One world | Projects, maps and coding

Introducing geobounds

Thu, 12 Feb 2026 00:00:00 +0100

3 min.

If you’ve ever worked with spatial data in R, this may ring a bell…

Search for boundary data
Figure out which version is “official”
Download a shapefile
Unzip it
Load it
Fix projections
Repeat

While searching for new data sources, I found the excellent geoBoundaries database. However, accessing the data can be tedious since it’s provided as zipped shapefiles, and as any GIS professional knows, shapefiles should die!

Previously, the rgeoboundaries package was on CRAN and allowed to access the geoBoundaries API, but it was archived. So I decided to create my own version, and geobounds was born.

Source code: https://github.com/dieghernan/geobounds
pkgdown website: https://dieghernan.github.io/geobounds/

It connects directly to the excellent geoBoundaries database and returns clean, ready-to-use sf objects with a single function call. No manual downloads. No shapefile messing.

This is how it works.

Installation

geobounds was recently accepted on CRAN, so just install it with:

install.packages("geobounds")

Load the package and other complementary packages:

library(geobounds)
library(sf)
library(ggplot2)
library(dplyr)

Getting administrative levels (ADM)

Administrative level 0 (ADM0) corresponds to countries:

# Panama

gb_get_adm0(country = "Panama") |>
  ggplot() +
  geom_sf(fill = "#072357") +
  labs(caption = "Source: www.geoboundaries.org")

You can also retrieve multiple administrative levels at once. For example:

# Simplified files
gb_get(country = "Panama", adm_lvl = "all", simplified = TRUE) |>
  ggplot() +
  geom_sf(aes(fill = shapeType), color = "grey50", linewidth = 0.1) +
  facet_wrap(vars(shapeType)) +
  scale_fill_viridis_d() +
  labs(
    title = "Administrative levels of Panama",
    fill = "level",
    caption = "Source: www.geoboundaries.org"
  )

Global Composite Boundaries (CGAZ)

When you download individual country files, each country reflects its own view of borders. This results in:

Overlapping boundaries
Geographic gaps
Disputed territories

For clean global visualizations, geoBoundaries provides a Composite Global Administrative Zones (CGAZ) dataset that can be accessed with gb_get_world().

Here’s an example with country-level files:

# Using individual (gb_get_adm) shapefiles
gb_get_adm0(country = c("India", "Pakistan")) |>
  # Disputed area: Kashmir
  ggplot() +
  geom_sf(aes(fill = shapeName), alpha = 0.5) +
  scale_fill_manual(values = c("#FF671F", "#00401A")) +
  labs(
    fill = "Country",
    title = "Map of India & Pakistan",
    subtitle = "Note overlapping in Kashmir region",
    caption = "Source: www.geoboundaries.org"
  )

And here’s the same comparison using CGAZ with gb_get_world():

gb_get_world(c("India", "Pakistan")) |>
  ggplot() +
  geom_sf(aes(fill = shapeName), alpha = 0.5) +
  scale_fill_manual(values = c("#FF671F", "#00401A")) +
  labs(
    fill = "Country",
    title = "Map of India & Pakistan",
    subtitle = "CGAZ does not overlap",
    caption = "Source: www.geoboundaries.org"
  )

Understanding the data

The geoBoundaries database undergoes rigorous quality assurance, including manual review and hand-digitization of physical maps. This ensures the highest level of spatial accuracy for scientific and academic research.

This precision comes at a cost: some files can be large and take longer to download. For visualization and general mapping, we recommend using simplified datasets by setting simplified = TRUE.

# Different resolutions
norway <- gb_get_adm0("NOR") |>
  mutate(res = "Full resolution")
print(object.size(norway), units = "Mb")
#> 26.5 Mb

norway_simp <- gb_get_adm0(country = "NOR", simplified = TRUE) |>
  mutate(res = "Simplified")
print(object.size(norway_simp), units = "Mb")
#> 1.5 Mb

norway_all <- bind_rows(norway, norway_simp)

# Plot ggplot2
ggplot(norway_all) +
  geom_sf(fill = "#BA0C2F", color = "#00205B") +
  facet_wrap(vars(res)) +
  theme_minimal() +
  labs(caption = "Source: www.geoboundaries.org")

Caching

Downloaded files are cached locally. That means:

You download once
Re-running your script is fast
Your workflow stays reproducible

You can set the cache directory with:

gb_set_cache_dir("a/path/to/a/folder")

When should you use geobounds?

Use geobounds when:

You need reliable global administrative boundaries
You want reproducible workflows
You prefer code over manual downloads
You’re building maps, dashboards, or spatial analyses

geobounds is not alone in this space. Depending on your needs, you might also want to look at:

rnaturalearth

A very popular package to access Natural Earth datasets directly from R. It’s lightweight and great for quick global maps, especially at small scales.

If you need physical layers (rivers, coastlines, elevation) alongside political boundaries, this is often a good choice.

giscoR

If your focus is Europe, giscoR provides direct access to Eurostat GISCO data. It’s particularly useful for NUTS regions and European statistical boundaries.

osmdata

When administrative boundaries are not enough and you need OpenStreetMap features (roads, POIs, land use, etc.), osmdata gives you powerful querying capabilities.

Bottom line

I built geobounds to provide direct access to geoBoundaries products. I hope this package would help you in your GIS joruney.

Happy mapping!

Mapping Antarctica

Sat, 25 Oct 2025 00:00:00 +0200

Cool maps from the South Pole

6 min.

Creating maps with R is usually straightforward, but representations that cross the International Date Line or that use polar projections can be tricky.

Different spatial-data providers use different conventions: some break geometries at certain longitudes (for example, cutting the Chukchi Peninsula), while others omit portions of the data. These inconsistencies can produce awkward artifacts near the poles.

In this post I fix the GISCO (European Commission) shapefile for Antarctica and produce clean orthographic maps. I walk through the manual corrections and then create a few example maps.

# Libraries
library(tidyverse)
library(sf)
library(giscoR)
library(ggrepel)
library(rmapshaper)

Fixing the geometry

First, we obtain the GISCO Antarctica polygon and transform it to an orthographic projection centered on the South Pole.

antarct <- gisco_get_countries(year = 2024, resolution = 1, country = "ATA") %>%
  select(NAME = NAME_ENGL) |>
  # Ortho proj centered in the South Pole
  st_transform(crs = "+proj=ortho +lat_0=-90 +lon_0=0")

ggplot(antarct) +
  geom_sf(fill = "lightblue")

The shapefile contains a visible “lollipop” cut that looks unnatural in an orthographic projection. I correct it manually by:

Identify the polygon that represents the main Antarctic landmass.
Convert that polygon to a sequence of coordinates (points).
Remove the small sequence of points that create the artifact.
Rebuild the polygon from the cleaned coordinates and replace the broken geometry with the corrected one.

