From e3c1df179d08447804b3ac480c4b7b1c96cd21a7 Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Wed, 4 Sep 2024 19:28:38 +0100
Subject: [PATCH 01/10] Add minimal R package (#67)

---
 r/.gitignore            |  1 +
 r/DESCRIPTION           | 23 +++++++++++
 r/NAMESPACE             |  2 +
 r/R/setup.R             | 90 +++++++++++++++++++++++++++++++++++++++++
 r/README.md             | 65 +++++++++++++++++++++++++++++
 r/README.qmd            | 84 ++++++++++++++++++++++++++++++++++++++
 r/man/make_elevation.Rd | 24 +++++++++++
 r/man/make_zones.Rd     | 17 ++++++++
 8 files changed, 306 insertions(+)
 create mode 100644 r/.gitignore
 create mode 100644 r/DESCRIPTION
 create mode 100644 r/NAMESPACE
 create mode 100644 r/R/setup.R
 create mode 100644 r/README.md
 create mode 100644 r/README.qmd
 create mode 100644 r/man/make_elevation.Rd
 create mode 100644 r/man/make_zones.Rd

diff --git a/r/.gitignore b/r/.gitignore
new file mode 100644
index 0000000..075b254
--- /dev/null
+++ b/r/.gitignore
@@ -0,0 +1 @@
+/.quarto/
diff --git a/r/DESCRIPTION b/r/DESCRIPTION
new file mode 100644
index 0000000..abaeea4
--- /dev/null
+++ b/r/DESCRIPTION
@@ -0,0 +1,23 @@
+Package: od2net
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Imports: 
+    dplyr,
+    osmextract,
+    R.utils,
+    readr,
+    sf
+Suggests:
+    simodels (>= 0.1.0)
+Depends: 
+    R (>= 2.10)
+LazyData: true
+URL: https://acteng.github.io/od2net/
diff --git a/r/NAMESPACE b/r/NAMESPACE
new file mode 100644
index 0000000..6ae9268
--- /dev/null
+++ b/r/NAMESPACE
@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+
diff --git a/r/R/setup.R b/r/R/setup.R
new file mode 100644
index 0000000..c54e644
--- /dev/null
+++ b/r/R/setup.R
@@ -0,0 +1,90 @@
+# Aim: generate input data for od2net with R
+
+#' Generate a 'zones.geojson' file
+#' 
+#' This function requires a zones file, e.g.
+#' "https://raw.githubusercontent.com/nptscot/npt/main/data-raw/zones_edinburgh.geojson"
+#' or a file on your computer.
+#' It will generate a file in the input/ folder
+#' 
+#' @param file Location or URL of zones file
+make_zones = function(file) {
+  zones = sf::read_sf(file)[1]
+  names(zones)[1] = "name"
+  sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
+}
+
+getbbox_from_zones = function() {
+  zones = sf::st_read("input/zones.geojson")
+  bbox = sf::st_bbox(zones)
+  paste0(bbox, collapse = ",")
+}
+
+make_osm = function(force_download = FALSE) {
+  zones = sf::read_sf("input/zones.geojson")
+  zones_union = sf::st_union(zones)
+  osmextract_match = osmextract::oe_match(place = zones_union)
+  osmextract::oe_download(file_url = osmextract_match$url, download_directory = "input", force_download = force_download)
+  input_pbf = list.files(path = "input", pattern = basename(osmextract_match$url), full.names = TRUE)
+  bb = getbbox_from_zones()
+  msg = paste0("osmium extract -b ", bb, " ", input_pbf, " -o input/input.osm.pbf --overwrite")
+  system(msg)
+}
+
+#' Get elevation data
+#' 
+#' This function downloads elevation data from a source such as
+#' https://play.abstreet.org/dev/data/input/shared/elevation/UK-dem-50m-4326.tif.gz
+#' or https://assets.od2net.org/input/LisboaIST_10m_4326.tif
+#' 
+#' @param url Full URL of the elevation dataset if available
+#' @param file File name if hosted on a known site
+#' @param base_url Base URL associated with the 'file' argument
+#' 
+make_elevation = function(
+    url = NULL,
+    file = "UK-dem-50m-4326.tif.gz",
+    base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/"
+    ) {
+  if (is.null(url)) {
+    url = paste0(base_url, file)
+  }
+  is_gzip = grepl(pattern = "gz", url)
+  # Download the file
+    if (!file.exists("input/elevation.tif") && is_gzip) {
+      download.file(
+          url = url,
+          destfile = "input/elevation.tif.gz"
+      )
+      R.utils::gunzip("input/elevation.tif.gz", destname = "input/elevation.tif")
+    } else {
+      download.file(
+        url = url,
+        destfile = "input/elevation.tif"
+      )
+    }
+}
+
+make_origins = function() {
+  buildings = sf::read_sf("input/input.osm.pbf", query = "SELECT osm_id FROM multipolygons WHERE building IS NOT NULL")
+  use_sf = sf::sf_use_s2(FALSE)
+  centroids = sf::st_centroid(buildings)
+  sf::sf_use_s2(use_sf)
+  sf::write_sf(centroids, "input/buildings.geojson", delete_dsn = TRUE)
+}
+
+make_od = function() {
+  od = readr::read_csv("https://raw.githubusercontent.com/nptscot/npt/main/data-raw/od_subset.csv")
+  od = od |>
+    dplyr::transmute(from = geo_code1, to = geo_code2, count = bicycle)
+  readr::write_csv(od, "input/od.csv")
+}
+
+main = function() {
+  dir.create("input", showWarnings = FALSE)
+  make_zones()
+  make_osm()
+  # make_elevation()
+  make_origins()
+  make_od()
+}
diff --git a/r/README.md b/r/README.md
new file mode 100644
index 0000000..e480e4d
--- /dev/null
+++ b/r/README.md
@@ -0,0 +1,65 @@
+# Preparing OD data for network generation with od2net
+
+
+This R package provides functions to prepare OD data for network
+generation with the `od2net` tool, as illustrated in the example below.
+
+``` r
+source("R/setup.R")
+dir.create("input", showWarnings = FALSE)
+make_zones("https://github.com/acteng/netgen/raw/main/input/zones_york.geojson")
+make_osm()
+make_origins()
+make_elevation()
+destinations = destinations_york # Provided in the R package
+names(destinations)[1] = "name"
+destinations = destinations[1]
+class(destinations$name) = "character"
+sf::write_sf(destinations, "https://github.com/acteng/netgen/raw/main/input/destinations.geojson", delete_dsn = TRUE)
+# Save the OD dataset:
+od = od_geo |>
+  sf::st_drop_geometry() |>
+  transmute(from = O, to = as.character(D), count = round(trips_modelled))
+readr::write_csv(od, "input/od.csv", quote = "all")
+```
+
+Then create a config.json file, e.g. with the following content:
+
+``` json
+{
+  "requests": {
+    "description": "Test data for SchoolRoutes project.",
+    "pattern": {
+      "ZoneToPoint": {
+        "zones_path": "zones.geojson",
+        "destinations_path": "destinations.geojson",
+        "csv_path": "od.csv",
+         "origin_zone_centroid_fallback": false
+      }
+    },
+    "origins_path": "buildings.geojson",
+    "destinations_path": "destinations.geojson"
+  },
+  "cost": "Distance",
+  "uptake": "Identity",
+  "lts": "BikeOttawa",
+  "elevation_geotiff": "elevation.tif"
+}
+```
+
+Then run the following code to generate the network:
+
+Run the tool with Docker as follows:
+
+``` bash
+# On Linux:
+sudo docker run -v $(pwd):/app ghcr.io/urban-analytics-technology-platform/od2net:main /app/config.json
+# or in Windows:
+sudo docker run -v ${pwd}:/app ghcr.io/urban-analytics-technology-platform/od2net:main /app/config.json
+```
+
+After that you should see the following in the output folder:
+
+``` r
+fs::dir_tree("output")
+```
diff --git a/r/README.qmd b/r/README.qmd
new file mode 100644
index 0000000..85da2a1
--- /dev/null
+++ b/r/README.qmd
@@ -0,0 +1,84 @@
+---
+title: Preparing OD data for network generation with od2net
+#| eval: false
+#| echo: false
+format: gfm
+execute: 
+  message: false
+  warning: false
+---
+
+This R package provides functions to prepare OD data for network generation with the `od2net` tool, as illustrated in the example below.
+
+
+```{r}
+#| eval: false
+source("R/setup.R")
+dir.create("input", showWarnings = FALSE)
+make_zones("https://github.com/acteng/netgen/raw/main/input/zones_york.geojson")
+make_osm()
+make_origins()
+make_elevation()
+destinations = destinations_york # Provided in the R package
+names(destinations)[1] = "name"
+destinations = destinations[1]
+class(destinations$name) = "character"
+sf::write_sf(destinations, "https://github.com/acteng/netgen/raw/main/input/destinations.geojson", delete_dsn = TRUE)
+# Save the OD dataset:
+od = od_geo |>
+  sf::st_drop_geometry() |>
+  transmute(from = O, to = as.character(D), count = round(trips_modelled))
+readr::write_csv(od, "input/od.csv", quote = "all")
+```
+
+Then create a config.json file, e.g. with the following content:
+
+```json
+{
+  "requests": {
+    "description": "Test data for SchoolRoutes project.",
+    "pattern": {
+      "ZoneToPoint": {
+        "zones_path": "zones.geojson",
+        "destinations_path": "destinations.geojson",
+        "csv_path": "od.csv",
+         "origin_zone_centroid_fallback": false
+      }
+    },
+    "origins_path": "buildings.geojson",
+    "destinations_path": "destinations.geojson"
+  },
+  "cost": "Distance",
+  "uptake": "Identity",
+  "lts": "BikeOttawa",
+  "elevation_geotiff": "elevation.tif"
+}
+```
+
+Then run the following code to generate the network:
+
+Run the tool with Docker as follows:
+
+
+```{bash}
+#| eval: false
+# On Linux:
+sudo docker run -v $(pwd):/app ghcr.io/urban-analytics-technology-platform/od2net:main /app/config.json
+# or in Windows:
+sudo docker run -v ${pwd}:/app ghcr.io/urban-analytics-technology-platform/od2net:main /app/config.json
+```
+
+```{r}
+#| eval: false
+#| echo: false
+system("docker run -v $(pwd):/app ghcr.io/urban-analytics-technology-platform/od2net:main /app/config.json")
+```
+
+After that you should see the following in the output folder:
+
+```{r}
+#| eval: false
+fs::dir_tree("output")
+```
+
+
diff --git a/r/man/make_elevation.Rd b/r/man/make_elevation.Rd
new file mode 100644
index 0000000..af111f8
--- /dev/null
+++ b/r/man/make_elevation.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/setup.R
+\name{make_elevation}
+\alias{make_elevation}
+\title{Get elevation data}
+\usage{
+make_elevation(
+  url = NULL,
+  file = "UK-dem-50m-4326.tif.gz",
+  base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/"
+)
+}
+\arguments{
+\item{url}{Full URL of the elevation dataset if available}
+
+\item{file}{File name if hosted on a known site}
+
+\item{base_url}{Base URL associated with the 'file' argument}
+}
+\description{
+This function downloads elevation data from a source such as
+https://play.abstreet.org/dev/data/input/shared/elevation/UK-dem-50m-4326.tif.gz
+or https://assets.od2net.org/input/LisboaIST_10m_4326.tif
+}
diff --git a/r/man/make_zones.Rd b/r/man/make_zones.Rd
new file mode 100644
index 0000000..bfcedee
--- /dev/null
+++ b/r/man/make_zones.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/setup.R
+\name{make_zones}
+\alias{make_zones}
+\title{Generate a 'zones.geojson' file}
+\usage{
+make_zones(file)
+}
+\arguments{
+\item{file}{Location or URL of zones file}
+}
+\description{
+This function requires a zones file, e.g.
+"https://raw.githubusercontent.com/nptscot/npt/main/data-raw/zones_edinburgh.geojson"
+or a file on your computer.
+It will generate a file in the input/ folder
+}

