Merge branch:main into branch:dev_atkinson

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

@@ -1,10 +1,10 @@
-# 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]
+    branches:
+      - main
   pull_request:
-    branches: [main, master]
+    branches:
+     - main
 
 name: R-CMD-check
 
@@ -18,32 +18,85 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
+          # - {os: macOS-latest,   r: 'devel'} # Issue with loading 'units' dependency
+          - {os: macOS-latest,   r: 'release'}
+          - {os: macOS-latest,   r: 'oldrel'}
+          - {os: windows-latest, r: 'devel'}
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: windows-latest, r: 'oldrel'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel'}
 
     env:
+      R_KEEP_PKG_SOURCE: yes      
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/checkout@v4
 
       - 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-pandoc@v2
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: "[Custom block] [MacOS] Install spatial libraries"
+        if: runner.os == 'macOS'
+        run: brew install udunits gdal proj geos
+
+      - name: "[Custom block] [Linux] Install spatial libraries"
+        if: runner.os == 'Linux'
+        run: sudo apt-get install libudunits2-dev libgdal-dev libproj-dev libgeos-dev
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v3
         with:
-          extra-packages: any::rcmdcheck
-          needs: check
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, build = FALSE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      # - name: "[Custom block] [MacOS] Install units with configuration"
+      #   if: runner.os == 'macOS'
+      #   run: |
+      #     install.packages('udunits2', type = 'source', configure.args = '--with-udunits2-lib=/usr/local/udunits2')
+      #     install.packages('units', type = 'source', configure.args = '--with-udunits2-lib=/usr/local/udunits2')
+      #   shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
 
-      - uses: r-lib/actions/check-r-package@v2
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
         with:
-          upload-snapshots: true
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ndi
 Title: Neighborhood Deprivation Indices
-Version: 0.1.4.9001
-Date: 2023-01-18
+Version: 0.1.6.9002
+Date: 2024-08-22
 Authors@R:
     c(person(given = "Ian D.",
              family = "Buller",
@@ -21,28 +21,43 @@ Description: Computes various metrics of socio-economic deprivation and disparit
              and (2) based on Andrews et al. (2020) <doi:10.1080/17445647.2020.1750066> 
              and Slotman et al. (2022) <doi:10.1016/j.dib.2022.108002>
              who use variables chosen by Roux and Mair (2010)
-             <doi:10.1111/j.1749-6632.2009.05333.x>. Both are a decomposition
-             of multiple demographic characteristics from the U.S. Census Bureau
-             American Community Survey 5-year estimates (ACS-5; 2006-2010 onward). Using data
-             from the ACS-5 (2005-2009 onward), the package can also (1) compute the spatial
-             Racial Isolation Index (RI) based on Anthopolos et al. (2011)
-             <doi:10.1016/j.sste.2011.06.002>, (2) compute the spatial Educational Isolation
-             Index (EI) based on Bravo et al. (2021) <doi:10.3390/ijerph18179384>, 
-             (3) compute the aspatial Index of Concentration at the Extremes (ICE) based on 
-             Feldman et al. (2015) <doi:10.1136/jech-2015-205728> and Krieger et al. 
-             (2016) <doi:10.2105/AJPH.2015.302955>, (4) compute the aspatial racial/ethnic
-             Dissimilarity Index based on Duncan & Duncan (1955) <doi:10.2307/2088328>, (5)
-             compute the aspatial Atkinson Index based on Atkinson (1970) 
-             <doi:10.1016/0022-0531(70)90039-6>, and (6) retrieve the aspatial Gini Index 
-             based on Gini (1921) <doi:10.2307/2223319>.
+             <doi:10.1111/j.1749-6632.2009.05333.x>. Both are a decomposition of multiple
+             demographic characteristics from the U.S. Census Bureau American Community 
+             Survey 5-year estimates (ACS-5; 2006-2010 onward). Using data from the ACS-5
+             (2005-2009 onward), the package can also (1) compute the spatial Racial Isolation
+             Index (RI) based on Anthopolos et al. (2011) <doi:10.1016/j.sste.2011.06.002>,
+             (2) compute the spatial Educational Isolation Index (EI) based on Bravo et al.
+             (2021) <doi:10.3390/ijerph18179384>, (3) compute the aspatial Index of 
+             Concentration at the Extremes (ICE) based on Feldman et al. (2015) 
+             <doi:10.1136/jech-2015-205728> and Krieger et al. (2016) 
+             <doi:10.2105/AJPH.2015.302955>, (4) compute the aspatial racial/ethnic 
+             Dissimilarity Index (D) based on Duncan & Duncan (1955) <doi:10.2307/2088328>, (5)
+             compute the aspatial income or racial/ethnic Atkinson Index (A) based on Atkinson 
+             (1970) <doi:10.1016/0022-0531(70)90039-6>, (6) aspatial racial/ethnic Interaction
+             Index (xPy*) based on Shevky & Williams (1949; ISBN-13:978-0-837-15637-8) and Bell
+             (1954) <doi:10.2307/2574118>, (7) aspatial racial/ethnic Correlation Ratio (V)
+             based on Bell (1954) <doi:10.2307/2574118> and White (1986) <doi:10.2307/3644339>,
+             (8) aspatial racial/ethnic Location Quotient (LQ) based on Merton (1939) 
+             <doi:10.2307/2084686> and Sudano et al. (2013) 
+             <doi:10.1016/j.healthplace.2012.09.015>, (9) aspatial racial/ethnic Local
+             Exposure and Isolation (LEx/Is) metric based on Bemanian & Beyer (2017) 
+             <doi:10.1158/1055-9965.EPI-16-0926>, (10) aspatial racial/ethnic Delta (DEL) 
+             based on Hoover (1941) <doi:10.1017/S0022050700052980> and Duncan et al. (1961; 
+             LC:60007089), (11) an index of spatial proximity (SP) based on White (1986)
+             <doi:10.2307/3644339> and Blau (1977; ISBN-13:978-0-029-03660-0), and (12) the 
+             aspatial racial/ethnic Isolatoin Index (xPx*) based on Lieberson (1981; 
+             ISBN-13:978-1-032-53884-6) and Bell (1954) <doi:10.2307/2574118>. Also using data
+             from the ACS-5 (2005-2009 onward), the package can retrieve the aspatial Gini 
+             Index (G) based Gini (1921) <doi:10.2307/2223319>.
 License: Apache License (>= 2.0)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 3.5.0)
 Imports: 
+    car,
     dplyr,
     MASS,
     Matrix,
@@ -52,11 +67,13 @@ Imports:
     stringr,
     tidycensus,
     tidyr,
+    tigris,
+    units,
     utils
-Suggests: 
+Suggests:
+    DescTools,
     ggplot2,
     testthat,
-    tigris,
     R.rsp,
     spelling, 
     usethis

