RaredonLab · RaredonLab · Apr 5, 2026 · Apr 5, 2026 · RaredonLab · RaredonLab
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,9 @@
+^spatial-modeling-with-claude$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# R CMD check workflow for TissueField
+# Runs on ubuntu (release + devel), macos, and windows.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# pkgdown site deployment for TissueField
+# Deploys to gh-pages on push to main/master.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ concurrency:
+ group: pkgdown-${{ 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,34 @@
+Package: TissueField
+Title: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+ email = "raredon@yale.edu")
+Description: Computes continuous steady-state molecular concentration fields
+ from discrete mRNA transcript or protein detection coordinates, using a
+ physically motivated diffusion-clearance model. Solves the screened
+ Poisson PDE (D * nabla^2 C - lambda * C + s = 0) via one of three
+ methods: finite-difference sparse linear system, Green's function FFT
+ convolution, or Gaussian kernel density estimation. Designed for use
+ with spatial transcriptomics and spatial proteomics data. Works
+ naturally with tissue masks produced by the TissueMask package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.1.0)
+Imports:
+ sf (>= 1.0-0),
+ Matrix (>= 1.3-0),
+ stats,
+ parallel
+Suggests:
+ ggplot2,
+ patchwork,
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ TissueMask
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+URL: https://github.com/RaredonLab/TissueField
+BugReports: https://github.com/RaredonLab/TissueField/issues
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,13 @@
+# Generated by roxygen2: do not edit by hand
+
+export(estimate_concentration_field)
+export(field_to_df)
+export(plot_concentration_field)
+export(sweep_diffusion_length)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_crs)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,complete.cases)
+importFrom(stats,filter)
diff --git a/R/TissueField-package.R b/R/TissueField-package.R
@@ -0,0 +1,14 @@
+#' TissueField: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+#'
+#' Computes continuous steady-state molecular concentration fields from discrete
+#' mRNA transcript or protein detection coordinates using a physically motivated
+#' diffusion-clearance model. The screened Poisson PDE is solved numerically
+#' using one of three methods: finite-difference sparse linear system (`"fd"`),
+#' Green's function FFT convolution (`"green"`), or Gaussian kernel density
+#' (`"kde"`).
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## Suppress R CMD check NOTE for bare variable names used in ggplot2 aes()
+utils::globalVariables(c("x", "y", "field", ".data"))
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,9 @@
+^spatial-modeling-with-claude$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# R CMD check workflow for TissueField
+# Runs on ubuntu (release + devel), macos, and windows.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# pkgdown site deployment for TissueField
+# Deploys to gh-pages on push to main/master.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ concurrency:
+ group: pkgdown-${{ 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,34 @@
+Package: TissueField
+Title: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+ email = "raredon@yale.edu")
+Description: Computes continuous steady-state molecular concentration fields
+ from discrete mRNA transcript or protein detection coordinates, using a
+ physically motivated diffusion-clearance model. Solves the screened
+ Poisson PDE (D * nabla^2 C - lambda * C + s = 0) via one of three
+ methods: finite-difference sparse linear system, Green's function FFT
+ convolution, or Gaussian kernel density estimation. Designed for use
+ with spatial transcriptomics and spatial proteomics data. Works
+ naturally with tissue masks produced by the TissueMask package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.1.0)
+Imports:
+ sf (>= 1.0-0),
+ Matrix (>= 1.3-0),
+ stats,
+ parallel
+Suggests:
+ ggplot2,
+ patchwork,
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ TissueMask
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+URL: https://github.com/RaredonLab/TissueField
+BugReports: https://github.com/RaredonLab/TissueField/issues
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,13 @@
+# Generated by roxygen2: do not edit by hand
+
+export(estimate_concentration_field)
+export(field_to_df)
+export(plot_concentration_field)
+export(sweep_diffusion_length)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_crs)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,complete.cases)
+importFrom(stats,filter)
diff --git a/R/TissueField-package.R b/R/TissueField-package.R
@@ -0,0 +1,14 @@
+#' TissueField: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+#'
+#' Computes continuous steady-state molecular concentration fields from discrete
+#' mRNA transcript or protein detection coordinates using a physically motivated
+#' diffusion-clearance model. The screened Poisson PDE is solved numerically
+#' using one of three methods: finite-difference sparse linear system (`"fd"`),
+#' Green's function FFT convolution (`"green"`), or Gaussian kernel density
+#' (`"kde"`).