From e6be6eb2bd6db0595b36ab2ee62cb5ac0cdf42dd Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:03:16 +0100
Subject: [PATCH 02/10] Add URL

---
 r/DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/r/DESCRIPTION b/r/DESCRIPTION
index abaeea4..cf6d735 100644
--- a/r/DESCRIPTION
+++ b/r/DESCRIPTION
@@ -20,4 +20,4 @@ Suggests:
 Depends: 
     R (>= 2.10)
 LazyData: true
-URL: https://acteng.github.io/od2net/
+URL: https://urban-analytics-technology-platform.github.io/od2net/r/, https://github.com/urban-analytics-technology-platform/od2net

From 2e54269447645403e841ce2e7990edada2548692 Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:05:01 +0100
Subject: [PATCH 03/10] Port make_zones() to README, style file

---
 r/R/setup.R  | 53 ++++++++++++++++++----------------------------------
 r/README.qmd | 29 +++++++++++++++++++++++++++-
 2 files changed, 46 insertions(+), 36 deletions(-)

diff --git a/r/R/setup.R b/r/R/setup.R
index c54e644..ce05477 100644
--- a/r/R/setup.R
+++ b/r/R/setup.R
@@ -1,27 +1,11 @@
-# Aim: generate input data for od2net with R
-
-#' Generate a 'zones.geojson' file
-#' 
-#' This function requires a zones file, e.g.
-#' "https://raw.githubusercontent.com/nptscot/npt/main/data-raw/zones_edinburgh.geojson"
-#' or a file on your computer.
-#' It will generate a file in the input/ folder
-#' 
-#' @param file Location or URL of zones file
-make_zones = function(file) {
-  zones = sf::read_sf(file)[1]
-  names(zones)[1] = "name"
-  sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
-}
-
 getbbox_from_zones = function() {
   zones = sf::st_read("input/zones.geojson")
   bbox = sf::st_bbox(zones)
   paste0(bbox, collapse = ",")
 }
 