We convert polygons to point coordinates and inspect them to find the offending sequence:

# Identify the max
ant_explode <- antarct |>
  st_cast("POLYGON")

nrow(ant_explode)
#> [1] 778

# Max polygon

ant_max <- ant_explode[which.max(st_area(ant_explode)), ]

coords <- st_coordinates(ant_max) |>
  as_tibble() |>
  # Add id for points
  mutate(np = row_number())


ggplot(coords, aes(X, Y)) +
  geom_point(size = 0.05, color = "darkblue") +
  geom_text(aes(label = np), check_overlap = TRUE) +
  coord_equal()

From the plotted indices, we can see the problematic points fall roughly in the range 8200–9200. We inspect that interval in detail to select the exact indices to remove.

test <- coords |>
  filter(np %in% seq(8200, 9200))

test |>
  ggplot(aes(X, Y)) +
  geom_point(size = 0.05, color = "darkblue") +
  geom_text(aes(label = np), check_overlap = TRUE)

Note: This cleaning is tailored to this specific shapefile and may need to be repeated for other shapefiles. The approach is straightforward but depends on the particular geometry and projection.

# Final solution after some iterations...

test |>
  filter(np %in% seq(8289, 9130)) |>
  ggplot(aes(X, Y)) +
  geom_point(color = "darkblue") +
  labs(title = "To remove")


test |>
  filter(!np %in% seq(8289, 9130)) |>
  ggplot(aes(X, Y)) +
  geom_point(color = "darkblue") +
  labs(title = "To keep")

After removing the offending points, we rebuild the polygon and reconstitute the full Antarctica shape from the corrected piece plus the remaining polygons.

# From coordinates to polygon
newpol <- coords |>
  as.data.frame() |>
  filter(!np %in% seq(8289, 9130)) |> # Removing offending points
  select(X, Y) |>
  as.matrix() |>
  list() |>
  st_polygon() |>
  st_sfc() |>
  st_set_crs(st_crs(ant_max))

ant_max_fixed <- st_sf(st_drop_geometry(ant_max), geometry = newpol)

# Regenerate initial shape
antarctica_fixed <- bind_rows(
  ant_max_fixed,
  ant_explode[-which.max(st_area(ant_explode)), ]
) |>
  group_by(NAME) |>
  summarise(m = 1) |>
  select(-m) |>
  st_make_valid()

antarctica_fixed
#> Simple feature collection with 1 feature and 1 field
#> Geometry type: MULTIPOLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -2583099 ymin: -2458296 xmax: 2690846 ymax: 2233395
#> Projected CRS: +proj=ortho +lat_0=-90 +lon_0=0
#> # A tibble: 1 × 2
#>   NAME                                                                     geometry
#> *                                                           
#> 1 Antarctica (((-2456385 1179033, -2456141 1178965, -2456464 1178341, -2456563 117…

ggplot(antarctica_fixed) +
  geom_sf(fill = "lightblue")

Plotting examples

With the corrected shape we can produce maps. Below are a few examples based on proposed Antarctic flag designs.

Graham Bartram’s proposal (1996)

A simple rendition of Bartram’s original concept:

bbox <- st_bbox(antarctica_fixed) # For limits on the panel

antarctica_fixed |>
  ggplot() +
  geom_sf(fill = "white", color = NA) +
  theme(
    panel.background = element_rect(fill = "#009fdc"),
    panel.grid = element_blank(),
    axis.text = element_blank(),
    axis.ticks = element_blank()
  ) +
  labs(title = "Graham Bartram's proposal") +
  coord_sf(
    xlim = c(bbox[c(1, 3)]) * 1.8,
    ylim = c(bbox[c(2, 4)]) * 1.4
  )

Emblem of the Antarctic Treaty

This example uses graticules to create a concentric “bullseye” pattern around Antarctica. Generating such graticules and merging meridians requires a few extra steps to avoid small gaps near the pole.

# Need graticules
grats <- giscoR::gisco_get_countries() |>
  st_transform(st_crs(antarctica_fixed)) |>
  # Specify the cuts of the graticules
  st_graticule(
    lat = c(-80, -70, -60),
    lon = seq(-180, 180, 30),
    ndiscr = 10000,
    margin = 0.000001
  )


ggplot(grats) +
  geom_sf(color = "darkblue")

We merge meridians so the area around the South Pole is filled. st_graticule() can leave a tiny hole at the pole; we fix this by joining complementary meridians.

# Merge meridians
merid <- lapply(seq(-180, 0, 30), function(x) {
  df <- grats |>
    filter(type == "E") |>
    filter(degree %in% c(x, x + 180))

  df2 <- df |>
    st_geometry() |>
    st_cast("MULTIPOINT") |>
    st_union() |>
    st_cast("LINESTRING")

  sf_x <- st_sf(
    degree = x,
    type = "E",
    geometry = df2
  )
}) |> bind_rows()


grats_end <- merid |>
  bind_rows(grats |>
    filter(type != "E"))

We then cut and color the resulting graticules so they form the emblem-like pattern.

# Cut since some grats should be colored differently

antarctica_simp <- rmapshaper::ms_simplify(antarctica_fixed, keep = 0.005)
grats_yes <- st_intersection(grats_end, antarctica_simp)
grats_no <- st_difference(grats_end, antarctica_simp)

antarctica_simp |>
  ggplot() +
  geom_sf(fill = "white", color = NA) +
  theme(
    panel.background = element_rect(fill = "#072b5f"),
    panel.grid = element_blank(),
    axis.text = element_blank(),
    axis.ticks = element_blank()
  ) +
  geom_sf(data = grats_yes, color = "#072b5f", linewidth = 1) +
  geom_sf(data = grats_no, color = "white", linewidth = 1) +
  coord_sf(
    xlim = c(bbox[c(1, 3)]) * 1.8,
    ylim = c(bbox[c(2, 4)]) * 1.4
  ) +
  labs(title = "Emblem of the Antarctic Treaty")

Antarctica Flag Redesigned

In 2024, Graham Bartram revealed a new version of his original flag as part of a global campaign to raise awareness about the growing problem of microplastic pollution. The new design keeps the familiar white outline of Antarctica but swaps the plain blue background for one filled with countless tiny, colorful dots. These dots represent the microscopic bits of plastic that have been discovered even in the planet’s most untouched places - including the Antarctic ice and its surrounding oceans.

Because the design relies on randomness, we approximate it using the following procedure:

Sample random points across the Antarctic polygon.
Build Voronoi polygons from those points, then apply a small negative buffer to create gaps.
Randomly sample the resulting polygons to increase visual noise.
Color polygons so larger areas remain white while smaller polygons use magenta/pink tones.

