🔀 Merge branch:dev_pw into branch:main

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ndi
 Title: Neighborhood Deprivation Indices
-Version: 0.1.6.9015
-Date: 2025-05-30
+Version: 0.2.0
+Date: 2025-08-29
 Authors@R:
     c(person(given = "Ian D.",
              family = "Buller",
@@ -38,6 +38,7 @@ Depends:
 Imports: 
     car,
     dplyr,
+    Hmisc,
     MASS,
     Matrix,
     psych,

NAMESPACE

@@ -26,6 +26,7 @@ export(theil)
 export(white)
 export(white_blau)
 import(dplyr)
+importFrom(Hmisc,wtd.quantile)
 importFrom(MASS,ginv)
 importFrom(Matrix,sparseMatrix)
 importFrom(car,logit)

NEWS.md

@@ -1,6 +1,6 @@
 # ndi (development version)
 
-## ndi v0.1.6.9015
+## ndi v0.2.0
 
 ### New Features
 
@@ -31,7 +31,8 @@
 ### Updates
 
 #### Bug Fixes
-* Fixed NOTE in CRAN checks to provide package anchors for Rd \link{} targets not in the package itself and the base packages  within 'ndi-package.Rd'
+* Fixed NOTE in CRAN checks to provide package anchors for Rd `\link{}` targets not in the package itself and the base packages  within 'ndi-package.Rd'
+* Updated population-weighted quantile method from `stats::quantile` to `Hmisc::wtd.quantile` in `powell_wiley()` thanks to a contribution (#32) by [Hunter Miller](https://github.com/huntermills707)
 * `bell()` function computes the Interaction Index (Bell) not the Isolation Index as previously documented. Updated documentation throughout.
 * Fixed bug in `bell()`, `bemanian_beyer()`, `duncan()`, `sudano()`, and `white()` functions when a smaller geography contains n=0 total population, will assign a value of zero (0) in the internal calculation instead of NA
 * Fixed bug in `atkinson()` function to properly compute the income Atkinson Index
@@ -40,7 +41,7 @@
 * Output of racial or ethnic residential segregation indices is now rounded to four significant digits
 
 #### New Dependencies
-* `tigris` and `units` are now Imports
+* `Hmisc`, `tigris`, and `units` are now Imports
 
 #### Updated Documentation
 * Split up vignette into three separate vignettes: 'ndi1', 'ndi2', and 'ndi3' for the *NDI*, racial or ethnic residential segregation, and additional socioeconomic disparity indices, respectively

R/ndi-package.R

@@ -83,17 +83,18 @@
 #' @name ndi-package
 #' @aliases ndi-package ndi
 #' 
-#' @section Dependencies: The 'ndi' package relies heavily upon \code{\link[tidycensus]{tidycensus}} to retrieve data from the U.S. Census Bureau American Community Survey five-year estimates and the \code{\link[psych]{psych}} for computing the neighborhood deprivation indices. The \code{\link{messer}} function builds upon code developed by Hruska et al. (2022) \doi{10.17605/OSF.IO/M2SAV} by fictionalizing, adding the percent of households earning <$30,000 per year to the \emph{NDI} computation, and providing the option for computing the ACS-5 2006-2010 \emph{NDI} values. There is no code companion to compute \emph{NDI} included in Andrews et al. (2020) \doi{10.1080/17445647.2020.1750066} or Slotman et al. (2022) \doi{10.1016/j.dib.2022.108002}, but the package author worked directly with the Slotman et al. (2022) \doi{10.1016/j.dib.2022.108002} authors to replicate their SAS code in \strong{R}. The indices of racial or ethnic residential segregation rely heavily on the \code{\link[sf]{sf}} and \code{\link[tigris]{tigris}} packages to assign the smaller geographical units within larger geographical units and, occasionally, perform geospatial projection for distance-based metrics. The computation of \emph{RI} and \emph{EI} also relies on the \code{\link[Matrix]{Matrix}} package to compute the geospatial adjacency matrix between census geographies. Internal function to calculate \emph{AI} using the Hölder mean is based on \code{\link[DescTools]{Atkinson}} function.
+#' @section Dependencies: The 'ndi' package relies heavily upon \code{\link[tidycensus]{tidycensus-package}} to retrieve data from the U.S. Census Bureau American Community Survey five-year estimates and the \code{\link[psych]{psych-package}} for computing the neighborhood deprivation indices. The \code{\link{messer}} function builds upon code developed by Hruska et al. (2022) \doi{10.17605/OSF.IO/M2SAV} by fictionalizing, adding the percent of households earning <$30,000 per year to the \emph{NDI} computation, and providing the option for computing the ACS-5 2006-2010 \emph{NDI} values. There is no code companion to compute \emph{NDI} included in Andrews et al. (2020) \doi{10.1080/17445647.2020.1750066} or Slotman et al. (2022) \doi{10.1016/j.dib.2022.108002}, but the package author worked directly with the Slotman et al. (2022) \doi{10.1016/j.dib.2022.108002} authors to replicate their SAS code in \strong{R}. The indices of racial or ethnic residential segregation rely heavily on the \code{\link[sf]{sf-package}} and \code{\link[tigris]{tigris-package}} packages to assign the smaller geographical units within larger geographical units and, occasionally, perform geospatial projection for distance-based metrics. The computation of \emph{RI} and \emph{EI} also relies on the \code{\link[Matrix]{sparseMatrix}} function to compute the geospatial adjacency matrix between census geographies. Internal function to calculate \emph{AI} using the Hölder mean is based on \code{\link[DescTools]{Atkinson}} function.
 #' 
 #' @author Ian D. Buller\cr \emph{DLH, LLC (formerly DLH Corporation and Social & Scientific Systems, Inc.), Bethesda, Maryland, USA (current); Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA (original).} \cr
 #' 
 #' Maintainer: I.D.B. \email{ian.buller@@alumni.emory.edu}
 #'
 #' @keywords internal
-'_PACKAGE'
+"_PACKAGE"
 