-make_osm = function(force_download = FALSE) {
-  zones = sf::read_sf("input/zones.geojson")
+make_osm = function(force_download = FALSE, zones_file = "input/zones.geojson") {
+  zones = sf::read_sf(zones_file)
   zones_union = sf::st_union(zones)
   osmextract_match = osmextract::oe_match(place = zones_union)
   osmextract::oe_download(file_url = osmextract_match$url, download_directory = "input", force_download = force_download)
@@ -32,37 +16,36 @@ make_osm = function(force_download = FALSE) {
 }
 
 #' Get elevation data
-#' 
+#'
 #' This function downloads elevation data from a source such as
 #' https://play.abstreet.org/dev/data/input/shared/elevation/UK-dem-50m-4326.tif.gz
 #' or https://assets.od2net.org/input/LisboaIST_10m_4326.tif
-#' 
+#'
 #' @param url Full URL of the elevation dataset if available
 #' @param file File name if hosted on a known site
 #' @param base_url Base URL associated with the 'file' argument
-#' 
+#'
 make_elevation = function(
     url = NULL,
     file = "UK-dem-50m-4326.tif.gz",
-    base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/"
-    ) {
+    base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/") {
   if (is.null(url)) {
     url = paste0(base_url, file)
   }
   is_gzip = grepl(pattern = "gz", url)
   # Download the file
-    if (!file.exists("input/elevation.tif") && is_gzip) {
-      download.file(
-          url = url,
-          destfile = "input/elevation.tif.gz"
-      )
-      R.utils::gunzip("input/elevation.tif.gz", destname = "input/elevation.tif")
-    } else {
-      download.file(
-        url = url,
-        destfile = "input/elevation.tif"
-      )
-    }
+  if (!file.exists("input/elevation.tif") && is_gzip) {
+    download.file(
+      url = url,
+      destfile = "input/elevation.tif.gz"
+    )
+    R.utils::gunzip("input/elevation.tif.gz", destname = "input/elevation.tif")
+  } else {
+    download.file(
+      url = url,
+      destfile = "input/elevation.tif"
+    )
+  }
 }
 
 make_origins = function() {
diff --git a/r/README.qmd b/r/README.qmd
index 85da2a1..b332280 100644
--- a/r/README.qmd
+++ b/r/README.qmd
@@ -10,10 +10,18 @@ execute:
 
 This R package provides functions to prepare OD data for network generation with the `od2net` tool, as illustrated in the example below.
 
+## Example
+
+Imagine you want to generate a route network with values on the links representing the number of pupils/parents on their way to school each school day. The following code shows how to prepare the data for the `od2net` tool.
+
 
 ```{r}
 #| eval: false
-source("R/setup.R")
+# Install pak if not already installed:
+if (!requireNamespace("pak", quietly = TRUE)) {
+  install.packages("pak")
+}
+pak::pkg_install("robinlovelace/od2net/r@67-r-port")
 dir.create("input", showWarnings = FALSE)
 make_zones("https://github.com/acteng/netgen/raw/main/input/zones_york.geojson")
 make_osm()
@@ -81,4 +89,23 @@ After that you should see the following in the output folder:
 fs::dir_tree("output")
 ```
 
+Helper functions
+
+```{r}
+# Aim: generate input data for od2net with R
+
+#' Generate a 'zones.geojson' file
+#' 
+#' This function requires a zones file, e.g.
+#' "https://raw.githubusercontent.com/nptscot/npt/main/data-raw/zones_edinburgh.geojson"
+#' or a file on your computer.
+#' It will generate a file in the input/ folder
+#' 
+#' @param file Location or URL of zones file
+make_zones = function(file) {
+  zones = sf::read_sf(file)[1]
+  names(zones)[1] = "name"
+  sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
+}
+
 

From 0ff2e2051fa9d1a9361dfcd4d3e6325fbdefd62f Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:09:12 +0100
Subject: [PATCH 04/10] More tweaks to pkg

---
 r/R/setup.R  | 19 ++-----------------
 r/README.qmd | 13 +++++++++++++
 2 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/r/R/setup.R b/r/R/setup.R
index ce05477..49320a9 100644
--- a/r/R/setup.R
+++ b/r/R/setup.R
@@ -24,7 +24,8 @@ make_osm = function(force_download = FALSE, zones_file = "input/zones.geojson")
 #' @param url Full URL of the elevation dataset if available
 #' @param file File name if hosted on a known site
 #' @param base_url Base URL associated with the 'file' argument
-#'
+#' @return NULL
+#' @export
 make_elevation = function(
     url = NULL,
     file = "UK-dem-50m-4326.tif.gz",
@@ -55,19 +56,3 @@ make_origins = function() {
   sf::sf_use_s2(use_sf)
   sf::write_sf(centroids, "input/buildings.geojson", delete_dsn = TRUE)
 }
-
-make_od = function() {
-  od = readr::read_csv("https://raw.githubusercontent.com/nptscot/npt/main/data-raw/od_subset.csv")
-  od = od |>
-    dplyr::transmute(from = geo_code1, to = geo_code2, count = bicycle)
-  readr::write_csv(od, "input/od.csv")
-}
-
-main = function() {
-  dir.create("input", showWarnings = FALSE)
-  make_zones()
-  make_osm()
-  # make_elevation()
-  make_origins()
-  make_od()
-}
diff --git a/r/README.qmd b/r/README.qmd
index b332280..5785e24 100644
--- a/r/README.qmd
+++ b/r/README.qmd
@@ -91,6 +91,12 @@ fs::dir_tree("output")
 
