export(logtiterTableLayers)
 export(make.acmap)
 export(mapBootstrap_agCoords)
 export(mapBootstrap_srCoords)
@@ -179,9 +186,11 @@ export(plotly_map_table_distance)
 export(procrustesData)
 export(procrustesMap)
 export(ptBaseCoords)
+export(ptBootstrapBlobs)
 export(ptBootstrapCoords)
 export(ptCoords)
 export(ptDrawingOrder)
+export(ptTriangulationBlobs)
 export(randomizeCoords)
 export(read.acmap)
 export(read.titerTable)
@@ -201,12 +210,12 @@ export(save.acmap)
 export(save.coords)
 export(save.titerTable)
 export(setLegend)
-export(snapshotMap)
 export(sortOptimizations)
 export(srAnnotations)
 export(srAspect)
 export(srBaseCoords)
 export(srBootstrapBlob)
+export(srBootstrapBlobs)
 export(srBootstrapCoords)
 export(srClades)
 export(srCohesion)
@@ -233,10 +242,10 @@ export(srShown)
 export(srSize)
 export(srSpecies)
 export(srStress)
-export(srStressBlobSize)
 export(srStressPerTiter)
 export(srStrings)
-export(srTriangulationBlobSize)
+export(srTriangulationBlob)
+export(srTriangulationBlobs)
 export(standardizeStrainNames)
 export(stressBlobs)
 export(stressTable)
@@ -251,5 +260,12 @@ export(triangulationBlobs)
 export(update_ferret_seraNames)
 export(view)
 import(htmlwidgets)
-importFrom(Rcpp,sourceCpp)
+importFrom(Rcpp,`sourceCpp`)
+importFrom(ggplot2,`.data`)
+importFrom(ggplot2,`ggplot`)
+importFrom(grid,`drawDetails`)
+importFrom(grid,`postDrawDetails`)
+importFrom(grid,`preDrawDetails`)
+importFrom(magrittr,`%>%`)
+importFrom(rlang,`.data`)
 useDynLib(Racmacs)