 #' @import dplyr
 #' @importFrom car logit
+#' @importFrom Hmisc wtd.quantile
 #' @importFrom MASS ginv
 #' @importFrom Matrix sparseMatrix
 #' @importFrom psych alpha principal

R/powell_wiley.R

@@ -31,7 +31,7 @@
 #'
 #' Use the internal \code{state} and \code{county} arguments within the \code{\link[tidycensus]{get_acs}} function to specify the referent for standardizing the \emph{NDI} (Powell-Wiley) values. For example, if all U.S. states are specified for the \code{state} argument, then the output would be a U.S.-standardized index. Please note: the \emph{NDI} (Powell-Wiley) values will not exactly match (but will highly correlate with) those found in Andrews et al. (2020) \doi{10.1080/17445647.2020.1750066} and Slotman et al. (2022) \doi{10.1016/j.dib.2022.108002} because the two studies used a different statistical platform (i.e., SPSS and SAS, respectively) that intrinsically calculate the principal component analysis differently from R.
 #'
-#' The categorical \emph{NDI} (Powell-Wiley) values are population-weighted quintiles of the continuous \emph{NDI} (Powell-Wiley) values.
+#' The categorical \emph{NDI} (Powell-Wiley) values are population-weighted quintiles of the continuous \emph{NDI} (Powell-Wiley) values. NOTE: As of version 0.2.0, population-weighted quintiles are computed using a weighted quantile function \code{\link[Hmisc]{wtd.quantile}} where values are calculated NDI and weights are Total Population instead of previously using \code{\link[stats]{quantile}} of the product of the calculated NDI and natural logarithm transformed total population.
 #'
 #' Check if the proportion of variance explained by the first principal component is high (more than 0.5).
 #'
@@ -53,9 +53,10 @@
 #' @references Slotman, BA, Stinchcomb, DG, Powell-Wiley, TM, Ostendorf, DM, Saelens, BE, Gorin, AA, Zenk, SN, & Berrigan, D (2022) Environmental Data and Methods from the Accumulating Data to Optimally Predict Obesity Treatment (ADOPT) Core Measures Environmental Working Group. \emph{Data in Brief}, 41:108002. \doi{10.1016/j.dib.2022.108002}
 #' 
 #' @import dplyr
+#' @importFrom Hmisc wtd.quantile
 #' @importFrom MASS ginv
 #' @importFrom psych alpha principal
-#' @importFrom stats complete.cases cor cov2cor loadings median promax quantile sd
+#' @importFrom stats complete.cases cor cov2cor loadings median promax sd
 #' @importFrom stringr str_trim
 #' @importFrom tidycensus get_acs
 #' @importFrom tidyr pivot_longer separate
@@ -350,9 +351,10 @@ powell_wiley <- function(geo = 'tract',
   NDIQuint <- ndi_data_NDI %>%
     dplyr::mutate(
       NDIQuint = cut(
-        NDI * log(TotalPop),
-        breaks = stats::quantile(
-          NDI * log(TotalPop),
+        NDI,
+        breaks = Hmisc::wtd.quantile(
+          NDI,
+          weights = TotalPop,
           probs = c(0, 0.2, 0.4, 0.6, 0.8, 1),
           na.rm = TRUE
         ),

README.md

@@ -9,10 +9,10 @@
 [![CRAN RStudio mirror downloads monthly](https://cranlogs.r-pkg.org/badges/ndi)](https://r-pkg.org:443/pkg/ndi)
 [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/license/apache-2-0)
 ![GitHub last commit](https://img.shields.io/github/last-commit/idblr/ndi)
-[![DOI](https://zenodo.org/badge/521439746.svg)](https://zenodo.org/badge/latestdoi/521439746)
+[![](https://img.shields.io/badge/DOI-10.32614/CRAN.package.ndi-1f57b6?style=flat&link=https://doi.org/10.32614/CRAN.package.ndi)](https://doi.org/10.32614/CRAN.package.ndi)
 <!-- badges: end -->
 