 Helper functions
 
+<details>
+
+The following functions could be useful when you're preparing the data, and show the kind of data preparation that is required.
+
+<!-- TODO: consider adding these functions to the package at some stage? -->
+
 ```{r}
 # Aim: generate input data for od2net with R
 
@@ -108,4 +114,11 @@ make_zones = function(file) {
   sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
 }
 
+make_od = function() {
+  od = readr::read_csv("https://raw.githubusercontent.com/nptscot/npt/main/data-raw/od_subset.csv")
+  od = od |>
+    dplyr::transmute(from = geo_code1, to = geo_code2, count = bicycle)
+  readr::write_csv(od, "input/od.csv")
+}
+```
 

From c2be2b0974892933e1e4d6e6d3eba25b84dbdc34 Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:11:33 +0100
Subject: [PATCH 05/10] Document functions

---
 r/R/setup.R | 50 +++++++++++++++++++++++++++-----------------------
 1 file changed, 27 insertions(+), 23 deletions(-)

diff --git a/r/R/setup.R b/r/R/setup.R
index 49320a9..84634db 100644
--- a/r/R/setup.R
+++ b/r/R/setup.R
@@ -1,33 +1,37 @@
-getbbox_from_zones = function() {
-  zones = sf::st_read("input/zones.geojson")
+#' Get bounding box from zones
+#'
+#' This function reads a GeoJSON file containing zones and calculates the bounding box of the zones.
+#' 
+#' @param zones_file Path to the GeoJSON file containing zones. Default is 'input/zones.geojson'.
+#'
+#' @return A character string representing the bounding box in the format "xmin, ymin, xmax, ymax".
+#' @export
+getbbox_from_zones = function(zones_file = "input/zones.geojson") {
+  zones = sf::st_read(zones_file)
   bbox = sf::st_bbox(zones)
   paste0(bbox, collapse = ",")
 }
 
-make_osm = function(force_download = FALSE, zones_file = "input/zones.geojson") {
-  zones = sf::read_sf(zones_file)
-  zones_union = sf::st_union(zones)
-  osmextract_match = osmextract::oe_match(place = zones_union)
-  osmextract::oe_download(file_url = osmextract_match$url, download_directory = "input", force_download = force_download)
-  input_pbf = list.files(path = "input", pattern = basename(osmextract_match$url), full.names = TRUE)
-  bb = getbbox_from_zones()
-  msg = paste0("osmium extract -b ", bb, " ", input_pbf, " -o input/input.osm.pbf --overwrite")
-  system(msg)
-}
-
-#' Get elevation data
+#' make_osm Function
+#'
+#' This function is used to download and extract OpenStreetMap (OSM) data based on specified zones.
+#'
+#' @param force_download A logical value indicating whether to force the download of OSM data even if it already exists. Default is \code{FALSE}.
+#' @param zones_file The file path or name of the zones file in GeoJSON format. Default is \code{"input/zones.geojson"}.
+#'
+#' @return This function does not return any value. It downloads and extracts OSM data based on the specified zones.
+#'
+#' @examples
+#' make_osm(force_download = TRUE, zones_file = "input/zones.geojson")
 #'
-#' This function downloads elevation data from a source such as
-#' https://play.abstreet.org/dev/data/input/shared/elevation/UK-dem-50m-4326.tif.gz
-#' or https://assets.od2net.org/input/LisboaIST_10m_4326.tif
+#' @import sf
+#' @import osmextract
+#' @importFrom osmextract oe_match oe_download
+#' @importFrom osmium getbbox_from_zones
+#' @importFrom base system
 #'
-#' @param url Full URL of the elevation dataset if available
-#' @param file File name if hosted on a known site
-#' @param base_url Base URL associated with the 'file' argument
-#' @return NULL
 #' @export
-make_elevation = function(
-    url = NULL,
+make_osm = function(force_download = FALSE, zones_file = "input/zones.geojson") {  # Function coderl}
     file = "UK-dem-50m-4326.tif.gz",
     base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/") {
   if (is.null(url)) {

From 6f48b48dea0ecbec3ed45044f3bdcc0a10a5fc31 Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:11:51 +0100
Subject: [PATCH 06/10] Reformat

---
 r/R/setup.R | 29 +++++++++--------------------
 1 file changed, 9 insertions(+), 20 deletions(-)

diff --git a/r/R/setup.R b/r/R/setup.R
index 84634db..684dfb2 100644
--- a/r/R/setup.R
+++ b/r/R/setup.R
@@ -31,26 +31,15 @@ getbbox_from_zones = function(zones_file = "input/zones.geojson") {
 #' @importFrom base system
 #'
 #' @export
-make_osm = function(force_download = FALSE, zones_file = "input/zones.geojson") {  # Function coderl}
-    file = "UK-dem-50m-4326.tif.gz",
-    base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/") {
-  if (is.null(url)) {
-    url = paste0(base_url, file)
-  }
-  is_gzip = grepl(pattern = "gz", url)
-  # Download the file
-  if (!file.exists("input/elevation.tif") && is_gzip) {
-    download.file(
-      url = url,
-      destfile = "input/elevation.tif.gz"
-    )
-    R.utils::gunzip("input/elevation.tif.gz", destname = "input/elevation.tif")
-  } else {
-    download.file(
-      url = url,
-      destfile = "input/elevation.tif"
-    )
-  }
+make_osm = function(force_download = FALSE, zones_file = "input/zones.geojson") {
+  zones = sf::read_sf(zones_file)
+  zones_union = sf::st_union(zones)
+  osmextract_match = osmextract::oe_match(place = zones_union)
+  osmextract::oe_download(file_url = osmextract_match$url, download_directory = "input", force_download = force_download)
+  input_pbf = list.files(path = "input", pattern = basename(osmextract_match$url), full.names = TRUE)
+  bb = getbbox_from_zones()
+  msg = paste0("osmium extract -b ", bb, " ", input_pbf, " -o input/input.osm.pbf --overwrite")
+  system(msg)
 }
 
 make_origins = function() {

From dc140363d9bd43119e5f7ae70e44edf77c8a941b Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:17:11 +0100
Subject: [PATCH 07/10] Re-document

---
 r/.devcontainer/devcontainer.json | 39 +++++++++++++++++++++++++++++++
 r/NAMESPACE                       |  2 ++
 r/R/setup.R                       | 20 ++++++++--------
 r/man/getbbox_from_zones.Rd       | 17 ++++++++++++++
 r/man/make_elevation.Rd           | 24 -------------------
 r/man/make_osm.Rd                 | 30 ++++++++++++++++++++++++
 r/man/make_zones.Rd               | 17 --------------
 7 files changed, 98 insertions(+), 51 deletions(-)
 create mode 100644 r/.devcontainer/devcontainer.json
 create mode 100644 r/man/getbbox_from_zones.Rd
 delete mode 100644 r/man/make_elevation.Rd
 create mode 100644 r/man/make_osm.Rd
 delete mode 100644 r/man/make_zones.Rd

diff --git a/r/.devcontainer/devcontainer.json b/r/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..fc3e717
--- /dev/null
+++ b/r/.devcontainer/devcontainer.json
@@ -0,0 +1,39 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/debian
+{
+	"name": "Debian",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "ghcr.io/geocompx/docker:rust",
+	"customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+		  // Add the IDs of extensions you want installed when the container is created.
+		  // Including reditorsupport.r and the quarto extension.
+		  "extensions": [
+			"reditor-support.r",
+			"quarto.quarto",
+			"ms-python.python",
+			"ms-toolsai.jupyter"
+		  ]
+		}
+	  }
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+
+	// These are now set in the Dockerfile:
+	// https://github.com/geocompx/docker/blob/master/rust/Dockerfile
+	// "postCreateCommand": [
+	// 	"bash .devcontainer/install-additional-dependencies.sh"
+	// ]
+
+}
diff --git a/r/NAMESPACE b/r/NAMESPACE
index 6ae9268..54e3111 100644
--- a/r/NAMESPACE
+++ b/r/NAMESPACE
@@ -1,2 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
+export(getbbox_from_zones)
+export(make_osm)
diff --git a/r/R/setup.R b/r/R/setup.R
index 684dfb2..ce57a31 100644
--- a/r/R/setup.R
+++ b/r/R/setup.R
@@ -18,27 +18,27 @@ getbbox_from_zones = function(zones_file = "input/zones.geojson") {
 #'
 #' @param force_download A logical value indicating whether to force the download of OSM data even if it already exists. Default is \code{FALSE}.
 #' @param zones_file The file path or name of the zones file in GeoJSON format. Default is \code{"input/zones.geojson"}.
+#' @param output_file The file path or name of the output OSM file in PBF format. Default is "input/input.osm.pbf".
 #'
 #' @return This function does not return any value. It downloads and extracts OSM data based on the specified zones.
 #'
 #' @examples
-#' make_osm(force_download = TRUE, zones_file = "input/zones.geojson")
-#'
-#' @import sf
-#' @import osmextract
-#' @importFrom osmextract oe_match oe_download
-#' @importFrom osmium getbbox_from_zones
