DuckDB implementation

.Rbuildignore

@@ -16,3 +16,7 @@
 ^CRAN-SUBMISSION$
 ^revdep$
 ^vignettes/articles$
+^vignettes/\.quarto$
+^vignettes/*_files$
+^vignettes/articles/\.quarto$
+^vignettes/articles/*_files$

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

@@ -2,9 +2,10 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
+  workflow_dispatch:
 
 name: R-CMD-check
 
@@ -31,7 +32,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pkgdown.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -24,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -43,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/test-coverage-local.yaml

@@ -3,9 +3,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches: [main, master, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: test-coverage-local
 
@@ -16,7 +16,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -28,7 +28,7 @@ jobs:
           needs: coverage
 
       - name: Cache C++ and R dependencies
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: |
             ~/.cache/R
@@ -53,7 +53,7 @@ jobs:
           echo "coverage=$COV" >> $GITHUB_OUTPUT
 
       - name: Checkout gh-pages
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: gh-pages
 
@@ -102,6 +102,6 @@ jobs:
       # Can't find 'action.yml', 'action.yaml' or 'Dockerfile' under '/home/runner/work/coverage-badge-action/coverage-badge-action/action.yml'.
       # Did you forget to run actions/checkout before running your local action?
       - name: Checkout Back
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           ref: ${{ github.ref }}

.gitignore

@@ -71,3 +71,4 @@ docs
 data/geo_tox_data_manuscript.RData
 
 README.html
+**/.quarto/

DESCRIPTION

@@ -1,54 +1,59 @@
 Package: GeoTox
 Title: Spatiotemporal Mixture Risk Assessment
-Version: 0.3.0.9000
+Version: 1.0.0
 Authors@R: c(
-    person("Skylar", "Marvel", , "skylar.marvel@nih.gov", role = c("aut"),
+    person("Skylar", "Marvel", , "skylar.marvel@nih.gov", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-2971-9743")),
-    person("David", "Reif", , "david.reif@nih.gov", role = c("aut"),
+    person("David", "Reif", , "david.reif@nih.gov", role = "aut",
            comment = c(ORCID = "0000-0001-7815-6767")),
-    person("Kyle", "Messier", , "kyle.messier@nih.gov", role = c("cre", "aut"),
+    person("Kyle", "Messier", , "kyle.messier@nih.gov", role = "aut",
            comment = c(ORCID = "0000-0001-9508-9623")),
-    person("Spatiotemporal Exposures and Toxicology Group", role = c("cph"))
+    person("Spatiotemporal Exposures and Toxicology Group", role = "cph")
   )
 Description: Connecting spatiotemporal exposure to individual and
-    population-level risk via source-to-outcome continuum modeling. The package,
-    methods, and case-studies are described in Messier, Reif, and Marvel (2025)
-    <doi:10.1186/s40246-024-00711-8> and Eccles et al. (2023)
-    <doi:10.1016/j.scitotenv.2022.158905>.
+    population-level risk via source-to-outcome continuum modeling. The
+    package, methods, and case-studies are described in Messier, Reif, and
+    Marvel (2025) <doi:10.1186/s40246-024-00711-8> and Eccles et al.
+    (2023) <doi:10.1016/j.scitotenv.2022.158905>.
 License: MIT + file LICENSE
 URL: https://niehs.github.io/GeoTox/, https://github.com/NIEHS/GeoTox
+BugReports: https://github.com/NIEHS/GeoTox/issues
 Depends: 
     R (>= 4.4.0)
 Imports: 
+    DBI,
+    dbplyr,
     dplyr,
-    ggplot2,
-    ggridges,
+    duckdb,
+    duckplyr,
     purrr,
     rlang,
-    sf,
-    stats,
-    stringr,
     tibble,
     tidyr,
     tidyselect,
-    truncnorm,
-    utils
+    truncnorm
 Suggests: 
-    ggpubr,
+    blob,
+    ggplot2,
+    ggridges,
     httk,
     httr2,
     knitr,
+    quarto,
     readr,
     readxl,
     rmarkdown,
-    scales,
-    testthat (>= 3.0.0)
+    sf,
+    stringr,
+    testthat (>= 3.0.0),
+    withr,
+    zip
 VignetteBuilder: 
-    knitr
+    knitr,
+    quarto
+Config/Needs/website: rmarkdown, quarto
+Config/roxygen2/version: 8.0.0
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
-BugReports: https://github.com/NIEHS/GeoTox/issues
-Config/Needs/website: rmarkdown

NAMESPACE

@@ -1,37 +1,35 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(plot,GeoTox)
 S3method(print,GeoTox)
 export(GeoTox)
-export(calc_concentration_response)
-export(calc_independent_action)
+export(add_age)
+export(add_exposure)
+export(add_exposure_rate_params)
+export(add_hill_params)
+export(add_obesity)
 export(calc_internal_dose)
 export(calc_invitro_concentration)
-export(calculate_response)
-export(compute_sensitivity)
+export(calc_response)
+export(calc_risk)
+export(calc_sensitivity)
 export(fit_hill)
-export(get_fixed_age)
-export(get_fixed_css)
-export(get_fixed_obesity)
-export(get_fixed_other)
-export(get_fixed_params)
-export(hill_conc)
-export(hill_val)
-export(plot_exposure)
-export(plot_hill)
-export(plot_resp)
-export(plot_sensitivity)
-export(resp_quantiles)
-export(sample_Css)
+export(get_assay_table)
+export(get_boundary)
+export(get_con)
+export(get_concentration_mean)
+export(get_risk_quantiles)
+export(get_risk_sensitivity)
+export(get_risk_values)
+export(sample_simulated_css)
 export(sensitivity_analysis)
-export(set_boundaries)
-export(set_hill_params)
-export(set_population)
+export(set_boundary)
+export(set_fixed_css)
+export(set_sample)
+export(set_simulated_css)
 export(simulate_age)
 export(simulate_exposure)
-export(simulate_inhalation_rate)
+export(simulate_exposure_rate)
 export(simulate_obesity)
 export(simulate_population)
 importFrom(rlang,.data)
 importFrom(rlang,.env)
-importFrom(sf,st_as_sf)

NEWS.md

@@ -1,4 +1,12 @@
-# GeoTox (development version)
+# GeoTox 1.0.0
+
+* Reimplementation where data are now stored in a DuckDB database rather than an
+in-memory R object.
+
+* Majority of functions have been redone for the new storage structure.
+
+* Hill curve fits using `fit_hill()` are now bidirectional. Previously only the
+positive direction was fit.
 
 # GeoTox 0.3.0
 

R/GeoTox-package.R

@@ -1,9 +1,13 @@
 #' @keywords internal
 "_PACKAGE"
 
+# Dummy function to avoid R CMD check notes about unused imports from dbplyr.
+ignore_unused_imports <- function() {
+  dbplyr::tbl_lazy
+}
+
 ## usethis namespace: start
 #' @importFrom rlang .data
 #' @importFrom rlang .env
-#' @importFrom sf st_as_sf
 ## usethis namespace: end
 NULL