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## Suppress R CMD check NOTE for bare variable names used in ggplot2 aes()
+utils::globalVariables(c("x", "y", "field", ".data"))
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,9 @@
+^spatial-modeling-with-claude$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# R CMD check workflow for TissueField
+# Runs on ubuntu (release + devel), macos, and windows.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# pkgdown site deployment for TissueField
+# Deploys to gh-pages on push to main/master.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ concurrency:
+ group: pkgdown-${{ 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,34 @@
+Package: TissueField
+Title: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+ email = "raredon@yale.edu")
+Description: Computes continuous steady-state molecular concentration fields
+ from discrete mRNA transcript or protein detection coordinates, using a
+ physically motivated diffusion-clearance model. Solves the screened
+ Poisson PDE (D * nabla^2 C - lambda * C + s = 0) via one of three
+ methods: finite-difference sparse linear system, Green's function FFT
+ convolution, or Gaussian kernel density estimation. Designed for use
+ with spatial transcriptomics and spatial proteomics data. Works
+ naturally with tissue masks produced by the TissueMask package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.1.0)
+Imports:
+ sf (>= 1.0-0),
+ Matrix (>= 1.3-0),
+ stats,
+ parallel
+Suggests:
+ ggplot2,
+ patchwork,
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ TissueMask
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+URL: https://github.com/RaredonLab/TissueField
+BugReports: https://github.com/RaredonLab/TissueField/issues
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,13 @@
+# Generated by roxygen2: do not edit by hand
+
+export(estimate_concentration_field)
+export(field_to_df)
+export(plot_concentration_field)
+export(sweep_diffusion_length)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_crs)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,complete.cases)
+importFrom(stats,filter)
diff --git a/R/TissueField-package.R b/R/TissueField-package.R
@@ -0,0 +1,14 @@
+#' TissueField: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+#'
+#' Computes continuous steady-state molecular concentration fields from discrete
+#' mRNA transcript or protein detection coordinates using a physically motivated
+#' diffusion-clearance model. The screened Poisson PDE is solved numerically
+#' using one of three methods: finite-difference sparse linear system (`"fd"`),
+#' Green's function FFT convolution (`"green"`), or Gaussian kernel density
+#' (`"kde"`).
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## Suppress R CMD check NOTE for bare variable names used in ggplot2 aes()
+utils::globalVariables(c("x", "y", "field", ".data"))
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,9 @@
+^spatial-modeling-with-claude$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# R CMD check workflow for TissueField
+# Runs on ubuntu (release + devel), macos, and windows.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# pkgdown site deployment for TissueField
+# Deploys to gh-pages on push to main/master.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ concurrency:
+ group: pkgdown-${{ 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,34 @@
+Package: TissueField
+Title: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+ email = "raredon@yale.edu")
+Description: Computes continuous steady-state molecular concentration fields
+ from discrete mRNA transcript or protein detection coordinates, using a
+ physically motivated diffusion-clearance model. Solves the screened
+ Poisson PDE (D * nabla^2 C - lambda * C + s = 0) via one of three
+ methods: finite-difference sparse linear system, Green's function FFT
+ convolution, or Gaussian kernel density estimation. Designed for use
+ with spatial transcriptomics and spatial proteomics data. Works
+ naturally with tissue masks produced by the TissueMask package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.1.0)
+Imports:
+ sf (>= 1.0-0),
+ Matrix (>= 1.3-0),
+ stats,
+ parallel
+Suggests:
+ ggplot2,
+ patchwork,
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ TissueMask
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+URL: https://github.com/RaredonLab/TissueField
+BugReports: https://github.com/RaredonLab/TissueField/issues
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,13 @@
+# Generated by roxygen2: do not edit by hand
+
+export(estimate_concentration_field)
+export(field_to_df)
+export(plot_concentration_field)
+export(sweep_diffusion_length)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_crs)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,complete.cases)
+importFrom(stats,filter)
diff --git a/R/TissueField-package.R b/R/TissueField-package.R
@@ -0,0 +1,14 @@
+#' TissueField: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+#'
+#' Computes continuous steady-state molecular concentration fields from discrete
+#' mRNA transcript or protein detection coordinates using a physically motivated
+#' diffusion-clearance model. The screened Poisson PDE is solved numerically
+#' using one of three methods: finite-difference sparse linear system (`"fd"`),
+#' Green's function FFT convolution (`"green"`), or Gaussian kernel density
+#' (`"kde"`).