-#' @importFrom base system
-#'
+#' if (file.exists("input/zones.geojson")) {
+#'   make_osm(force_download = TRUE, zones_file = "input/zones.geojson")
+#' }
 #' @export
-make_osm = function(force_download = FALSE, zones_file = "input/zones.geojson") {
+make_osm = function(
+  force_download = FALSE,
+  zones_file = "input/zones.geojson",
+  output_file = "input/input.osm.pbf"
+  ) {
   zones = sf::read_sf(zones_file)
   zones_union = sf::st_union(zones)
   osmextract_match = osmextract::oe_match(place = zones_union)
   osmextract::oe_download(file_url = osmextract_match$url, download_directory = "input", force_download = force_download)
   input_pbf = list.files(path = "input", pattern = basename(osmextract_match$url), full.names = TRUE)
   bb = getbbox_from_zones()
-  msg = paste0("osmium extract -b ", bb, " ", input_pbf, " -o input/input.osm.pbf --overwrite")
+  msg = paste0("osmium extract -b ", bb, " ", input_pbf, " -o ", output_file, " --overwrite")
   system(msg)
 }
 
diff --git a/r/man/getbbox_from_zones.Rd b/r/man/getbbox_from_zones.Rd
new file mode 100644
index 0000000..0e89a8e
--- /dev/null
+++ b/r/man/getbbox_from_zones.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/setup.R
+\name{getbbox_from_zones}
+\alias{getbbox_from_zones}
+\title{Get bounding box from zones}
+\usage{
+getbbox_from_zones(zones_file = "input/zones.geojson")
+}
+\arguments{
+\item{zones_file}{Path to the GeoJSON file containing zones. Default is 'input/zones.geojson'.}
+}
+\value{
+A character string representing the bounding box in the format "xmin, ymin, xmax, ymax".
+}
+\description{
+This function reads a GeoJSON file containing zones and calculates the bounding box of the zones.
+}
diff --git a/r/man/make_elevation.Rd b/r/man/make_elevation.Rd
deleted file mode 100644
index af111f8..0000000
--- a/r/man/make_elevation.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/setup.R
-\name{make_elevation}
-\alias{make_elevation}
-\title{Get elevation data}
-\usage{
-make_elevation(
-  url = NULL,
-  file = "UK-dem-50m-4326.tif.gz",
-  base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/"
-)
-}
-\arguments{
-\item{url}{Full URL of the elevation dataset if available}
-
-\item{file}{File name if hosted on a known site}
-
-\item{base_url}{Base URL associated with the 'file' argument}
-}
-\description{
-This function downloads elevation data from a source such as
-https://play.abstreet.org/dev/data/input/shared/elevation/UK-dem-50m-4326.tif.gz
-or https://assets.od2net.org/input/LisboaIST_10m_4326.tif
-}
diff --git a/r/man/make_osm.Rd b/r/man/make_osm.Rd
new file mode 100644
index 0000000..10a7af9
--- /dev/null
+++ b/r/man/make_osm.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/setup.R
+\name{make_osm}
+\alias{make_osm}
+\title{make_osm Function}
+\usage{
+make_osm(
+  force_download = FALSE,
+  zones_file = "input/zones.geojson",
+  output_file = "input/input.osm.pbf"
+)
+}
+\arguments{
+\item{force_download}{A logical value indicating whether to force the download of OSM data even if it already exists. Default is \code{FALSE}.}
+
+\item{zones_file}{The file path or name of the zones file in GeoJSON format. Default is \code{"input/zones.geojson"}.}
+
+\item{output_file}{The file path or name of the output OSM file in PBF format. Default is "input/input.osm.pbf".}
+}
+\value{
+This function does not return any value. It downloads and extracts OSM data based on the specified zones.
+}
+\description{
+This function is used to download and extract OpenStreetMap (OSM) data based on specified zones.
+}
+\examples{
+if (file.exists("input/zones.geojson")) {
+  make_osm(force_download = TRUE, zones_file = "input/zones.geojson")
+}
+}
diff --git a/r/man/make_zones.Rd b/r/man/make_zones.Rd
deleted file mode 100644
index bfcedee..0000000
--- a/r/man/make_zones.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/setup.R
-\name{make_zones}
-\alias{make_zones}
-\title{Generate a 'zones.geojson' file}
-\usage{
-make_zones(file)
-}
-\arguments{
-\item{file}{Location or URL of zones file}
-}
-\description{
-This function requires a zones file, e.g.
-"https://raw.githubusercontent.com/nptscot/npt/main/data-raw/zones_edinburgh.geojson"
-or a file on your computer.
-It will generate a file in the input/ folder
-}

From 0a66a15ee14ff3c9559a46560a66325e3169c803 Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:36:39 +0100
Subject: [PATCH 08/10] Changes for all R pkg checks to pass

---
 r/.Rbuildignore       |   5 ++
 r/.gitignore          |   1 +
 r/DESCRIPTION         |  10 +--
 r/LICENSE.md          | 194 ++++++++++++++++++++++++++++++++++++++++++
 r/NAMESPACE           |   1 +
 r/R/setup.R           |  21 ++++-
 r/man/make_origins.Rd |  26 ++++++
 7 files changed, 250 insertions(+), 8 deletions(-)
 create mode 100644 r/.Rbuildignore
 create mode 100644 r/LICENSE.md
 create mode 100644 r/man/make_origins.Rd

diff --git a/r/.Rbuildignore b/r/.Rbuildignore
new file mode 100644
index 0000000..2a2d5c2
--- /dev/null
+++ b/r/.Rbuildignore
@@ -0,0 +1,5 @@
+^README\.qmd$
+^input$
+^LICENSE\.md$
+^\.quarto$
+^\.devcontainer$
diff --git a/r/.gitignore b/r/.gitignore
index 075b254..d97264f 100644
--- a/r/.gitignore
+++ b/r/.gitignore
@@ -1 +1,2 @@
 /.quarto/
+input/
diff --git a/r/DESCRIPTION b/r/DESCRIPTION
index cf6d735..eee7619 100644
--- a/r/DESCRIPTION
+++ b/r/DESCRIPTION
@@ -5,18 +5,18 @@ Authors@R:
     person("First", "Last", , "first.last@example.com", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))
 Description: What the package does (one paragraph).
-License: MIT + file LICENSE
+License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Imports: 
-    dplyr,
     osmextract,
-    R.utils,
-    readr,
     sf
 Suggests:
-    simodels (>= 0.1.0)
+    simodels (>= 0.1.0),
+    readr,
+    dplyr,
+    R.utils,
 Depends: 
     R (>= 2.10)
 LazyData: true
diff --git a/r/LICENSE.md b/r/LICENSE.md
new file mode 100644
index 0000000..b62a9b5
--- /dev/null
+++ b/r/LICENSE.md
@@ -0,0 +1,194 @@
+Apache License
+==============
+
+_Version 2.0, January 2004_
+_&lt;<http://www.apache.org/licenses/>&gt;_
+
+### Terms and Conditions for use, reproduction, and distribution
+
+#### 1. Definitions
+
+“License” shall mean the terms and conditions for use, reproduction, and
+distribution as defined by Sections 1 through 9 of this document.
+
+“Licensor” shall mean the copyright owner or entity authorized by the copyright
+owner that is granting the License.
+
+“Legal Entity” shall mean the union of the acting entity and all other entities
+that control, are controlled by, or are under common control with that entity.
+For the purposes of this definition, “control” means **(i)** the power, direct or
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+contract or otherwise, or **(ii)** ownership of fifty percent (50%) or more of the
+outstanding shares, or **(iii)** beneficial ownership of such entity.
+
+“You” (or “Your”) shall mean an individual or Legal Entity exercising
+permissions granted by this License.
+
+“Source” form shall mean the preferred form for making modifications, including
+but not limited to software source code, documentation source, and configuration
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+
+“Object” form shall mean any form resulting from mechanical transformation or
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+
+“Work” shall mean the work of authorship, whether in Source or Object form, made
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+
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+is based on (or derived from) the Work and for which the editorial revisions,
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+“Contribution” shall mean any work of authorship, including the original version
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+
+“Contributor” shall mean Licensor and any individual or Legal Entity on behalf
+of whom a Contribution has been received by Licensor and subsequently
+incorporated within the Work.
+
+#### 2. Grant of Copyright License
+
+Subject to the terms and conditions of this License, each Contributor hereby
+grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free,
+irrevocable copyright license to reproduce, prepare Derivative Works of,
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+    limitations under the License.
diff --git a/r/NAMESPACE b/r/NAMESPACE
index 54e3111..1730d8a 100644
--- a/r/NAMESPACE
+++ b/r/NAMESPACE