-**Date repository last updated**: 2025-05-30
+**Date repository last updated**: 2025-08-29
 
 ### Overview
 
@@ -182,6 +182,8 @@ See also the list of [contributors](https://github.com/idblr/ndi/graphs/contribu
 
 * **Jessica Gleason** - *Epidemiology Branch, Division of Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland* - [ORCID](https://orcid.org/0000-0001-9877-7931)
 
+* **Hunter Mills** - [GitHub](https://github.com/huntermills707)
+
 * **Chris Prener** - *Real World Evidence Center of Excellence, Pfizer, Inc.* - [GitHub](https://github.com/chris-prener) - [ORCID](https://orcid.org/0000-0002-4310-9888)
 
 * **Davis Vaughan** - *Posit* - [GitHub](https://github.com/DavisVaughan) - [ORCID](https://orcid.org/0000-0003-4777-038X)

cran-comments.md

@@ -1,6 +1,8 @@
 ## This is the seventh resubmission
 
 * Actions taken since previous submission:
+
+#### New Functions
   * Added `denton()` function to compute the aspatial racial or ethnic Relative Clustering (*RCL*) based on [Massey & Denton (1988)](https://doi.org/10.1093/sf/67.2.281)
   * Added `denton_cuzzort()` function to compute the aspatial racial or ethnic Relative Concentration (*RCO*) based on [Massey & Denton (1988)](https://doi.org/10.1093/sf/67.2.281) and Duncan, Cuzzort, & Duncan (1961; LC:60007089)
   * Added `duncan_cuzzort()` function to compute the aspatial racial or ethnic Absolute Centralization (*ACE*) based on Duncan, Cuzzort, & Duncan (1961; LC:60007089) and [Massey & Denton (1988)](https://doi.org/10.1093/sf/67.2.281)
@@ -14,19 +16,28 @@
   * Added `morgan_massey()` function to compute the aspatial racial or ethnic Distance-Decay Isolation Index (_DPxx\*_) based on [Morgan (1983)](https://www.jstor.org/stable/20001935) and [Massey & Denton (1988)](https://doi.org/10.1093/sf/67.2.281)
   * Added `theil()` function the aspatial racial or ethnic Entropy (*H*) based on Theil (1972; ISBN:978-0-444-10378-9) and [Theil & Finizza (1971)](https://doi.org/110.1080/0022250X.1971.9989795)
   * Added `white_blau()` function to compute an index of spatial proximity (*SP*) based on [White (1986)](https://doi.org/10.2307/3644339) and Blau (1977; ISBN-13:978-0-029-03660-0)
+
+#### New Function Capabilities
   * Added `geo_large = 'place'` for census-designated places, `geo_large = 'cbsa'` for core-based statistical areas, `geo_large = 'csa'` for combined statistical areas, and `geo_large = 'metro'` for metropolitan divisions as the larger geographical unit in `atkinson()`, `bell()`, `bemanian_beyer()`, `denton()`, `denton_cuzzort()`, `duncan()`, `duncan_cuzzort()`, `duncan_duncan()`, `hoover()`, `james_taeuber()`, `lieberson()`, `massey()`, `massey_duncan()`, `morgan_denton()`, `morgan_massey()`, `sudano()`, `theil()`, and `white()`, `white_blau()` functions.
   * Added census block group computation for `anthopolos()` by specifying `geo == 'cbg'` or `geo == 'block group'`
   * Added `holder` argument to `atkinson()` function to toggle the computation with or without the Hölder mean. The function can now compute *A* without the Hölder mean. The default is `holder = FALSE`.
   * Added `crs` argument to `anthopolos()`, `bravo()`, and `white_blau()` functions to provide spatial projection of the distance-based metrics
   * The `gini()` function now computes the aspatial racial or ethnic Gini Index (*G*) based on [Gini (1921)](https://doi.org/10.2307/2223319) as the main outcome. Arguments `geo_large`, `geo_small`, `subgroup`, and `omit_NAs` were added and argument `geo` was deprecated. The `gini()` function still retrieves the original output of the aspatial income Gini Index (*G*) at each smaller geography and is moved from the `g` output to `g_data` output.
   * Specifying census block groups in `geo` or `geo_small` arguments is now `'block group'` or `'cbg'` to match internal `get_acs()` function from the [tidycensus](https://CRAN.R-project.org/package=tidycensus) package
-  * Fixed NOTE in CRAN checks to provide package anchors for Rd \link{} targets not in the package itself and the base packages  within 'ndi-package.Rd'
+
+#### Bug Fixes
+  * Fixed NOTE in CRAN checks to provide package anchors for Rd `\link{}` targets not in the package itself and the base packages  within 'ndi-package.Rd'
+  * Updated population-weighted quantile method from `stats::quantile` to `Hmisc::wtd.quantile` in `powell_wiley()`
   * `bell()` function computes the Interaction Index (Bell) not the Isolation Index as previously documented. Updated documentation throughout.
   * Fixed bug in `bell()`, `bemanian_beyer()`, `duncan()`, `sudano()`, and `white()` functions when a smaller geography contains n=0 total population, will assign a value of zero (0) in the internal calculation instead of NA
   * Fixed bug in `atkinson()` function to properly compute the income Atkinson Index
   * Renamed *AI* as *A*, *DI* as *D*, *Gini* as *G*, and *II* as _xPy\*_ to align with the definitions from [Massey & Denton (1988)](https://doi.org/10.1093/sf/67.2.281). The output for `atkinson()` now produces `a` instead of `ai`. The output for `duncan()` now produces `d` instead of `ai`. The output for `gini()` now produces `g` instead of `gini`. The output for `bell()` now produces `xPy_star` instead of `II`. The internal functions `ai_fun()`, `di_fun()` and `ii_fun()` were renamed `a_fun()`, `ddd_fun()` and `xpy_star_fun()`, respectively.
   * Output of racial or ethnic residential segregation indices is now rounded to four significant digits
-  * `tigris` and `units` are now Imports
+
+#### New Dependencies
+  * `Hmisc`, `tigris`, and `units` are now Imports
+
+#### Updated Documentation
   * Reformatted functions for consistent internal structure
   * 'package.R' deprecated. Replaced with 'ndi-package.R' and reordered the contents
   * Consolidated DESCRIPTION
@@ -52,19 +63,25 @@
   * <https://doi.org/10.1080/17445647.2020.1750066>
   * <https://doi.org/10.2307/3644339>
   * <https://doi.org/10.2307/2084686>
+* The win-builder oldrelease throws a NOTE that "Author field differs from that derived from Authors@R". The behavior is OK because ORCID has different formatting but same information
 