# Maximum chunk of Antarctica, the one that we fixed

ant_max_fixed
#> Simple feature collection with 1 feature and 1 field
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -2447764 ymin: -2125910 xmax: 2690846 ymax: 2233395
#> Projected CRS: +proj=ortho +lat_0=-90 +lon_0=0
#>         NAME                       geometry
#> 1 Antarctica POLYGON ((-2423737 1557908,...

set.seed(2024)
# Sample, Voronoi and negative buffer
plastics <- st_sample(ant_max_fixed, 3000) |>
  st_union() |>
  st_voronoi(envelope = st_geometry(ant_max_fixed)) |>
  st_collection_extract() |>
  st_buffer(dist = -10000)


# Keep only those properly included in the outline

toinc <- st_contains_properly(ant_max_fixed, plastics, sparse = FALSE) |>
  as.vector()

# Select random chunks
plastic_end <- plastics[toinc, ] |>
  st_as_sf() |>
  slice_sample(prop = 0.75)

ggplot(plastic_end) +
  geom_sf(fill = "darkblue")

# Random coloring

plastic_end$area <- st_area(plastic_end) |> as.double()

plastic_end$fill <- sample(c("#ff00ec", "#9e00ec"), nrow(plastic_end), replace = TRUE)
plastic_end$fill <- ifelse(plastic_end$area > quantile(plastic_end$area, probs = 0.4),
  "white",
  plastic_end$fill
)

bbox2 <- st_bbox(plastic_end)
ggplot() +
  geom_sf(data = plastic_end, aes(fill = fill), color = NA) +
  scale_fill_identity() +
  theme(
    panel.background = element_rect(fill = "#009fdc"),
    panel.grid = element_blank(),
    axis.text = element_blank(),
    axis.ticks = element_blank()
  ) +
  labs(title = "New redesign") +
  coord_sf(
    xlim = c(bbox2[c(1, 3)] * 1.8),
    ylim = c(bbox2[c(2, 4)]) * 1.4
  )

Implementing group_by count in Liquid

Fri, 28 Feb 2025 00:00:00 +0100

See the magic happening

5 min.

Liquid is an open-source template language created by Shopify back in 2006 and written in Ruby. It is widely used by several frameworks, with Jekyll being one of the most famous.

This website is created using Jekyll, specifically my Jekyll template Chulapa (link).

Some time ago, @cargocultprogramming opened dieghernan/chulapa#29 because one of the components of the theme was broken in Jekyll =>4.1.0. Digging a bit, I saw jekyll/jekyll#8214, exposing the same issue. What seemed to be a feature was indeed a bug that some developers were exploiting.

The change is that when applying the group_by Liquid filter on an array, it used to produce a “grouped” version of the array, while on Jekyll =>4.1.0 it produces a different result that can’t be used in the same way.

{% assign alldocs = site.exercises %}
{% assign grouptag = alldocs | map: 'tags' | join: ',' | split: ',' | group_by: tag %}

{{ grouptag }}

{"name"=>"tag A", "items"=>["tag A"], "size"=>1}{"name"=>"Tag B", "items"=>["Tag B"], "size"=>1}{"name"=>"Virtualbox", "items"=>["Virtualbox"], "size"=>1}{"name"=>"netcat", "items"=>["netcat"], "size"=>1}{"name"=>"whois", "items"=>["whois"], "size"=>1}{"name"=>"dig", "items"=>["dig"], "size"=>1} ... {"name"=>"Hydra", "items"=>["Hydra"], "size"=>1}

{"name"=>"", "items"=>["tag A", "Tag B", "Virtualbox", "netcat", "whois", "dig", ... , "Hydra"], "size"=>26}

So basically, counting items was not easy anymore. I developed a solution in pure Liquid (which happens to be a quite verbose language out of the predefined filters) that is compatible with any Jekyll version.

The algorithm is now implemented in Chulapa. You can check the results on my /tags page.

Note that the tables produced in the example are taken from my live site, hence they may change as I add more posts. The results of the table should be the same as the order and number of tags displayed on the /tags page.

Alternative `group_by` with Liquid

First, we define an array of all the tags included in the documents of my site:

{% assign alldocs = site.documents %}
{% assign alltags = alldocs | map: 'tags' | join: ',' | split: ',' %}

Cool! Now we can count the number of unique elements in alltags by counting the occurrences of unique tags in the array:

{% assign single_tags = alltags | uniq %}

{% assign count_tags = '' | split: ',' %}

{% assign n_tags = single_tags | size | minus: 1 %}

{% for i in (0..n_tags) %}

  {% assign count_this_tag = alltags | where_exp:"item", "item == single_tags[i]" | size %}
  {% assign count_tags = count_tags | push: count_this_tag %}
{% endfor %}

  {% for i in (0..n_tags) %}
    
  {% endfor %}

  Display count of tags on this site 
  
    Tag
    Count
  
      {{ single_tags[i] }}
      {{ count_tags[i] }}

Display count of tags on this site
Tag	Count
{{ single_tags[i] }}	{{ count_tags[i] }}

See results

Happy Valentine’s Day

Mon, 17 Feb 2025 00:00:00 +0100

Do you know the Bonne projection?

1 min.

Do you know the Bonne Projection? This is a very special one, as used on whole world’s mapping produces this result. Happy Valentine’s Day!

library(sf)
library(dplyr)
library(giscoR)
library(ggplot2)
library(showtext)


world <- gisco_get_countries()

# Shaped ocean

h_earth <- world %>%
  # Fine grid
  st_make_grid(n = c(50, 50)) %>%
  # Bonne projection
  st_transform("ESRI:54024") %>%
  # To sf object (data-frame like)
  st_sf(couple = 2, someval = 1, .)


# And finally

font_add_google(name = "Emilys Candy", family = "emilys")

showtext_auto()

ggplot() +
  geom_sf(data = h_earth, fill = "#f9b7bb", color = "#f9b7bb") +
  geom_sf(data = world, fill = "#d24658", color = "#d24658") +
  theme_void() +
  labs(
    title = "Happy Valentine's Day",
    caption = "Bonne Projection (ESRI:54024)"
  ) +
  theme(
    plot.background = element_rect(
      fill = "#faddcf",
      color = "transparent"
    ),
    text = element_text(family = "emilys", colour = "#d24658"),
    plot.title = element_text(hjust = 0.5, size = rel(3)),
    plot.caption = element_text(hjust = 0.5, size = rel(2))
  )

Optimize your images with R and reSmush.it

Mon, 05 Feb 2024 00:00:00 +0100

Introducing the resmush package

5 min.

The resmush package has recently been accepted on CRAN! This small utility package allows for the optimization (i.e., compression) of local and online images using reSmush.it.

You can install resmush from CRAN with:

install.packages("resmush")

What is reSmush.it?

reSmush.it is a free online API that provides image optimization and has been implemented on WordPress, Drupal, or Magento. Some features of reSmush.it include:

Free optimization services, no API key required.
Optimization of local and online images.
Supported image file formats: PNG, JPG/JPEG, GIF, BMP, TIFF, WebP.
Maximum image size: 5 MB.
Compression using several algorithms:
- PNGQuant: Strip unneeded chunks from PNGs while preserving full alpha transparency.
- JPEGOptim: Lossless optimization based on optimizing the Huffman tables.
- OptiPNG: png reducer used by several online optimizers.

reSmush.it is free of charge, but its team is planning to offer more serves as well as extend the service to support other types of image files. If you enjoy this API (as I do), you can consider supporting them.

Support reSmush.it on Ko-fi

Why the resmush package?

