Update with CRAN fixes (#36)

.Rbuildignore

@@ -19,3 +19,4 @@
 ^zonebuilder-paper_files$
 ^vignettes/josis*$
 ^\.ccache$
+^CRAN-SUBMISSION$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: zonebuilder
 Title: Create and Explore Geographic Zoning Systems
-Version: 0.0.2.9001
+Version: 0.1.0
 Authors@R: 
     c(person(given = "Robin",
              family = "Lovelace",
@@ -13,6 +13,8 @@ Authors@R:
              email = "mtennekes@gmail.com"))
 Description: Functions, documentation and example data to help divide
     geographic space into discrete polygons (zones).
+    The package supports new zoning systems that are documented in the
+    accompanying paper <doi:10.5311/JOSIS.2022.24.172>.
     The functions are motivated by research into the merits of different zoning systems
     <doi:10.1068/a090169>. A flexible 'ClockBoard' zoning system is
     provided, which breaks-up space by concentric rings
@@ -39,7 +41,6 @@ Suggests:
     rmarkdown,
     tmap,
     tmaptools,
-    pct,
     dplyr,
     lwgeom,
     leaflet,
@@ -50,4 +51,4 @@ VignetteBuilder:
 URL: https://github.com/zonebuilders/zonebuilder, https://zonebuilders.github.io/zonebuilder/
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(geo_select_aeq,sf)
+S3method(geo_select_aeq,sfc)
 export(london_a)
 export(london_c)
 export(zb_color)
@@ -8,7 +10,6 @@ export(zb_lines)
 export(zb_plot)
 export(zb_quadrat)
 export(zb_segment)
-export(zb_view)
 export(zb_zone)
 import(sf)
 importFrom(RColorBrewer,brewer.pal)

NEWS.md

@@ -1,4 +1,8 @@
-# zonebuilder (development version)
+# zonebuilder 0.1.0 (2025-02)
+
+* Various issues fixed for CRAN (#36)
+* Removal of `zb_view()` function
+* Addition of citation to documentation
 
 # zonebuilder 0.0.2
 

R/from_stplanr.R

@@ -1,3 +1,12 @@
+#' Azimuthal Equidistant Projection
+#'
+#' @title Azimuthal Equidistant Projection
+#' @name geo_select_aeq
+#' @description Returns a CRS string for an Azimuthal Equidistant projection centered on the midpoint of an sf object's coordinates.
+#'
+#' @param shp An sf object.
+#' @return A CRS string for an Azimuthal Equidistant projection.
+#' @export
 geo_select_aeq.sf = function (shp) {
   #cent <- sf::st_geometry(shp)
   coords <- sf::st_coordinates(shp)
@@ -8,7 +17,8 @@ geo_select_aeq.sf = function (shp) {
   sf::st_crs(aeqd)
 }
 
-
+#' @rdname geo_select_aeq
+#' @export
 geo_select_aeq.sfc = function (shp) {
   #cent <- sf::st_geometry(shp)
   coords <- sf::st_coordinates(shp)
@@ -19,12 +29,13 @@ geo_select_aeq.sfc = function (shp) {
   sf::st_crs(aeqd)
 }
 
+#' @rdname geo_select_aeq
 geo_select_aeq = function (shp) {
   UseMethod("geo_select_aeq")
 }
 
 
 geo_project = function(shp) {
   crs = geo_select_aeq(shp)
-  st_transform(shp, crs = crs)
+  sf::st_transform(shp, crs = crs)
 }

R/plot.R

@@ -35,55 +35,6 @@ zb_color = function(z, palette = c("rings", "hcl", "dartboard")) {
   }
 }
 
