🔀 Merge branch:dev_cleanup into branch:main

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ndi
 Title: Neighborhood Deprivation Indices
-Version: 0.1.6.9014
-Date: 2024-09-02
+Version: 0.1.6.9015
+Date: 2025-05-30
 Authors@R:
     c(person(given = "Ian D.",
              family = "Buller",

LICENSE.md

@@ -169,7 +169,7 @@ accepting any such warranty or additional liability.
 
 _END OF TERMS AND CONDITIONS_
 
-    Copyright 2024 Ian D. Buller; NCI
+    Copyright 2025 Ian D. Buller; National Cancer Institute
 
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.

NEWS.md

@@ -1,6 +1,6 @@
 # ndi (development version)
 
-## ndi v0.1.6.9014
+## ndi v0.1.6.9015
 
 ### New Features
 
@@ -31,11 +31,13 @@
 ### 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'
 * `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.
 * 'package.R' deprecated. Replaced with 'ndi-package.R'
+* Output of racial or ethnic residential segregation indices is now rounded to four significant digits
 
 #### New Dependencies
 * `tigris` and `units` are now Imports
@@ -49,6 +51,8 @@
 * Updated documentation about value range of *V* (White) from `{0 to 1}` to `{-Inf to Inf}`
 * Added examples for `atkinson()`, `duncan_cuzzort()`, `duncan_duncan()`, `gini()`, `hoover()`, `james_taeuber()`, `lieberson()`, `massey()`, `massey_duncan()`, `morgan_massey()`, `theil()`, and `white_blau()` functions in vignettes and README
 * Added example for `holder` argument in `atkinson()` function in README
+* Added internal and external references within each functions documentation
+* Reordered and reformatted CITATION alphabetically by index abbreviation
 * Reordered the contents of 'ndi-package.R' thematically
 * Reordered the README examples alphabetically
 * Reordered the vignette examples to group the racial or ethnic residential segregation indices

R/anthopolos.R

@@ -45,6 +45,13 @@
 #' \item{\code{ri}}{An object of class 'tbl' for the GEOID, name, \emph{RI}, and raw census values of specified census geographies.}
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{RI}.}
 #' }
+#' 
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Other isolation indices: \code{\link{bemanian_beyer}}, \code{\link{lieberson}}, \code{\link{morgan_massey}}, \code{\link{white}}
+#' @seealso Interaction indices: \code{\link{bell}}, \code{\link{morgan_denton}}
+#' @seealso Education Isolation Index: \code{\link{bravo}}
+#' 
+#' @references Anthopolos, R, James, SA, Gelfand, AE, & Miranda, ML (2011) A Spatial Measure of Neighborhood Level Racial Isolation Applied to Low Birthweight, Preterm Birth, and Birthweight in North Carolina. \emph{Spatial and Spatio-temporal Epidemiology}, 2(4):235-246. \doi{10.1016/j.sste.2011.06.002}
 #'
 #' @import dplyr
 #' @importFrom Matrix sparseMatrix
@@ -53,9 +60,7 @@
 #' @importFrom tidycensus get_acs
 #' @importFrom tidyr pivot_longer separate
 #' @export
-#'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
+#' 
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/atkinson.R

@@ -53,6 +53,14 @@
 #' \item{\code{a_data}}{An object of class 'tbl' for the raw census values at specified smaller census geographies.}
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{A}.}
 #' }
+#' 
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Other one-group evenness indices: \code{\link{gini}}, \code{\link{james_taeuber}}, \code{\link{sudano}}, \code{\link{theil}}
+#' @seealso Between groups dissimilarity indices: \code{\link{duncan}}
+#' 
+#' @references Atkinson, AB (1970) On the Measurement of Inequality. \emph{Journal of Economic Theory}, 2(3):244-263. \doi{10.1016/0022-0531(70)90039-6}
+#' @references James, D, & Taeuber, KE (1985) Measures of Segregation. \emph{Sociological Methodology}, 15:1-32. \doi{10.2307/270845}
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
 #'
 #' @import dplyr
 #' @importFrom sf st_drop_geometry st_within
@@ -64,8 +72,6 @@
 #' @importFrom utils stack
 #' @export
 #'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/bell.R