One of the main reasons I developed resmush is because I usually include precomputed vignettes with my packages (see tidyterra as an example). I found that the plots created on CRAN with the standard configuration (i.e., not precomputed vignettes but built on CRAN itself) were not very satisfying. In some of the packages I developed, especially those related to mapping, they didn’t do justice to the actual results when a user runs them.

Precomputing vignettes has the drawback of producing higher-quality images at the expense of size. To avoid exceeding CRAN’s 5Mb maximum size policy, I developed resmush, which enables me to reduce the size of the images without a significant loss in quality.

Another use case for resmush is optimizing images in the context of web page development and SEO optimization. For example, I optimized all the images on this blog using resmush_dir(), which is a shorthand for optimizing all files in a specific folder.

There are other alternatives that I would discuss at the end of this post, but in one line, the reSmush.it API performs fast with minimal configuration for a wide range of formats without needing an API key.

Using the resmush package

With local files

Let’s present an example of how a local file can be optimized. First we create a large plot with ggplot2

library(tidyterra)
library(ggplot2)
library(terra)
library(maptiles)

cyl <- vect(system.file("extdata/cyl.gpkg", package = "tidyterra")) %>%
  project("EPSG:3857")
cyl_img <- get_tiles(cyl, "Esri.WorldImagery", zoom = 8, crop = TRUE)
cyl_gg <- autoplot(cyl_img, maxcell = Inf) +
  geom_spatvector(data = cyl, alpha = 0.3)

cyl_gg

Original file

# And we save it for resmushing
ggsave("cyl.png", width = 5, height = 0.7 * 5)

Cool, but the file has a size of 1.7 Mb. So we can use resmush_file() to reduce it, see:

library(resmush)
resmush_file("cyl.png")
#> ══ resmush summary ══════════════════════════════════════════
#> ℹ Input: 1 file with size 1.7 Mb
#> ✔ Success for 1 file: Size now is 762.2 Kb (was 1.7 Mb). Saved 948.9 Kb (55.46%).
#> See result in directory '.'.

# Check
png::readPNG("cyl_resmush.png") %>%
  grid::grid.raster()

Optimized file

By default, resmush_file() and resmush_dir() do not overwrite the original file, although this behavior may be modified with the overwrite = TRUE parameter. Now, the resmushed file ("cyl_resmush.png") has a size of 762.2 Kb.

Let’s compare the results side-by-side:

Original picture (left/top) 1.7 Mb and optimized picture (right/bottom) 762.2 Kb (Compression 55.46%). Click in the images to enlarge.

We can verify that the image has been compressed without reducing its dimensions.

size_src <- file.size("cyl.png") %>%
  `class<-`("object_size") %>%
  format(units = "auto")
size_dest <- file.size("cyl_resmush.png") %>%
  `class<-`("object_size") %>%
  format(units = "auto")

dim_src <- dim(png::readPNG("cyl.png"))[1:2] %>% paste0(collapse = "x")
dim_dest <- dim(png::readPNG("cyl_resmush.png"))[1:2] %>% paste0(collapse = "x")

data.frame(
  source = c("original file", "compressed file"),
  size = c(size_src, size_dest),
  dimensions = c(dim_src, dim_dest)
) %>%
  knitr::kable()

source	size	dimensions
original file	1.7 Mb	1050x1500
compressed file	762.2 Kb	1050x1500

With online files

We can also optimize online files with resmush_url() and download them to disk. In this example, I demonstrate a feature of all the functions in resmush: they return an invisible data frame with a summary of the process.

url <- "https://dieghernan.github.io/assets/img/samples/sample_1.3mb.jpg"

# Invisible data frame
dm <- resmush_url(url, "sample_optimized.jpg", report = FALSE)

knitr::kable(dm)

src_img	dest_img	src_size	dest_size	compress_ratio	notes	src_bytes	dest_bytes
https://dieghernan.github.io/assets/img/samples/sample_1.3mb.jpg	sample_optimized.jpg	1.3 Mb	985 Kb	26.63%	OK	1374693	1008593

Original picture (left/top) 1.3 Mb and optimized picture (right/bottom) 985 Kb (Compression 26.63%). Click in the images to enlarge.

Other alternatives

There are other alternatives for optimizing images with R, but first…

Yihui Xie, one of the most prominent figures in the R community, was recently laid off from his position at Posit PBC (formerly RStudio) (more info here).

Yihui is the developer of knitr, markdown, blogdown, and bookdown, among others, and he has been one of the key contributors (if not the most) to the reproducible research space with R through his libraries.

If you have ever used and enjoyed his packages, consider sponsoring him on GitHub.

Sponsor Yihui Xie

One of the many packages developed by Yihui is xfun, which includes the following functions for optimizing image files:
- xfun::tinify() is similar to resmush_file() but uses TinyPNG. An API key is required.
- xfun::optipng() compresses local files with OptiPNG (which needs to be installed locally).
tinieR package by jmablog. An R package that provides a full interface with TinyPNG.
optout package by @coolbutuseless. Similar to xfun::optipng() with additional options. Requires additional software to be installed locally.

Table 1: R packages: Comparison of alternatives for optimizing images.
tool	CRAN	Additional software?	Online?	API Key?	Limits?
`xfun::tinify()`	Yes	No	Yes	Yes	500 files/month (Free tier)
`xfun::optipng()`	Yes	Yes	No	No	No
tinieR	No	No	Yes	Yes	500 files/month (Free tier)
optout	No	Yes	No	No	No
resmush	Yes	No	Yes	No	Max size 5Mb

Table 2: R packages: Formats admitted.
tool	png	jpg	gif	bmp	tiff	webp	pdf
`xfun::tinify()`	✅	✅	❌	❌	❌	✅	❌
`xfun::optipng()`	✅	❌	❌	❌	❌	❌	❌
tinieR	✅	✅	❌	❌	❌	✅	❌
optout	✅	✅	❌	❌	❌	❌	✅
resmush	✅	✅	✅	✅	✅	✅	❌

Additionally, if you host your projects on GitHub, you can try Imgbot, which is free for open-source projects. Imgbot provides automatic optimization for files in your repositories, and the optimized files will be included in specific pull requests before merging into your work.

Beautiful Maps with R (V): Point densities

Sat, 16 Dec 2023 00:00:00 +0100

Bertin’s dot density maps with R and GHSL

8 min.

Recently the R Graph Gallery has incorporated a new post by Benjamin Nowak showing how to create a dot density map based on the work of the french cartographer Jacques Bertin (1918 - 2010):

In this post I would create a similar map for Iberia, and additionally I would show how to create a variation using a hexagonal grid instead of a rectangular one. This is the first issue of the series Beautiful Maps with R.

Libraries

I would use the following libraries for loading, manipulating and plotting spatial data (both raster and vector):

# Base spatial packages
library(terra)
library(sf)
# Spatial data
library(giscoR)
# Wrangling and plotting
library(tidyverse)
library(tidyterra)
library(ggtext)
# Additional for hex grids
# Supporting for units and bridge raster to polygon
library(units)
library(exactextractr)

Get the data

The first step is always to get the data we need. My final map would use as a base a circular layout with Iberia in the middle (that would be our observation window), so we can get the corresponding shapes and create a buffer around it.