-
-
-#' View zones
-#' 
-#' This function opens an interactive map of the zones
-#' 
-#' @param z An `sf` object containing zones covering the region
-#' @param alpha Alpha transparency, number between 0 (fully transparent) and 1 (not transparent)
-#' @param palette Palette type, one of \code{"hcl"} (a palette based on the HCL color space), \code{"rings"} (a palette which colors the rings using the YlOrBr color brewer palette), \code{"dartboard"} (a palette which resembles a dartboard)
-#' @param title The title of the plot
-#' @return An interactive map created with `tmap`
-#' @export
-#' @examples
-#' \donttest{
-#' z = zb_zone(london_c(), london_a())
-#' zb_view(z, palette = "rings")
-#' }
-zb_view = function(z, alpha = 0.4, palette = c("rings", "hcl", "dartboard"), title  = NULL) {
-  palette = match.arg(palette)
-  if (requireNamespace("tmap")) {
-    suppressMessages(tmap::tmap_mode("view"))
-    tmap::tmap_options(show.messages = FALSE)
-
-    cent = sf::st_set_crs(sf::st_set_geometry(z, "centroid"), sf::st_crs(z))
-    check_and_fix = tmap::tmap_options()$check.and.fix
-    if(!check_and_fix) {
-      message("Updating tmap settings with:\ntmap::tmap_options(check.and.fix = TRUE)")
-      tmap::tmap_options(check.and.fix = TRUE)
-    }
-
-    z$color = zb_color(z, palette)
-    tm = tmap::tm_basemap("OpenStreetMap") +
-    tmap::tm_shape(z) + 
-      tmap::tm_fill("color", alpha = alpha, id = "label", group = "colors", popup.vars = c("circle_id", "segment_id", "label")) + 
-      tmap::tm_borders(group = "Borders", col = "black", lwd = 1.5) +
-    tmap::tm_shape(cent) +
-      tmap::tm_text("label", col = "black", size = "circle_id", group = "Labels") +
-      tmap::tm_scale_bar()
-
-    if (!is.null(title)) {
-      tm + tmap::tm_layout(title = title)
-    } else {
-      tm
-    }
-  } else {
-    stop("Please install tmap")
-  }
-}
-
 #' Plot zones
 #' 
 #' This function opens a static map of the zones
@@ -113,7 +64,7 @@ zb_plot = function(z, palette = c("rings", "hcl", "dartboard"), title = NULL, te
   on.exit(par(oldpar)) # code line i + 1
   p = graphics::par(mar=c(.2,.2,.2,.2))
   plot(sf::st_geometry(z), col = z$color, border = "grey40")
-  co = st_coordinates(cent[sel,])
+  co = sf::st_coordinates(cent[sel,])
   mx = max(z$circle_id[sel])
   cex = seq(text_size[1], text_size[2], length.out = 9)[pmin(9, z$circle_id[sel] + (9-mx))]
   text(co[, 1], co[, 2], cex = cex, labels = z$label[sel])

R/zone.R

@@ -28,20 +28,9 @@
 #' @examples
 #' # default settings
 #' z = zb_zone(london_c(), london_a())
-#' \donttest{
-#' zb_plot(z)
-#' if (require(tmap)) {
-#'   zb_view(z)
-#'   
-#'   z = zb_zone("Berlin")
-#'   zb_view(z)
-#'}
-#' 
-#' # variations
 #' zb_plot(zb_zone(london_c(), london_a(), n_circles = 2))
 #' zb_plot(zb_zone(london_c(), london_a(), n_circles = 4, distance = 2, distance_growth = 0))
 #' zb_plot(zb_zone(london_c(), london_a(), n_circles = 3, n_segments = c(1,4,8)))
-#' }
 zb_zone = function(x = NULL,
                    area = NULL,
                    n_circles = NA,

README.Rmd

@@ -24,11 +24,11 @@ knitr::opts_chunk$set(
 [![CRAN status](https://www.r-pkg.org/badges/version/zonebuilder)](https://CRAN.R-project.org/package=zonebuilder)
 [![CRAN RStudio mirror
 downloads](https://cranlogs.r-pkg.org/badges/grand-total/zonebuilder)](https://www.r-pkg.org/pkg/zonebuilder)
-[DOI](https://doi.org/10.31219/osf.io/vncgw)
+[DOI](https://doi.org/10.5311/JOSIS.2022.24.172)
 <!-- badges: end -->
 