@@ -1,4 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
 export(getbbox_from_zones)
+export(make_origins)
 export(make_osm)
diff --git a/r/R/setup.R b/r/R/setup.R
index ce57a31..7353769 100644
--- a/r/R/setup.R
+++ b/r/R/setup.R
@@ -42,10 +42,25 @@ make_osm = function(
   system(msg)
 }
 
-make_origins = function() {
-  buildings = sf::read_sf("input/input.osm.pbf", query = "SELECT osm_id FROM multipolygons WHERE building IS NOT NULL")
+#' make_origins function
+#'
+#' This function reads an OpenStreetMap file, selects the multipolygons with a non-null building attribute,
+#' calculates the centroids of the selected buildings, and writes the resulting centroids to a GeoJSON file.
+#' 
+#' @param osm_file The file path or name of the OSM file in PBF format. Default is "input/input.osm.pbf".
+#' @param query The SQL query to select the multipolygons with a non-null building attribute. Default is "SELECT osm_id FROM multipolygons WHERE building IS NOT NULL".
+#' @param output_file The file path or name of the output GeoJSON file containing the centroids of the selected buildings. Default is "input/buildings.geojson".
+#'
+#' @return None
+#' @export
+make_origins = function(
+  osm_file = "input/input.osm.pbf",
+  query = "SELECT osm_id FROM multipolygons WHERE building IS NOT NULL",
+  output_file = "input/buildings.geojson"
+  ) {
+  buildings = sf::read_sf(osm_file, query = query)
   use_sf = sf::sf_use_s2(FALSE)
   centroids = sf::st_centroid(buildings)
   sf::sf_use_s2(use_sf)
-  sf::write_sf(centroids, "input/buildings.geojson", delete_dsn = TRUE)
+  sf::write_sf(centroids, output_file, delete_dsn = TRUE)
 }
diff --git a/r/man/make_origins.Rd b/r/man/make_origins.Rd
new file mode 100644
index 0000000..3eabb2a
--- /dev/null
+++ b/r/man/make_origins.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/setup.R
+\name{make_origins}
+\alias{make_origins}
+\title{make_origins function}
+\usage{
+make_origins(
+  osm_file = "input/input.osm.pbf",
+  query = "SELECT osm_id FROM multipolygons WHERE building IS NOT NULL",
+  output_file = "input/buildings.geojson"
+)
+}
+\arguments{
+\item{osm_file}{The file path or name of the OSM file in PBF format. Default is "input/input.osm.pbf".}
+
+\item{query}{The SQL query to select the multipolygons with a non-null building attribute. Default is "SELECT osm_id FROM multipolygons WHERE building IS NOT NULL".}
+
+\item{output_file}{The file path or name of the output GeoJSON file containing the centroids of the selected buildings. Default is "input/buildings.geojson".}
+}
+\value{
+None
+}
+\description{
+This function reads an OpenStreetMap file, selects the multipolygons with a non-null building attribute,
+calculates the centroids of the selected buildings, and writes the resulting centroids to a GeoJSON file.
+}

From c698bccc421e544022d086915f9f1de4d54adf02 Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:53:38 +0100
Subject: [PATCH 09/10] Document, ready for review

---
 r/.Rbuildignore |   3 +
 r/.gitignore    |   2 +
 r/README.md     | 144 ++++++++++++++++++++++++++++++++++++++----------
 r/README.qmd    | 144 ++++++++++++++++++++++++++++--------------------
 4 files changed, 205 insertions(+), 88 deletions(-)

diff --git a/r/.Rbuildignore b/r/.Rbuildignore
index 2a2d5c2..687a27e 100644
--- a/r/.Rbuildignore
+++ b/r/.Rbuildignore
@@ -3,3 +3,6 @@
 ^LICENSE\.md$
 ^\.quarto$
 ^\.devcontainer$
+^output$
+^intermediate$
+^config\.json$
diff --git a/r/.gitignore b/r/.gitignore
index d97264f..638e7a2 100644
--- a/r/.gitignore
+++ b/r/.gitignore
@@ -1,2 +1,4 @@
 /.quarto/
 input/
+output/
+intermediate/
diff --git a/r/README.md b/r/README.md
index e480e4d..1bd6a25 100644
--- a/r/README.md
+++ b/r/README.md
@@ -4,49 +4,136 @@
 This R package provides functions to prepare OD data for network
 generation with the `od2net` tool, as illustrated in the example below.
 
+## Example
+
+Imagine you want to generate a route network with values on the links
+representing the number of pupils/parents on their way to school each
+school day. The following code shows how to prepare the data for the
+`od2net` tool.
+
+The following functions could be useful when you’re preparing the data,
+and show the kind of data preparation that is required.
+
+<details>
+<!-- TODO: consider adding these functions to the package at some stage? -->
+
 ``` r
-source("R/setup.R")
+# Aim: generate input data for od2net with R
+
+#' Generate a 'zones.geojson' file
+#' 
+#' This function requires a zones file, e.g.
+#' "https://raw.githubusercontent.com/nptscot/npt/main/data-raw/zones_edinburgh.geojson"
+#' or a file on your computer.
+#' It will generate a file in the input/ folder
+#' 
+#' @param file Location or URL of zones file
+make_zones = function(file) {
+  zones = sf::read_sf(file)[1]
+  names(zones)[1] = "name"
+  sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
+}
+
+make_od = function() {
+  od = readr::read_csv("https://raw.githubusercontent.com/nptscot/npt/main/data-raw/od_subset.csv")
+  od = od |>
+    dplyr::transmute(from = geo_code1, to = geo_code2, count = bicycle)
+  readr::write_csv(od, "input/od.csv")
+}
+#' Get elevation data
+#' 
+#' This function downloads elevation data from a source such as
+#' https://play.abstreet.org/dev/data/input/shared/elevation/UK-dem-50m-4326.tif.gz
+#' or https://assets.od2net.org/input/LisboaIST_10m_4326.tif
+#' 
+#' @param url Full URL of the elevation dataset if available
+#' @param file File name if hosted on a known site
+#' @param base_url Base URL associated with the 'file' argument
+#' 
+make_elevation = function(
+    url = NULL,
+    file = "UK-dem-50m-4326.tif.gz",
+    base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/"
+    ) {
+  if (is.null(url)) {
+    url = paste0(base_url, file)
+  }
+  is_gzip = grepl(pattern = "gz", url)
+  # Download the file
+    if (!file.exists("input/elevation.tif") && is_gzip) {
+      download.file(
+          url = url,
+          destfile = "input/elevation.tif.gz"
+      )
+      R.utils::gunzip("input/elevation.tif.gz", destname = "input/elevation.tif")
+    } else {
+      download.file(
+        url = url,
+        destfile = "input/elevation.tif"
+      )
+    }
+}
+```
+
+</details>
+
+``` r
+# Install pak if not already installed:
+if (!requireNamespace("pak", quietly = TRUE)) {
+  install.packages("pak")
+}
+pak::pkg_install("robinlovelace/od2net/r@67-r-port")
 dir.create("input", showWarnings = FALSE)
-make_zones("https://github.com/acteng/netgen/raw/main/input/zones_york.geojson")
-make_osm()
-make_origins()
+# Get some zones from a URL:
+uz = "https://github.com/acteng/netgen/raw/main/input/zones_york.geojson"
+make_zones(uz)
+sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
+make_osm(zones_file = "input/zones.geojson", output_file = "input/input.osm.pbf")
+make_origins(
+  osm_file = "input/input.osm.pbf",
+  query = "SELECT osm_id FROM multipolygons WHERE building IS NOT NULL",
+  output_file = "input/buildings.geojson"
+)
 make_elevation()
-destinations = destinations_york # Provided in the R package
+destinations = simodels::destinations_york # Provided in the R package
 names(destinations)[1] = "name"
 destinations = destinations[1]
 class(destinations$name) = "character"
-sf::write_sf(destinations, "https://github.com/acteng/netgen/raw/main/input/destinations.geojson", delete_dsn = TRUE)
+sf::write_sf(destinations, "input/destinations.geojson", delete_dsn = TRUE)
+od_geo = sf::read_sf("https://github.com/acteng/netgen/releases/download/v0.1.0/res_output.geojson")
 # Save the OD dataset:
 od = od_geo |>
   sf::st_drop_geometry() |>
-  transmute(from = O, to = as.character(D), count = round(trips_modelled))
+  dplyr::transmute(from = O, to = as.character(D), count = round(trips_modelled))
 readr::write_csv(od, "input/od.csv", quote = "all")
 ```
 
 Then create a config.json file, e.g. with the following content:
 
-``` json
-{
-  "requests": {
-    "description": "Test data for SchoolRoutes project.",
-    "pattern": {
-      "ZoneToPoint": {
-        "zones_path": "zones.geojson",
-        "destinations_path": "destinations.geojson",
-        "csv_path": "od.csv",
-         "origin_zone_centroid_fallback": false
-      }
-    },
-    "origins_path": "buildings.geojson",
-    "destinations_path": "destinations.geojson"
-  },
-  "cost": "Distance",
-  "uptake": "Identity",
-  "lts": "BikeOttawa",
-  "elevation_geotiff": "elevation.tif"
-}
+``` r
+readLines("config.json")
 ```
 