After that, we would extract the population spatial distribution from GHSL - Global Human Settlement Layer. We would use the global file with a resolution of 1 km on Mollweide projection (ESRI:54009).

# Create observation window based the Iberian Peninsula and surroundings
# We create a buffered circle
owin <- gisco_get_countries(
  country = c("ES", "PT"),
  # We buffer in 3035 since I want my final map on this projection
  epsg = 3035,
  resolution = 60
) %>%
  st_geometry() %>%
  st_union() %>%
  st_centroid(of_largest_polygon = TRUE) %>%
  st_buffer(750000) %>%
  # But for extracting raster data we need this in Mollweide so far
  st_transform(crs = "ESRI:54009")

# Get additional shapes and cut them to the owin
regions <- gisco_get_nuts(resolution = 3, nuts_level = 2) %>%
  st_transform(st_crs(owin)) %>%
  st_intersection(owin)

countries <- gisco_get_countries(resolution = 3) %>%
  st_transform(st_crs(owin)) %>%
  st_intersection(owin)

# Base map
base_gg <- ggplot() +
  geom_sf(data = regions, fill = NA, color = "black", linewidth = 0.1) +
  geom_sf(data = countries, fill = NA, linewidth = 0.5, color = "black") +
  geom_sf(data = owin, fill = NA, linewidth = 0.75, color = "black")

base_gg

That would be our base map. Now we download programmatically the GHSL data and we would check that everything is correct. At this point, it is interesting to use the win argument when reading the raster with terra::rast(), as this would allow us to load only the desired area with the subsequent improvement in terms of performance.

# Download data
# We need the following file (download 305Mb)
url <- "https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/GHSL/GHS_POP_GLOBE_R2023A/GHS_POP_E2030_GLOBE_R2023A_54009_1000/V1-0/GHS_POP_E2030_GLOBE_R2023A_54009_1000_V1_0.zip"

# This is where I would store the file, you would need to modify the folder
fname <- file.path("~/R/mapslib/GHS", basename(url))
if (!file.exists(fname)) {
  download.file(url, fname)
}
zip_content <- unzip(fname, list = TRUE)
zip_content
#>                                                 Name    Length                Date
#> 1     GHS_POP_E2030_GLOBE_R2023A_54009_1000_V1_0.tif 263188307 2023-04-28 21:11:00
#> 2 GHS_POP_E2030_GLOBE_R2023A_54009_1000_V1_0.tif.ovr  88461532 2023-04-28 21:11:00
#> 3                         GHSL_Data_Package_2023.pdf   9761851 2023-10-27 14:30:00
#> 4           GHS_POP_GLOBE_R2023A_input_metadata.xlsx    137963 2023-04-30 10:42:00

# Unzip
unzip(fname, exdir = "~/R/mapslib/GHS", junkpaths = TRUE, overwrite = FALSE)

# Create the path to the file
global_tiff <- zip_content$Name[grepl("tif$", zip_content$Name)]
global_tiff_path <- file.path("~/R/mapslib/GHS", global_tiff)

# And read cropping to our owin
pop_init <- rast(global_tiff_path, win = as_spatvector(owin))

# Consistent naming of the layer
names(pop_init) <- "population"

ncell(pop_init)
#> [1] 2255923

# And check with tidyterra
base_gg +
  geom_spatraster(data = pop_init, maxcell = 50000) +
  scale_fill_viridis_c(na.value = "transparent", alpha = 0.3)

Data wrangling

The GHSL information contains the estimated population on each grid. However the file has a high resolution (more than 2 millions of cells) so for plotting purposes we are going to reduce (i.e. aggregate) the number of cells so we can have a better dot visualization. Once that we aggregate, we would compute the area of each new aggregated cell and compute the corresponding population density.

Instead of using the numeric range of densities, we would use categories for the final map, so we would classify the density into different groups:

# Reduce resolution for visualization
# Compute factor to reduce raster to (aprox) 100 rows:
nrow(pop_init)
#> [1] 1511
factor <- round(nrow(pop_init) / 100)

# Each new cell would contain the sum of population of the aggregated cells
pop_agg <- terra::aggregate(pop_init,
  fact = factor, fun = "sum",
  na.rm = TRUE
)


# Compute area of each new cell
pop_agg$area_km2 <- cellSize(pop_agg, unit = "km")

# Compute densities, mask to owin, convert to points and create categories
pop_points <- pop_agg %>%
  # Compute density by cell
  mutate(dens = population / area_km2) %>%
  select(dens) %>%
  # Mask to the countries shapes
  mask(as_spatvector(countries), touches = FALSE) %>%
  # SpatVector as points
  as.points() %>%
  # Categorize
  mutate(cat = case_when(
    dens < 25 ~ "A",
    dens < 50 ~ "B",
    dens < 100 ~ "C",
    dens < 250 ~ "D",
    dens < 500 ~ "E",
    dens < 1500 ~ "F",
    TRUE ~ "G"
  ))

Final plot

And finally the map. In this case I would save it as a high resolution square map.

# Final plot
final_plot <- base_gg +
  # Layer, this object is a SpatVector instead of sf object
  geom_spatvector(
    pop_points,
    mapping = aes(size = cat),
    # Use a point with a border AND a fill
    pch = 21, color = "white", fill = "black", linewidth = 0.05
  ) +
  scale_size_manual(
    values = c(0.3, 1, 1.25, 1.5, 2, 2.5, 3.5),
    labels = c(
      "< 25", "[25, 50)", "[50, 100)", "[100, 250)",
      "[250, 500)", "[500, 1500)", "≥ 1500"
    ),
    guide = guide_legend(
      nrow = 1,
      title.position = "top",
      keywidth = 1,
      label.position = "bottom"
    )
  ) +
  labs(
    title = "**Population density in Iberia**",
    subtitle = "in the way of Jacques Bertin",
    size = "Inhabitants per km2",
    caption = "**Data** GHSL **| Plot** @dhernangomez based on @BjnNowak"
  ) +
  theme_void() +
  # This CRS for representation only
  coord_sf(expand = TRUE, crs = 3035) +
  theme(
    # plot.margin = margin(20,0,20,0,"cm"),
    plot.background = element_rect(fill = "white", color = NA),
    legend.position = "bottom",
    legend.margin = margin(r = 20, unit = "pt"),
    legend.title = element_markdown(),
    legend.key.width = unit(50, "pt"),
    plot.title = element_markdown(hjust = 0.5, size = 20),
    plot.subtitle = element_text(hjust = 0.5, color = "grey40"),
    plot.caption = element_markdown(
      color = "grey20",
      margin = margin(t = 20, b = 5, unit = "pt"),
      hjust = .5
    )
  )



ggsave("202312_finalmap.png", dpi = 300, width = 8, height = 8)

Alternative hexagonal grid

The previous plot is based on the centroids of each cell of the raster, that is, by definition, a rectangular grid. I would like also to experiment with hexagonal grids (i.e. grid of hexagons) since I have the feeling that looks more “natural” than the rectangular ones, that presents a regularity hardly seen in the wild.