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## Suppress R CMD check NOTE for bare variable names used in ggplot2 aes()
+utils::globalVariables(c("x", "y", "field", ".data"))
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,9 @@
+^spatial-modeling-with-claude$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# R CMD check workflow for TissueField
+# Runs on ubuntu (release + devel), macos, and windows.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# pkgdown site deployment for TissueField
+# Deploys to gh-pages on push to main/master.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ concurrency:
+ group: pkgdown-${{ 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,34 @@
+Package: TissueField
+Title: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+ email = "raredon@yale.edu")
+Description: Computes continuous steady-state molecular concentration fields
+ from discrete mRNA transcript or protein detection coordinates, using a
+ physically motivated diffusion-clearance model. Solves the screened
+ Poisson PDE (D * nabla^2 C - lambda * C + s = 0) via one of three
+ methods: finite-difference sparse linear system, Green's function FFT
+ convolution, or Gaussian kernel density estimation. Designed for use
+ with spatial transcriptomics and spatial proteomics data. Works
+ naturally with tissue masks produced by the TissueMask package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.1.0)
+Imports:
+ sf (>= 1.0-0),
+ Matrix (>= 1.3-0),
+ stats,
+ parallel
+Suggests:
+ ggplot2,
+ patchwork,
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ TissueMask
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+URL: https://github.com/RaredonLab/TissueField
+BugReports: https://github.com/RaredonLab/TissueField/issues
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,13 @@
+# Generated by roxygen2: do not edit by hand
+
+export(estimate_concentration_field)
+export(field_to_df)
+export(plot_concentration_field)
+export(sweep_diffusion_length)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_crs)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,complete.cases)
+importFrom(stats,filter)
diff --git a/R/TissueField-package.R b/R/TissueField-package.R
@@ -0,0 +1,14 @@
+#' TissueField: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+#'
+#' Computes continuous steady-state molecular concentration fields from discrete
+#' mRNA transcript or protein detection coordinates using a physically motivated
+#' diffusion-clearance model. The screened Poisson PDE is solved numerically
+#' using one of three methods: finite-difference sparse linear system (`"fd"`),
+#' Green's function FFT convolution (`"green"`), or Gaussian kernel density
+#' (`"kde"`).
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## Suppress R CMD check NOTE for bare variable names used in ggplot2 aes()
+utils::globalVariables(c("x", "y", "field", ".data"))
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,9 @@
+^spatial-modeling-with-claude$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# R CMD check workflow for TissueField
+# Runs on ubuntu (release + devel), macos, and windows.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# pkgdown site deployment for TissueField
+# Deploys to gh-pages on push to main/master.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ concurrency:
+ group: pkgdown-${{ 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,34 @@
+Package: TissueField
+Title: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+ email = "raredon@yale.edu")
+Description: Computes continuous steady-state molecular concentration fields
+ from discrete mRNA transcript or protein detection coordinates, using a
+ physically motivated diffusion-clearance model. Solves the screened
+ Poisson PDE (D * nabla^2 C - lambda * C + s = 0) via one of three
+ methods: finite-difference sparse linear system, Green's function FFT
+ convolution, or Gaussian kernel density estimation. Designed for use
+ with spatial transcriptomics and spatial proteomics data. Works
+ naturally with tissue masks produced by the TissueMask package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.1.0)
+Imports:
+ sf (>= 1.0-0),
+ Matrix (>= 1.3-0),
+ stats,
+ parallel
+Suggests:
+ ggplot2,
+ patchwork,
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ TissueMask
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+URL: https://github.com/RaredonLab/TissueField
+BugReports: https://github.com/RaredonLab/TissueField/issues
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,13 @@
+# Generated by roxygen2: do not edit by hand
+
+export(estimate_concentration_field)
+export(field_to_df)
+export(plot_concentration_field)
+export(sweep_diffusion_length)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_crs)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,complete.cases)
+importFrom(stats,filter)
diff --git a/R/TissueField-package.R b/R/TissueField-package.R
@@ -0,0 +1,14 @@
+#' TissueField: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+#'
+#' Computes continuous steady-state molecular concentration fields from discrete
+#' mRNA transcript or protein detection coordinates using a physically motivated
+#' diffusion-clearance model. The screened Poisson PDE is solved numerically
+#' using one of three methods: finite-difference sparse linear system (`"fd"`),
+#' Green's function FFT convolution (`"green"`), or Gaussian kernel density
+#' (`"kde"`).