 * Some tests and examples for `anthopolos()`, `atkinson()`, `bell()`, `bemanian_beyer()`, `bravo()`, `denton()`, `denton_cuzzort()`, `duncan()`, `duncan_cuzzort()`, `duncan_duncan()`, `gini()`, `hoover()`, `james_taeuber()`, `krieger()`, `lieberson()`, `massey()`, `massey_duncan()`, `messer()`, `powell_wiley()`, `sudano()`, `theil()`, `white()`, and `white_blau()` functions require a Census API key so they are skipped if NULL or not run
 
 ## Test environments
-* local Windows install, R 4.4.1
+* local Windows install, R 4.5.1
 * win-builder, (devel, release, oldrelease)
-* Rhub
-  * Fedora Linux, R-devel, clang, gfortran
-  * Ubuntu Linux 20.04.1 LTS, R-release, GCC
-  * Windows Server 2022, R-devel, 64 bit
-  * Windows Server 2008 R2 SP1, R-release, 32⁄64 bit
-  * Oracle Solaris 10, x86, 32 bit, R-release
-  * macOS 10.13.6 High Sierra, R-release, CRAN's setup
+* R-CMD-check on GitHub
+  * macos-latest (release)
+  * windows-latest (release)
+  * ubuntu-latest (devel)
+  * ubuntu-latest (release)
+  * ubuntu-latest (oldrel-1)
+* Rhub v2
+  * macos-15 on GitHub, ASAN + UBSAN on macOS (`m1-san`)
+  * macos-13 on GitHub(`macos`)
+  * Fedora Linux 40 (Container Image) (`gcc-asan`)
+  * Ubuntu 22.04.5 LTS (`ubuntu-clang`)
+  * Ubuntu 22.04.5 LTS (`ubuntu-gcc12`)
 
 ## R CMD check results
 0 errors | 0 warnings | 0 notes

inst/CITATION

@@ -3,15 +3,15 @@ bibentry(bibtype = 'manual',
   author         = as.person('Ian D. Buller'),
   publisher      = 'The Comprehensive R Archive Network',
   year           = '2025',
-  number         = '0.1.6.9015.',
+  number         = '0.2.0.',
   doi            = '10.32614/CRAN.package.ndi',
   url            = 'https://cran.r-project.org/package=ndi',
 
   textVersion    = 
   paste('Ian D. Buller (2025)',
         'ndi: Neighborhood Deprivation Indices.',
         'The Comprehensive R Archive Network.',
-        'v0.1.6.9015.',
+        'v0.2.0.',
         'DOI:10.32614/CRAN.package.ndi',
         'Accessed by: https://cran.r-project.org/package=ndi'),