The issue here is that terra does not produce this type of grids, however it is possible to create them with sf::st_make_grid(), so the workflow for this altenative is:

Create a hexagonal grid, where each hexagon represents a similar area than each cell on the aggregated raster.
Extract the values of the raster to the new grid.
Finally, follow the same steps on data wrangling and plotting.

When working with sf::st_make_grid(square = FALSE), the parameter cellsize should be the “diameter” of the hexagon instead of the area. Luckly, we can infer this value since the area of a hexagon is

[A = \frac{\sqrt{3}}{2}d^{2}]

So we can extract \(d\) from the previous expression knowing the area \(A\) of the aggregated cells:

# Hex grid with sf ----

# Avg size of the cells on the aggregated grid
target_area <- cellSize(pop_agg, unit = "km") %>%
  pull() %>%
  mean() %>%
  as_units("km^2")

target_area
#> 224.7461 [km^2]

# Infer diam hex
diam_hex <- sqrt(2 * target_area / sqrt(3))
# Create hexagonal grid
pop_agg_sf <- st_make_grid(owin, cellsize = diam_hex, square = FALSE)

length(pop_agg_sf)
#> [1] 10340
ncell(pop_agg)
#> [1] 10100

area_km2 <- st_area(pop_agg_sf) %>%
  set_units("km^2") %>%
  as.double()

pop_agg_sf <- st_sf(area_km2 = area_km2, geom = pop_agg_sf)

Now, we use exact_extract() to extract the population on each hexagonal grid.

# Extract aggregated population by hex cell
pop_agg_sf$population <- exact_extract(pop_init,
  y = pop_agg_sf,
  progress = FALSE,
  fun = "sum"
)


base_gg +
  geom_sf(
    data = pop_agg_sf %>% filter(population > 0),
    aes(fill = population), color = NA
  ) +
  scale_fill_viridis_c(na.value = "transparent", alpha = 0.3)

Finally we just compute densities, create categories and finally the map:

# Mask and categorize
pop_sf_points <- pop_agg_sf %>%
  # Compute density by cell
  mutate(dens = population / area_km2) %>%
  select(dens) %>%
  # To points and filter to country shape
  st_centroid(of_largest_polygon = TRUE) %>%
  st_filter(countries) %>%
  # Categorize
  mutate(cat = case_when(
    dens < 25 ~ "A",
    dens < 50 ~ "B",
    dens < 100 ~ "C",
    dens < 250 ~ "D",
    dens < 500 ~ "E",
    dens < 1500 ~ "F",
    TRUE ~ "G"
  ))

# Final plot
final_plot_hex <- base_gg +
  # Layer, this object is a sf object
  geom_sf(
    pop_sf_points,
    mapping = aes(size = cat),
    # Use a point with a border AND a fill
    pch = 21, color = "white", fill = "black", linewidth = 0.05
  ) +
  scale_size_manual(
    values = c(0.3, 1, 1.25, 1.5, 2, 2.5, 3.5),
    labels = c(
      "< 25", "[25, 50)", "[50, 100)", "[100, 250)",
      "[250, 500)", "[500, 1500)", "≥ 1500"
    ),
    guide = guide_legend(
      nrow = 1,
      title.position = "top",
      keywidth = 1,
      label.position = "bottom"
    )
  ) +
  labs(
    title = "**Population density in Iberia**",
    subtitle = "in the way of Jacques Bertin",
    size = "Inhabitants per km2",
    caption = "**Data** GHSL **| Plot** @dhernangomez based on @BjnNowak"
  ) +
  theme_void() +
  # This CRS for representation only
  coord_sf(expand = TRUE, crs = 3035) +
  theme(
    # plot.margin = margin(20,0,20,0,"cm"),
    plot.background = element_rect(fill = "white", color = NA),
    legend.position = "bottom",
    legend.margin = margin(r = 20, unit = "pt"),
    legend.title = element_markdown(),
    legend.key.width = unit(50, "pt"),
    plot.title = element_markdown(hjust = 0.5, size = 20),
    plot.subtitle = element_text(hjust = 0.5, color = "grey40"),
    plot.caption = element_markdown(
      color = "grey20",
      margin = margin(t = 20, b = 5, unit = "pt"),
      hjust = .5
    )
  )

ggsave("202312_finalmap_hex.png", dpi = 300, width = 8, height = 8)

And that’s it! Which one do you like the most? Let me know in the comments.

References

Bertin J (1967). Sémiologie graphique. Les diagrammes. Les réseaux. Les cartes. Gauthier-Villars, Paris.
European Commission. Joint Research Centre. (2023). GHSL data package 2023.. Publications Office, LU https://doi.org/10.2760/098587
Hernangómez D (2023). “Using the tidyverse with terra objects: the tidyterra package Journal of Open Source Software, 8(91), 5751. ISSN 2475-9066 https://doi.org/10.21105/joss.05751
Pesaresi M, Politis P (2023). “GHS-BUILT-C R2023A - GHS Settlement Characteristics, derived from Sentinel2 composite (2018) and other GHS R2023A data.” https://doi.org/10.2905/3C60DDF6-0586-4190-854B-F6AA0EDC2A30

Star Map with R

Wed, 25 Jan 2023 00:00:00 +0100

Creating Star Map Visualizations Based on Location and Date

13 min.

A couple of weeks ago I was doing my daily check on StackOverflow when I found a question by Benjamin Smith that blew my mind: Creating Star Map Visualizations Based on Location and Date !!

Oh my! Can we do this with R? Answer is: Of course! In fact, Kim Fitter already worked on this two years ago, see his Celestial Maps. So I decided to put some work on this.

Since then, I also learnt that Benjamin and myself have been working on parallel on the same topic. He is preparing a R package named starBliss and hopefully this post would be of some help.

I have very little knowledge on this topic, so if you find errors or have any suggestions please let me know in the Comments section below

First things first: The data

The initial data source of all these projects (Kim, Benjamin and myself) is the same, and it is provided on the D3 plugin d3-celestial by Olaf Frohn. As Kim Fitter pointed out on his post, these data files present the problem (experienced by almost any sf user) of lines crossing the international date line (longitude 180º). I also found that some files are not valid as per sf::st_make_valid().

Solution? I processed and fixed almost every file (some of them as the corresponding to the Milky Way or the lines for Chinese constellations manually) to provide a set of files. That is the origin of my project Celestial Data, that provides all these files on several spatial formats. Please check out the repo to know more about it.

Creating a Star Map with R

The first step is loading a bunch of libraries that would help us on this cosmic task:

# Spatial manipulation
library(sf)
library(s2)
library(nominatimlite)

## Wrange data and dates
library(dplyr)
library(lubridate)
library(lutz)

## Visualization
library(ggplot2)
library(ggfx)
library(ggshadow)

Helper funs

Now we prepare some helper functions:

load_celestial() just downloads the corresponding .geojson from the Celestial Data repo¹ to a specific directory cachedir and loads it with sf::st_read().
pretty_lonlat() is a labeller that returns a decimal longitude or latitude coordinate in the format degrees/minutes/seconds (e.g a latitude 34.72782 would be converted into 34° 43’ 40.15” N).