 The goal of zonebuilder is to break up large geographic regions such as cities into manageable zones.
-Zoning systems are important in many fields, including demographics, economy, health, and transport. The zones have standard configuration, which enabled comparability across cities. See its website at [zonebuilders.github.io/zonebuilder](https://zonebuilders.github.io/zonebuilder/).
+Zoning systems are important in many fields, including demographics, economy, health, and transport. The zones have standard configuration, which enabled comparability across cities. See its website at [zonebuilders.github.io/zonebuilder](https://zonebuilders.github.io/zonebuilder/) and the academic paper that describes the package in detail [here (Lovelace et al. 2022)](https://doi.org/10.5311/JOSIS.2022.24.172).
 
 ## Installation
 
@@ -53,7 +53,11 @@ Attaching the package provides the example datasets `london_a()` and `london_c()
 ```{r}
 library(zonebuilder)
 library(tmap)
-tm_shape(london_a()) + tm_borders() + tm_shape(london_c()) + tm_dots("red")
+tmap_mode("plot")
+tm_shape(london_a()) +
+  tm_borders() +
+  tm_shape(london_c()) +
+  tm_dots("red")
 ```
 
 The main function `zb_zone` breaks this geographical scale into zones. The default settings follow the **ClockBoard** configuration:
@@ -99,11 +103,25 @@ It may be worth checking-in in a [discussion post](https://github.com/zonebuilde
 
 ## Citation
 
-Watch this space.
-
-
-<!-- tmap_arrange( -->
-<!--   zb_view(zb_doughnut(london_c(), london_a(), n_circles = 5), title = "Doughnuts"), -->
-<!--   zb_view(zb_segment(london_c(), n_segments = 20), title = "Segments") -->
-<!--  ) -->
+Please cite the package as follows (Lovelace et al. 2022):
 
+```
+@article{lovelace_clockboard_2022,
+  title = {{{ClockBoard}}: {{A}} Zoning System for Urban Analysis},
+  shorttitle = {{{ClockBoard}}},
+  author = {Lovelace, Robin and Tennekes, Martijn and Carlino, Dustin},
+  date = {2022-06-20},
+  journaltitle = {Journal of Spatial Information Science},
+  number = {24},
+  pages = {63--85},
+  issn = {1948-660X},
+  doi = {10.5311/JOSIS.2022.24.172},
+  url = {https://josis.org/index.php/josis/article/view/172},
+  urldate = {2022-07-02},
+  abstract = {Zones are the building blocks of urban analysis. Fields ranging from demographics to transport planning routinely use zones - spatially contiguous areal units that break-up continuous space into discrete chunks - as the foundation for diverse analysis techniques. Key methods such as origin-destination analysis and choropleth mapping rely on zones with appropriate sizes, shapes and coverage. However, existing zoning systems are sub-optimal in many urban analysis contexts, for three main reasons: 1) administrative zoning systems are often based on somewhat arbitrary factors; 2) zoning systems that are evidence-based (e.g., based on equal population size) are often highly variable in size and shape, reducing their utility for inter-city comparison; and 3) official zoning systems in many places simply do not exist or are unavailable. We set out to develop a flexible, open and scalable solution to these problems. The result is the zonebuilder project (with R, Rust and Python implementations), which was used to create the ClockBoard zoning system. ClockBoard consists of 12 segments emanating from a central place and divided by concentric rings with radii that increase in line with the triangular number sequence (1, 3, 6 km etc). 'ClockBoards' thus create a consistent visual frame of reference for monocentric cities that is reminiscent of clocks and a dartboard. This paper outlines the design and potential uses of the ClockBoard zoning system in the historical context, and discusses future avenues for research into the design and assessment of zoning systems.},
+  issue = {24},
+  langid = {english},
+  keywords = {modifiable area unit problem},
+  file = {C:\Users\georl_admin\Zotero\storage\QRQDMJSH\Lovelace et al. - 2022 - ClockBoard A zoning system for urban analysis.pdf}
+}
+```