+\[1\] “{”  
+\[2\] ” "requests": {”  
+\[3\] ” "description": "Test data for SchoolRoutes project.",” \[4\] ”
+"pattern": {”  
+\[5\] ” "ZoneToPoint": {”  
+\[6\] ” "zones_path": "zones.geojson",”  
+\[7\] ” "destinations_path": "destinations.geojson",”  
+\[8\] ” "csv_path": "od.csv",”  
+\[9\] ” "origin_zone_centroid_fallback": false”  
+\[10\] ” }”  
+\[11\] ” },”  
+\[12\] ” "origins_path": "buildings.geojson",”  
+\[13\] ” "destinations_path": "destinations.geojson"”  
+\[14\] ” },”  
+\[15\] ” "cost": "Distance",”  
+\[16\] ” "uptake": "Identity",”  
+\[17\] ” "lts": "BikeOttawa",”  
+\[18\] ” "elevation_geotiff": "elevation.tif"”  
+\[19\] “}”
+
 Then run the following code to generate the network:
 
 Run the tool with Docker as follows:
@@ -58,7 +145,8 @@ sudo docker run -v $(pwd):/app ghcr.io/urban-analytics-technology-platform/od2ne
 sudo docker run -v ${pwd}:/app ghcr.io/urban-analytics-technology-platform/od2net:main /app/config.json
 ```
 
-After that you should see the following in the output folder:
+After that you should see something like the following in the output
+folder:
 
 ``` r
 fs::dir_tree("output")
diff --git a/r/README.qmd b/r/README.qmd
index 5785e24..e0a80e4 100644
--- a/r/README.qmd
+++ b/r/README.qmd
@@ -14,6 +14,72 @@ This R package provides functions to prepare OD data for network generation with
 
 Imagine you want to generate a route network with values on the links representing the number of pupils/parents on their way to school each school day. The following code shows how to prepare the data for the `od2net` tool.
 