LICENSE.md

@@ -169,7 +169,7 @@ accepting any such warranty or additional liability.
 
 _END OF TERMS AND CONDITIONS_
 
-    Copyright 2022 Ian D. Buller; NCI
+    Copyright 2024 Ian D. Buller; NCI
 
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.

NAMESPACE

@@ -2,20 +2,31 @@
 
 export(anthopolos)
 export(atkinson)
+export(bell)
+export(bemanian_beyer)
 export(bravo)
 export(duncan)
 export(gini)
+export(hoover)
 export(krieger)
+export(lieberson)
 export(messer)
 export(powell_wiley)
+export(sudano)
+export(white)
+export(white_blau)
 import(dplyr)
 importFrom(MASS,ginv)
 importFrom(Matrix,sparseMatrix)
+importFrom(car,logit)
 importFrom(psych,alpha)
 importFrom(psych,principal)
+importFrom(sf,st_centroid)
+importFrom(sf,st_distance)
 importFrom(sf,st_drop_geometry)
 importFrom(sf,st_geometry)
 importFrom(sf,st_intersects)
+importFrom(sf,st_within)
 importFrom(stats,complete.cases)
 importFrom(stats,cor)
 importFrom(stats,cov2cor)
@@ -30,4 +41,9 @@ importFrom(stringr,str_trim)
 importFrom(tidycensus,get_acs)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,separate)
+importFrom(tigris,combined_statistical_areas)
+importFrom(tigris,core_based_statistical_areas)
+importFrom(tigris,metro_divisions)
+importFrom(units,drop_units)
+importFrom(units,set_units)
 importFrom(utils,stack)