README.md

@@ -4,21 +4,24 @@
 # zonebuilder
 
 <!-- badges: start -->
+
 <!-- [![Codecov test coverage](https://codecov.io/gh/zonebuilders/zonebuilder/branch/master/graph/badge.svg)](https://codecov.io/gh/zonebuilders/zonebuilder?branch=master) -->
 
 [![R-CMD-check](https://github.com/zonebuilders/zonebuilder/workflows/R-CMD-check/badge.svg)](https://github.com/zonebuilders/zonebuilder/actions)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/zonebuilder)](https://CRAN.R-project.org/package=zonebuilder)
 [![CRAN RStudio mirror
 downloads](https://cranlogs.r-pkg.org/badges/grand-total/zonebuilder)](https://www.r-pkg.org/pkg/zonebuilder)
-[DOI](https://doi.org/10.31219/osf.io/vncgw) <!-- badges: end -->
+[DOI](https://doi.org/10.5311/JOSIS.2022.24.172) <!-- badges: end -->
 
 The goal of zonebuilder is to break up large geographic regions such as
 cities into manageable zones. Zoning systems are important in many
 fields, including demographics, economy, health, and transport. The
 zones have standard configuration, which enabled comparability across
 cities. See its website at
-[zonebuilders.github.io/zonebuilder](https://zonebuilders.github.io/zonebuilder/).
+[zonebuilders.github.io/zonebuilder](https://zonebuilders.github.io/zonebuilder/)
+and the academic paper that describes the package in detail [here
+(Lovelace et al. 2022)](https://doi.org/10.5311/JOSIS.2022.24.172).
 
 ## Installation
 
@@ -47,7 +50,11 @@ geographic boundary and the centre of London:
 ``` r
 library(zonebuilder)
 library(tmap)
-tm_shape(london_a()) + tm_borders() + tm_shape(london_c()) + tm_dots("red")
+tmap_mode("plot")
+tm_shape(london_a()) +
+  tm_borders() +
+  tm_shape(london_c()) +
+  tm_dots("red")
 ```
 
 <img src="man/figures/README-unnamed-chunk-3-1.png" width="100%" />
@@ -64,22 +71,21 @@ zb_plot(london_zones)
 
 The idea behind this zoning system is based on the following principles:
 
--   Most cities have a centre, the ‘heart’ of the city. Therefore, the
-    zones are distributed around the centre.
--   Typically, the population is much denser in and around the centre
-    and also the traffic intensity is higher. Therefore, the zones are
-    smaller in and around the centre.
--   The rings (so A, B, C, D, etc) reflect the proximity to the centre
-    point. The distances from the outer borders of the rings A, B, C, D,
-    etc. follow the triangular number sequence 1, 3, 6, 10, etc. This
-    means that in everyday life use, within zone A everything is in
-    walking distance, from ring B to the centre requires a bike, from
-    zone C and further to the centre typically requires public
-    transport.
--   Regarding direction relative to the centre, we use the clock
-    analogy, since most people are familiar with that. So each ring
-    (annuli) is divided into 12 segments, where segment 12 is directed
-    at 12:00, segment 1 at 1:00 etc.
+- Most cities have a centre, the ‘heart’ of the city. Therefore, the
+  zones are distributed around the centre.
+- Typically, the population is much denser in and around the centre and
+  also the traffic intensity is higher. Therefore, the zones are smaller
+  in and around the centre.
+- The rings (so A, B, C, D, etc) reflect the proximity to the centre
+  point. The distances from the outer borders of the rings A, B, C, D,
+  etc. follow the triangular number sequence 1, 3, 6, 10, etc. This
+  means that in everyday life use, within zone A everything is in
+  walking distance, from ring B to the centre requires a bike, from zone
+  C and further to the centre typically requires public transport.
+- Regarding direction relative to the centre, we use the clock analogy,
+  since most people are familiar with that. So each ring (annuli) is
+  divided into 12 segments, where segment 12 is directed at 12:00,
+  segment 1 at 1:00 etc.
 