@@ -50,6 +50,14 @@
 #' \item{\code{xpy_star_data}}{An object of class 'tbl' for the raw census values at specified smaller census geographies.}
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute _xPy\*_.}
 #' }
+#' 
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Other interaction indices: \code{\link{morgan_denton}}
+#' @seealso Isolation indices: \code{\link{anthopolos}}, \code{\link{bemanian_beyer}}, \code{\link{lieberson}}, \code{\link{morgan_massey}}, \code{\link{white}}
+#' 
+#' @references Eshref, S, & Williams, M (1949). \emph{The Social Areas of Los Angeles: Analysis and Typology}. 1st Ed. Los Angeles:John Randolph Haynes and Dora Haynes Foundation. ISBN-13:978-0-837-15637-8
+#' @references Bell, W (1954) A probability model for the measurement of ecological segregation. \emph{Social Forces}, 32(4):357-364. \doi{10.2307/2574118}
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
 #'
 #' @import dplyr
 #' @importFrom sf st_drop_geometry st_within
@@ -61,8 +69,6 @@
 #' @importFrom utils stack
 #' @export
 #'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/bemanian_beyer.R

@@ -53,6 +53,12 @@
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{LEx/Is}.}
 #' }
 #'
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Other isolation indices: \code{\link{anthopolos}}, \code{\link{lieberson}}, \code{\link{morgan_massey}}, \code{\link{white}}
+#' @seealso Interaction indices: \code{\link{bell}}, \code{\link{morgan_denton}}
+#' 
+#' @references Bemanian, A, & Beyer, KMM (2017) Measures Matter: The Local Exposure/Isolation (LEx/Is) Metrics and Relationships between Local-Level Segregation and Breast Cancer Survival. \emph{Cancer Epidemiology, Biomarkers & Prevention}, 26(4):516-524. \doi{10.1158/1055-9965.EPI-16-0926}
+#'
 #' @import dplyr
 #' @importFrom car logit
 #' @importFrom sf st_drop_geometry st_within
@@ -63,9 +69,7 @@
 #' @importFrom tigris combined_statistical_areas core_based_statistical_areas metro_divisions places
 #' @importFrom utils stack
 #' @export
-#'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
+#' 
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/bravo.R

@@ -31,7 +31,12 @@
 #' \item{\code{ei}}{An object of class 'tbl' for the GEOID, name, \emph{EI}, and raw census values of specified census geographies.}
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{EI}.}
 #' }
-#'
+#' 
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Racial Isolation Index: \code{\link{anthopolos}}
+#' 
+#' @references Bravo, MA, Leong, MC, Gelfand, AE, & Miranda, ML (2021) Assessing Disparity Using Measures of Racial and Educational Isolation. \emph{International Journal of Environmental Research and Public Health}, 18(17):9384. \doi{10.3390/ijerph18179384}
+#' 
 #' @import dplyr
 #' @importFrom Matrix sparseMatrix
 #' @importFrom sf st_drop_geometry st_geometry st_intersects st_transform
@@ -41,7 +46,7 @@
 #' @importFrom tidyr pivot_longer separate
 #' @export
 #'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' 
 #'
 #' @examples
 #' \dontrun{

R/denton.R

@@ -54,6 +54,12 @@
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{RCL}.}
 #' }
 #'
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Absolute Clustering: \code{\link{massey}}
+#' @seealso Proximity measures: \code{\link{morgan_massey}}, \code{\link{morgan_denton}}, \code{\link{white_blau}}
+#' 
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
+#' 
 #' @import dplyr
 #' @importFrom sf st_centroid st_distance st_drop_geometry st_transform st_within
 #' @importFrom stats complete.cases
@@ -65,8 +71,6 @@
 #' @importFrom utils stack
 #' @export
 #'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/denton_cuzzort.R

@@ -51,6 +51,13 @@
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{RCO}.}
 #' }
 #'
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Absolute Concentration: \code{\link{massey_duncan}}
+#' @seealso Delta: \code{\link{hoover}}
+#' 
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
+#' @references Duncan, OD, Cuzzort, RP, & Duncan, B (1961) \emph{Statistical Geography: Problems in Analyzing Area Data}. Free Press. LC:60007089
+#' 
 #' @import dplyr
 #' @importFrom sf st_centroid st_distance st_drop_geometry st_transform st_within
 #' @importFrom stats complete.cases
@@ -62,8 +69,6 @@
 #' @importFrom utils stack
 #' @export
 #'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/duncan.R

@@ -51,6 +51,11 @@
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{D}.}
 #' }
 #'
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso One-group evenness indices: \code{\link{atkinson}}, \code{\link{gini}}, \code{\link{james_taeuber}}, \code{\link{sudano}}, \code{\link{theil}}
+#' 
+#' @references Duncan, OD, & Duncan, B (1955) Residential Distribution and Occupational Stratification. \emph{American Journal of Sociology}, 60(5):493-503. \doi{10.2307/2088328}
+#'
 #' @import dplyr
 #' @importFrom sf st_drop_geometry st_within
 #' @importFrom stats complete.cases
@@ -60,9 +65,7 @@
 #' @importFrom tigris combined_statistical_areas core_based_statistical_areas metro_divisions places
 #' @importFrom utils stack
 #' @export
-#'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
+#' 
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/duncan_cuzzort.R