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## Suppress R CMD check NOTE for bare variable names used in ggplot2 aes()
+utils::globalVariables(c("x", "y", "field", ".data"))
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,9 @@
+^spatial-modeling-with-claude$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# R CMD check workflow for TissueField
+# Runs on ubuntu (release + devel), macos, and windows.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# pkgdown site deployment for TissueField
+# Deploys to gh-pages on push to main/master.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ concurrency:
+ group: pkgdown-${{ 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,34 @@
+Package: TissueField
+Title: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+ email = "raredon@yale.edu")
+Description: Computes continuous steady-state molecular concentration fields
+ from discrete mRNA transcript or protein detection coordinates, using a
+ physically motivated diffusion-clearance model. Solves the screened
+ Poisson PDE (D * nabla^2 C - lambda * C + s = 0) via one of three
+ methods: finite-difference sparse linear system, Green's function FFT
+ convolution, or Gaussian kernel density estimation. Designed for use
+ with spatial transcriptomics and spatial proteomics data. Works
+ naturally with tissue masks produced by the TissueMask package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.1.0)
+Imports:
+ sf (>= 1.0-0),
+ Matrix (>= 1.3-0),
+ stats,
+ parallel
+Suggests:
+ ggplot2,
+ patchwork,
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ TissueMask
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+URL: https://github.com/RaredonLab/TissueField
+BugReports: https://github.com/RaredonLab/TissueField/issues
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,13 @@
+# Generated by roxygen2: do not edit by hand
+
+export(estimate_concentration_field)
+export(field_to_df)
+export(plot_concentration_field)
+export(sweep_diffusion_length)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_crs)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,complete.cases)
+importFrom(stats,filter)
diff --git a/R/TissueField-package.R b/R/TissueField-package.R
@@ -0,0 +1,14 @@
+#' TissueField: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+#'
+#' Computes continuous steady-state molecular concentration fields from discrete
+#' mRNA transcript or protein detection coordinates using a physically motivated
+#' diffusion-clearance model. The screened Poisson PDE is solved numerically
+#' using one of three methods: finite-difference sparse linear system (`"fd"`),
+#' Green's function FFT convolution (`"green"`), or Gaussian kernel density
+#' (`"kde"`).
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## Suppress R CMD check NOTE for bare variable names used in ggplot2 aes()
+utils::globalVariables(c("x", "y", "field", ".data"))
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -0,0 +1,9 @@
+^spatial-modeling-with-claude$
+^_pkgdown\.yml$
+^pkgdown$
+^docs$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# R CMD check workflow for TissueField
+# Runs on ubuntu (release + devel), macos, and windows.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+ R-CMD-check:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: ubuntu-latest, r: 'release'}
+ - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
+ - {os: macos-latest, r: 'release'}
+ - {os: windows-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,48 @@
+# pkgdown site deployment for TissueField
+# Deploys to gh-pages on push to main/master.
+
+on:
+ push:
+ branches: [main, master]
+ pull_request:
+ branches: [main, master]
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ concurrency:
+ group: pkgdown-${{ 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -0,0 +1,34 @@
+Package: TissueField
+Title: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+Version: 0.1.0
+Authors@R: person("Raredon Laboratory", role = c("aut", "cre"),
+ email = "raredon@yale.edu")
+Description: Computes continuous steady-state molecular concentration fields
+ from discrete mRNA transcript or protein detection coordinates, using a
+ physically motivated diffusion-clearance model. Solves the screened
+ Poisson PDE (D * nabla^2 C - lambda * C + s = 0) via one of three
+ methods: finite-difference sparse linear system, Green's function FFT
+ convolution, or Gaussian kernel density estimation. Designed for use
+ with spatial transcriptomics and spatial proteomics data. Works
+ naturally with tissue masks produced by the TissueMask package.
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.3
+Depends: R (>= 4.1.0)
+Imports:
+ sf (>= 1.0-0),
+ Matrix (>= 1.3-0),
+ stats,
+ parallel
+Suggests:
+ ggplot2,
+ patchwork,
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ TissueMask
+Config/testthat/edition: 3
+VignetteBuilder: knitr
+URL: https://github.com/RaredonLab/TissueField
+BugReports: https://github.com/RaredonLab/TissueField/issues
diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,2 @@
-MIT License
-
-Copyright (c) 2026 Raredon Lab
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2026
+COPYRIGHT HOLDER: Raredon Laboratory
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2026 Raredon Laboratory
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/NAMESPACE b/NAMESPACE
@@ -0,0 +1,13 @@
+# Generated by roxygen2: do not edit by hand
+
+export(estimate_concentration_field)
+export(field_to_df)
+export(plot_concentration_field)
+export(sweep_diffusion_length)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_bbox)
+importFrom(sf,st_crs)
+importFrom(sf,st_union)
+importFrom(sf,st_within)
+importFrom(stats,complete.cases)
+importFrom(stats,filter)
diff --git a/R/TissueField-package.R b/R/TissueField-package.R
@@ -0,0 +1,14 @@
+#' TissueField: Steady-State Molecular Concentration Fields for Spatial Transcriptomics
+#'
+#' Computes continuous steady-state molecular concentration fields from discrete
+#' mRNA transcript or protein detection coordinates using a physically motivated
+#' diffusion-clearance model. The screened Poisson PDE is solved numerically
+#' using one of three methods: finite-difference sparse linear system (`"fd"`),
+#' Green's function FFT convolution (`"green"`), or Gaussian kernel density
+#' (`"kde"`).
+#'
+#' @keywords internal
+"_PACKAGE"
+
+## Suppress R CMD check NOTE for bare variable names used in ggplot2 aes()
+utils::globalVariables(c("x", "y", "field", ".data"))