+The following functions could be useful when you're preparing the data, and show the kind of data preparation that is required.
+
+<details>
+
+<!-- TODO: consider adding these functions to the package at some stage? -->
+
+```{r}
+# Aim: generate input data for od2net with R
+
+#' Generate a 'zones.geojson' file
+#' 
+#' This function requires a zones file, e.g.
+#' "https://raw.githubusercontent.com/nptscot/npt/main/data-raw/zones_edinburgh.geojson"
+#' or a file on your computer.
+#' It will generate a file in the input/ folder
+#' 
+#' @param file Location or URL of zones file
+make_zones = function(file) {
+  zones = sf::read_sf(file)[1]
+  names(zones)[1] = "name"
+  sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
+}
+
+make_od = function() {
+  od = readr::read_csv("https://raw.githubusercontent.com/nptscot/npt/main/data-raw/od_subset.csv")
+  od = od |>
+    dplyr::transmute(from = geo_code1, to = geo_code2, count = bicycle)
+  readr::write_csv(od, "input/od.csv")
+}
+#' Get elevation data
+#' 
+#' This function downloads elevation data from a source such as
+#' https://play.abstreet.org/dev/data/input/shared/elevation/UK-dem-50m-4326.tif.gz
+#' or https://assets.od2net.org/input/LisboaIST_10m_4326.tif
+#' 
+#' @param url Full URL of the elevation dataset if available
+#' @param file File name if hosted on a known site
+#' @param base_url Base URL associated with the 'file' argument
+#' 
+make_elevation = function(
+    url = NULL,
+    file = "UK-dem-50m-4326.tif.gz",
+    base_url = "https://play.abstreet.org/dev/data/input/shared/elevation/"
+    ) {
+  if (is.null(url)) {
+    url = paste0(base_url, file)
+  }
+  is_gzip = grepl(pattern = "gz", url)
+  # Download the file
+    if (!file.exists("input/elevation.tif") && is_gzip) {
+      download.file(
+          url = url,
+          destfile = "input/elevation.tif.gz"
+      )
+      R.utils::gunzip("input/elevation.tif.gz", destname = "input/elevation.tif")
+    } else {
+      download.file(
+        url = url,
+        destfile = "input/elevation.tif"
+      )
+    }
+}
+```
+
+</details>
+
 
 ```{r}
 #| eval: false
@@ -23,44 +89,35 @@ if (!requireNamespace("pak", quietly = TRUE)) {
 }
 pak::pkg_install("robinlovelace/od2net/r@67-r-port")
 dir.create("input", showWarnings = FALSE)
-make_zones("https://github.com/acteng/netgen/raw/main/input/zones_york.geojson")
-make_osm()
-make_origins()
+# Get some zones from a URL:
+uz = "https://github.com/acteng/netgen/raw/main/input/zones_york.geojson"
+make_zones(uz)
+sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
+make_osm(zones_file = "input/zones.geojson", output_file = "input/input.osm.pbf")
+make_origins(
+  osm_file = "input/input.osm.pbf",
+  query = "SELECT osm_id FROM multipolygons WHERE building IS NOT NULL",
+  output_file = "input/buildings.geojson"
+)
 make_elevation()
-destinations = destinations_york # Provided in the R package
+destinations = simodels::destinations_york # Provided in the R package
 names(destinations)[1] = "name"
 destinations = destinations[1]
 class(destinations$name) = "character"
-sf::write_sf(destinations, "https://github.com/acteng/netgen/raw/main/input/destinations.geojson", delete_dsn = TRUE)
+sf::write_sf(destinations, "input/destinations.geojson", delete_dsn = TRUE)
+od_geo = sf::read_sf("https://github.com/acteng/netgen/releases/download/v0.1.0/res_output.geojson")
 # Save the OD dataset:
 od = od_geo |>
   sf::st_drop_geometry() |>
-  transmute(from = O, to = as.character(D), count = round(trips_modelled))
+  dplyr::transmute(from = O, to = as.character(D), count = round(trips_modelled))
 readr::write_csv(od, "input/od.csv", quote = "all")
 ```
 
 Then create a config.json file, e.g. with the following content:
 
-```json
-{
-  "requests": {
-    "description": "Test data for SchoolRoutes project.",
-    "pattern": {
-      "ZoneToPoint": {
-        "zones_path": "zones.geojson",
-        "destinations_path": "destinations.geojson",
-        "csv_path": "od.csv",
-         "origin_zone_centroid_fallback": false
-      }
-    },
-    "origins_path": "buildings.geojson",
-    "destinations_path": "destinations.geojson"
-  },
-  "cost": "Distance",
-  "uptake": "Identity",
-  "lts": "BikeOttawa",
-  "elevation_geotiff": "elevation.tif"
-}
+```{r}
+#| output: asis
+readLines("config.json")
 ```
 
 Then run the following code to generate the network:
@@ -82,43 +139,10 @@ sudo docker run -v ${pwd}:/app ghcr.io/urban-analytics-technology-platform/od2ne
 system("docker run -v $(pwd):/app ghcr.io/urban-analytics-technology-platform/od2net:main /app/config.json")
 ```
 
-After that you should see the following in the output folder:
+After that you should see something like the following in the output folder:
 
 ```{r}
 #| eval: false
 fs::dir_tree("output")
 ```
 
-Helper functions
-
-<details>
-
-The following functions could be useful when you're preparing the data, and show the kind of data preparation that is required.
-
-<!-- TODO: consider adding these functions to the package at some stage? -->
-
-```{r}
-# Aim: generate input data for od2net with R
-
-#' Generate a 'zones.geojson' file
-#' 
-#' This function requires a zones file, e.g.
-#' "https://raw.githubusercontent.com/nptscot/npt/main/data-raw/zones_edinburgh.geojson"
-#' or a file on your computer.
-#' It will generate a file in the input/ folder
-#' 
-#' @param file Location or URL of zones file
-make_zones = function(file) {
-  zones = sf::read_sf(file)[1]
-  names(zones)[1] = "name"
-  sf::write_sf(zones, "input/zones.geojson", delete_dsn = TRUE)
-}
-
-make_od = function() {
-  od = readr::read_csv("https://raw.githubusercontent.com/nptscot/npt/main/data-raw/od_subset.csv")
-  od = od |>
-    dplyr::transmute(from = geo_code1, to = geo_code2, count = bicycle)
-  readr::write_csv(od, "input/od.csv")
-}
-```
-

From 9b919559907c465b3bdc07b92f19aa39036bd97d Mon Sep 17 00:00:00 2001
From: robinlovelace <rob00x@gmail.com>
Date: Tue, 10 Sep 2024 10:53:48 +0100
Subject: [PATCH 10/10] Add demo config

---
 r/config.json | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 r/config.json

diff --git a/r/config.json b/r/config.json
new file mode 100644
index 0000000..aafce3b
--- /dev/null
+++ b/r/config.json
@@ -0,0 +1,19 @@
+{
+    "requests": {
+      "description": "Test data for SchoolRoutes project.",
+      "pattern": {
+        "ZoneToPoint": {
+          "zones_path": "zones.geojson",
+          "destinations_path": "destinations.geojson",
+          "csv_path": "od.csv",
+           "origin_zone_centroid_fallback": false
+        }
+      },
+      "origins_path": "buildings.geojson",
+      "destinations_path": "destinations.geojson"
+    },
+    "cost": "Distance",
+    "uptake": "Identity",
+    "lts": "BikeOttawa",
+    "elevation_geotiff": "elevation.tif"
+}
\ No newline at end of file