 The package `zonebuilder` does not only create zoning systems based on
 the CloadBoard layout as illustrated below.
@@ -126,10 +132,23 @@ opening an issue.
 
 ## Citation
 
-Watch this space.
-
-<!-- tmap_arrange( -->
-<!--   zb_view(zb_doughnut(london_c(), london_a(), n_circles = 5), title = "Doughnuts"), -->
-<!--   zb_view(zb_segment(london_c(), n_segments = 20), title = "Segments") -->
-<!--  ) -->
-
+Please cite the package as follows (Lovelace et al. 2022):
+
+    @article{lovelace_clockboard_2022,
+      title = {{{ClockBoard}}: {{A}} Zoning System for Urban Analysis},
+      shorttitle = {{{ClockBoard}}},
+      author = {Lovelace, Robin and Tennekes, Martijn and Carlino, Dustin},
+      date = {2022-06-20},
+      journaltitle = {Journal of Spatial Information Science},
+      number = {24},
+      pages = {63--85},
+      issn = {1948-660X},
+      doi = {10.5311/JOSIS.2022.24.172},
+      url = {https://josis.org/index.php/josis/article/view/172},
+      urldate = {2022-07-02},
+      abstract = {Zones are the building blocks of urban analysis. Fields ranging from demographics to transport planning routinely use zones - spatially contiguous areal units that break-up continuous space into discrete chunks - as the foundation for diverse analysis techniques. Key methods such as origin-destination analysis and choropleth mapping rely on zones with appropriate sizes, shapes and coverage. However, existing zoning systems are sub-optimal in many urban analysis contexts, for three main reasons: 1) administrative zoning systems are often based on somewhat arbitrary factors; 2) zoning systems that are evidence-based (e.g., based on equal population size) are often highly variable in size and shape, reducing their utility for inter-city comparison; and 3) official zoning systems in many places simply do not exist or are unavailable. We set out to develop a flexible, open and scalable solution to these problems. The result is the zonebuilder project (with R, Rust and Python implementations), which was used to create the ClockBoard zoning system. ClockBoard consists of 12 segments emanating from a central place and divided by concentric rings with radii that increase in line with the triangular number sequence (1, 3, 6 km etc). 'ClockBoards' thus create a consistent visual frame of reference for monocentric cities that is reminiscent of clocks and a dartboard. This paper outlines the design and potential uses of the ClockBoard zoning system in the historical context, and discusses future avenues for research into the design and assessment of zoning systems.},
+      issue = {24},
+      langid = {english},
+      keywords = {modifiable area unit problem},
+      file = {C:\Users\georl_admin\Zotero\storage\QRQDMJSH\Lovelace et al. - 2022 - ClockBoard A zoning system for urban analysis.pdf}
+    }

cran-comments.md

@@ -1,4 +1,6 @@
-Resubmitting after fixes to enable the package to work with sf 1.0-1 and beyond.
+Many updates enabling tests to pass on CRAN, after the package was removed due to failing tests.
+
+I have fixed broken URLs since last submission.
 
 ## Test environments
 * local R installation, R 4.1.0

data-raw/fix-polygons.R

@@ -17,9 +17,6 @@ qtm(sf::st_make_valid(z))
 tmap_options(check.and.fix = TRUE)
 qtm(z)
 
-zb_view(z)
-
-
 lnd_a = zonebuilder::london_a()
 sf::st_is_valid(lnd_a)
 sf::st_is_valid(london_c())