@@ -53,6 +53,12 @@
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{ACE}.}
 #' }
 #'
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Relative Centralization: \code{\link{duncan_duncan}}
+#' 
+#' @references Duncan, OD, Cuzzort, RP, & Duncan, B (1961) \emph{Statistical Geography: Problems in Analyzing Area Data}. Free Press. LC:60007089
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
+#' 
 #' @import dplyr
 #' @importFrom sf st_centroid st_distance st_drop_geometry st_transform st_within
 #' @importFrom stats complete.cases
@@ -64,8 +70,6 @@
 #' @importFrom utils stack
 #' @export
 #'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/duncan_duncan.R

@@ -54,6 +54,12 @@
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{RCE}.}
 #' }
 #'
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Absolute Centralization: \code{\link{duncan_cuzzort}}
+#' 
+#' @references Duncan, OD, Cuzzort, RP, & Duncan, B (1961) \emph{Statistical Geography: Problems in Analyzing Area Data}. Free Press. LC:60007089
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
+#'
 #' @import dplyr
 #' @importFrom sf st_centroid st_distance st_drop_geometry st_transform st_within
 #' @importFrom stats complete.cases
@@ -65,8 +71,6 @@
 #' @importFrom utils stack
 #' @export
 #'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/gini.R

@@ -49,7 +49,15 @@
 #' \item{\code{g_data}}{An object of class 'tbl' for the raw census values at specified smaller census geographies including \emph{G_inc}.}
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for \emph{G_inc} and each census variable used to compute \emph{G_re}.}
 #' }
-#'
+#' 
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Other one-group evenness indices: \code{\link{atkinson}}, \code{\link{james_taeuber}}, \code{\link{sudano}}, \code{\link{theil}}
+#' @seealso Between groups dissimilarity indices: \code{\link{duncan}}
+#' 
+#' @references Gini, C (1921) Measurement of Inequality of Incomes. \emph{The Economic Journal}, 31(121):124-126. \doi{10.2307/2223319}
+#' @references Duncan, OD, & Duncan, B (1955) Residential Distribution and Occupational Stratification. \emph{American Journal of Sociology}, 60(5):493-503. \doi{10.2307/2088328}
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
+#' 
 #' @import dplyr
 #' @importFrom sf st_drop_geometry st_within
 #' @importFrom stats complete.cases
@@ -59,9 +67,7 @@
 #' @importFrom tigris combined_statistical_areas core_based_statistical_areas metro_divisions places
 #' @importFrom utils stack
 #' @export
-#'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
+#' 
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/hoover.R

@@ -50,6 +50,14 @@
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{DEL}.}
 #' }
 #' 
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Absolute Concentration: \code{\link{massey_duncan}}
+#' @seealso Relative Concentration: \code{\link{denton_cuzzort}}
+#' 
+#' @references Hoover, EM (1941) Interstate Redistribution of Population, 1850-1940. \emph{Journal of Economic History}, 1:199-205. \doi{10.2307/2223319}
+#' @references Duncan, OD, Cuzzort, RP, & Duncan, B (1961) \emph{Statistical Geography: Problems in Analyzing Area Data}. Free Press. LC:60007089
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
+#' 
 #' @import dplyr
 #' @importFrom sf st_drop_geometry st_within
 #' @importFrom stats complete.cases
@@ -60,8 +68,6 @@
 #' @importFrom utils stack
 #' @export
 #' 
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.

R/james_taeuber.R

@@ -50,6 +50,13 @@
 #' \item{\code{missing}}{An object of class 'tbl' of the count and proportion of missingness for each census variable used to compute \emph{D}.}
 #' }
 #'
+#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
+#' @seealso Other one-group evenness indices: \code{\link{atkinson}}, \code{\link{gini}}, \code{\link{sudano}}, \code{\link{theil}}
+#' @seealso Between groups dissimilarity indices: \code{\link{duncan}}
+#' 
+#' @references James, D, & Taeuber, KE (1985) Measures of Segregation. \emph{Sociological Methodology}, 15:1-32. \doi{10.2307/270845}
+#' @references Massey, DS, & Denton, NA (1988) The Dimensions of Residential Segregation. \emph{Social Forces}, 67(1):281-315. \doi{10.1093/sf/67.2.281}
+#' 
 #' @import dplyr
 #' @importFrom sf st_drop_geometry st_within
 #' @importFrom stats complete.cases
@@ -60,8 +67,6 @@
 #' @importFrom utils stack
 #' @export
 #'
-#' @seealso \code{\link[tidycensus]{get_acs}} for additional arguments for geographic extent selection (i.e., \code{state} and \code{county}).
-#'
 #' @examples
 #' \dontrun{
 #' # Wrapped in \dontrun{} because these examples require a Census API key.