Add minimal R package (Urban-Analytics-Technology-Platform#67)

r/.gitignore

@@ -0,0 +1 @@
+/.quarto/

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", , "[email protected]", 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/

r/NAMESPACE

@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+

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()
+}

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")
+```

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")
+```
+
+