Show load_celestial and pretty_lonlat()

Celestial Data

Mon, 23 Jan 2023 00:00:00 +0100

A compilation of celestial data files

1 min.

This project provides several datasets in GeoJSON and GeoPackage format of celestial objects as of J2000 epoch.

The original files were provided on the d3-celestial plugin (Frohn 2015) under BSD 3-Clause. The datasets produced on this project consists on the same data provided on d3-celestial plugin processed with the R package sf (Pebesma 2018) to ensure its validity:

The spatial data objects are bounded to \([-180, -90, 180, 90]\).
Date is provided on WGS84 - World Geodetic System 1984 (EPSG:4326).
All geometries valid as per ST_IsValid (GEOS 3.9.3).

Distribution

The data can be accessed from several API endpoints:

https://raw.githubusercontent.com/dieghernan/celestial_data/main/data/mw.min.geojson

https://dieghernan.github.io/celestial_data/data/mw.min.geojson

https://cdn.jsdelivr.net/gh/dieghernan/celestial_data@main/data/mw.min.geojson

Data

Data is provided in GeoJSON (*.geojson) and GeoPackage (*.gpkg) format. Additionally, for GeoJSON formats a minified version (*.min.geojson) is also provided.

The data source can be found on the corresponding GitHub repo.

List of files provided

Hillshade, colors and marginal plots with tidyterra (II)

Mon, 12 Dec 2022 00:00:00 +0100

The rain in Spain does not stay mainly in the plain

13 min.

This is the second post of the series “Hillshade, colors and marginal plots with tidyterra”. In this post I would explore an approach for annotating marginal plots to a ggplot2 map of a SpatRaster, including information of the values by longitude and latitude. See the first post of the series here.

If you love watching classic movies, specially from the Hollywood’s Golden Age, you may recognize the following lyrics:

The rain in Spain stays mainly in the plain!

By George, she’s got it! By George, she’s got it!

Now, once again where does it rain? On the plain! On the plain!

And where’s that soggy plain? In Spain! In Spain!

The rain in Spain stays mainly in the plain!

The rain in Spain stays mainly in the plain!

This hard statement is made on My Fair Lady (1964) by Audrey Hepburn, Rex Harrison and Stanley Holloway. But as a Spaniard I can tell it is completely false.

The rain in Spain stays mainly in the north, most notably in Galicia. And I can prove it!

On this post I would overlay a SpatRaster showing average precipitation data with an extra set of plots on the margin to identify where the rain in Spain stays (mainly).

Libraries

On this post we would use the following libraries:

## Libraries

# Data manipulation
library(terra)
library(tidyterra)
library(dplyr)

# Get the data
library(geodata)
library(mapSpain)

# Plotting
library(ggplot2)
library(scales)
library(cowplot)
library(colorspace)

The plain in Spain

Well, the plain (or as we name it La Meseta Central) covers a large area of the inner land of Spain, with an average altitude of 650 meters over the sea level.

I didn’t find any accurate spatial data file with the bounds of the plain, so for this case I would approximate it using a mixture of political borders (historically the Meseta is associated to Castile and Madrid) and elevation data to get a rough shape.

# Using mapSpain
the_plain <- esp_get_prov(
  c(
    "Madrid", "Castilla-La Mancha",
    "Extremadura", "Castilla y Leon",
    "Teruel"
  ),
  epsg = 4326, resolution = 1
) %>%
  mutate(the_plain = TRUE) %>%
  group_by(the_plain) %>%
  # Combine
  summarise() %>%
  # To terra, until this step was sf
  vect()

# Get altitude

# I use here a local directory to cache downloaded files on my PC.
# Modify this to your likes, e.g. using
# mydir <- tempdir()

mydir <- "~/R/mapslib/misc"


r_init <- elevation_30s("ESP", path = mydir)

# For better handling we set here the names
names(r_init) <- "alt"

# We don't want values lower than 0 on the raster
r <- r_init %>%
  mutate(alt = pmax(0, alt))


# Now intersect the raster and the vector and filter by range

exploded <- r %>%
  crop(the_plain, mask = TRUE) %>%
  # Let's define here a range of elevations
  filter(alt > 600 & alt < 1100) %>%
  drop_na() %>%
  as.polygons(dissolve = TRUE, na.rm = TRUE) %>%
  # Aggregate first
  aggregate() %>%
  # Explode vectors
  disagg() %>%
  # And fill holes
  fillHoles()



# Select biggest polygons (area bigger than 50 kms 2)
r_plain <- exploded %>%
  # Add area
  mutate(area = expanse(exploded)) %>%
  filter(area > 50000**2) %>%
  # And convert to lines
  as.lines()

autoplot(r_plain)

We can create a now plot similar to the one produced in the previous post to identify the plain. In first place I create a base layer with a representation of the hillshade, that we would reuse later:

# Creating hillshade

slope <- terrain(r, "slope", unit = "radians")
aspect <- terrain(r, "aspect", unit = "radians")
hill <- shade(slope, aspect, 30, 45)

# normalize names
names(hill) <- "shades"

# Hillshading palette
pal_greys <- hcl.colors(1000, "Grays")

# Index of color by cell
index <- hill %>%
  mutate(index_col = rescale(shades, to = c(1, length(pal_greys)))) %>%
  mutate(index_col = round(index_col)) %>%
  pull(index_col)


# Get cols
vector_cols <- pal_greys[index]

# Need to avoid resampling
# and dont use aes

# Base hill plot
hill_plot <- ggplot() +
  geom_spatraster(
    data = hill, fill = vector_cols, maxcell = Inf,
    alpha = 1
  )

hill_plot

And finally we overlay the altitude and the outline of the plain in Spain.

# Overlaying and theming

# Aware of limits of the raster

alt_limits <- minmax(r) %>% as.vector()
# Round to lower and higher 500 integer with a min of 0
alt_limits <- pmax(
  c(floor(alt_limits[1] / 500), ceiling(alt_limits[2] / 500)) * 500,
  0
)

alt_limits
#> [1]    0 3500


base_text_size <- 9


plot_esp <- hill_plot +
  geom_spatraster(data = r, maxcell = Inf) +
  # Overlay the_plain
  geom_spatvector(
    data = r_plain,
    color = alpha("black", 0.7),
    linewidth = 0.15
  ) +
  scale_fill_hypso_tint_c(
    palette = "wiki-schwarzwald-cont",
    limits = alt_limits,
    alpha = 0.4,
    breaks = seq(0, 3500, 250),
    labels = label_comma()
  ) +
  guides(fill = guide_legend(
    title = "   m.",
    title.position = "top",
    keywidth = .5,
    reverse = TRUE,
    override.aes = list(alpha = 0.8)
  )) +
  labs(
    title = "Elevation of Spain",
    subtitle = "The plain represented with black line"
  ) +
  theme_minimal(base_family = "serif") +
  theme(
    plot.background = element_rect(fill = "white", color = "white"),
    plot.title = element_text(
      face = "bold", size = base_text_size * 1.5,
      hjust = 0.5
    ),
    plot.subtitle = element_text(
      size = base_text_size * 0.9,
      hjust = 0.5
    ),
    plot.caption = element_text(
      margin = margin(t = base_text_size * 3),
      face = "italic"
    ),
    legend.key = element_rect("grey50"),
    legend.text = element_text(hjust = 0),
    legend.position = "left"
  )

plot_esp

The rain in Spain

Let’s check now wheter the rain falls mainly in the plain or not. We use here geodata::worldclim_country() to get the average precipitation by month from WordClim:

# Precipitation of Spain

# Get precip data
precip <- geodata::worldclim_country("ESP", "prec", mydir)

precip
#> class       : SpatRaster 
#> dimensions  : 1980, 2760, 12  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : -18.5, 4.5, 27.5, 44  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source      : ESP_wc2.1_30s_prec.tif 
#> names       : ESP_w~rec_1, ESP_w~rec_2, ESP_w~rec_3, ESP_w~rec_4, ESP_w~rec_5, ESP_w~rec_6, ... 
#> min values  :           0,           1,           1,           0,           0,           0, ... 
#> max values  :         296,         255,         199,         166,         181,         140, ...

We have now a SpatRaster with 12 layers representing the value of each month. So we now just add the values by cell to get the annual average. Note that we also need to normalize the SpatRaster to the projection, extent and resolution of our hill object:

# Sum all layers
precip_avg <- sum(precip)

precip_avg
#> class       : SpatRaster 
#> dimensions  : 1980, 2760, 1  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : -18.5, 4.5, 27.5, 44  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source(s)   : memory
#> name        :  sum 
#> min value   :    8 
#> max value   : 2055


compare_spatrasters(precip_avg, hill)

# Align raster using hill

precip_avg_mask <- precip_avg %>%
  project(hill) %>%
  crop(hill) %>%
  mask(hill)

# Normalize
names(precip_avg_mask) <- "prec"

compare_spatrasters(precip_avg_mask, hill)

autoplot(precip_avg_mask)

Creating a modified palette

We can now start representing our precipitation map. I chose here to create a custom palette with colorspace to better highlight the differences:

mypal <- sequential_hcl(
  n = 16,
  h = c(320, 80),
  c = c(60, 65, 20),
  l = c(30, 95), power = c(0.7, 1.3),
  rev = TRUE
)

show_col(mypal)

And now we can create the final map showing if the rain in Spain stays mainly in the plain:

# Precipitation limits, rounded to 100
prec_limits <- floor(as.vector(minmax(precip_avg_mask)) / 100) * 100 + c(0, 100)


meteo_plot <- hill_plot +
  geom_spatraster(data = precip_avg_mask, maxcell = Inf) +
  # Overlay the_plain
  geom_spatvector(
    data = r_plain, color = alpha("black", 0.7),
    linewidth = .1
  ) +
  # This part is theming only
  scale_fill_gradientn(
    colours = alpha(mypal, 0.7),
    na.value = NA,
    labels = label_comma(),
    breaks = seq(0, prec_limits[2], 250)
  ) +
  guides(fill = guide_legend(
    direction = "horizontal",
    keyheight = .5,
    keywidth = 2,
    title.position = "right",
    label.position = "bottom",
    nrow = 1,
    family = "serif",
    title = " mm.",
    override.aes = list(alpha = 0.9)
  )) +
  labs(
    title = "Average yearly precipitation of Spain",
    subtitle = "The rain in Spain does not stay mainly in the plain"
  ) +
  theme_minimal(base_family = "serif") +
  theme(
    plot.background = element_rect(fill = "white", color = "white"),
    plot.title = element_text(
      face = "bold", size = base_text_size * 1.5,
      hjust = 0.5
    ),
    plot.subtitle = element_text(
      size = base_text_size,
      hjust = 0.5
    ),
    axis.text = element_text(size = base_text_size * 0.7, face = "italic"),
    legend.key = element_rect("grey50"),
    legend.position = "bottom",
    legend.title = element_text(size = base_text_size * .7),
    legend.text = element_text(size = base_text_size * .7),
    legend.spacing.x = unit(0, "pt")
  )


meteo_plot

We can now check that the rain in Spain falls mainly in the Atlantic coast (North of Spain) and specifically in Galicia. That’s why in Spanish the lyrics The rain in Spain stays mainly in the plain were translated into:

La lluvia en Sevilla es una pura maravilla.

That can be translated as “The rain in Seville is a true marvel”. And it is, indeed. Seville (located in the south on the Guadalquivir Valley has circa 50 rainy days per year, featuring very hot and dry summers.

Marginal plots (finally)

We can now start profiling our final plot. The idea is to create two bar charts, representing the value to be plotted (in this case, average annual precipitation) by longitude and latitude.

But first we add some additional margins and title axes to the main plot, so we can insert those marginal plots easily on our main plot:

# Now we can add titles on the secondary axis

plot_main <- meteo_plot +
  xlab("") +
  ylab("") +
  # titles on secondary axis, for later
  scale_x_continuous(sec.axis = dup_axis(
    name = "avg. precipitation by longitude"
  )) +
  scale_y_continuous(sec.axis = dup_axis(
    name = "avg. precipitation by latitude"
  )) +
  theme(
    axis.title.x = element_text(
      margin = margin(t = base_text_size),
      size = base_text_size * 0.9, face = "italic"
    ),
    axis.title.y = element_text(
      angle = 270,
      margin = margin(
        l = base_text_size,
        t = base_text_size
      ),
      size = base_text_size * 0.9, face = "italic"
    )
  )

plot_main

Profiling marginal plots

On the following code, I am just drafting how the marginal plots would look like, so we can have a preview of the final result:

# Profiling marginal plots

# Getting averages by x,y
marg_x <- precip_avg_mask %>%
  as_tibble(xy = TRUE) %>%
  drop_na() %>%
  group_by(x) %>%
  summarise(avg = mean(prec))

marg_y <- precip_avg_mask %>%
  as_tibble(xy = TRUE) %>%
  drop_na() %>%
  group_by(y) %>%
  summarise(avg = mean(prec))


# Cowplot would delete axis, we create an axis at 1000 and 2000
br_4marginal <- c(1000, 2000)

labs <- data.frame(labs = paste(
  prettyNum(br_4marginal, big.mark = " "),
  "mm."
))

labs$for_x <- max(marg_x$x) - diff(range(marg_x$x)) * 0.05
labs$for_y <- min(marg_y$y) + diff(range(marg_y$y)) * 0.05
labs$y <- br_4marginal

# Profiling
ggplot() +
  geom_col(
    data = marg_x,
    aes(x, avg, fill = avg),
    color = NA,
    show.legend = FALSE
  ) +
  geom_text(
    data = labs, aes(x = for_x, y = y, label = labs),
    nudge_y = 100,
    size = 3
  ) +
  scale_fill_gradientn(
    colours = alpha(mypal, 0.9),
    na.value = NA,
    labels = label_comma(),
    limits = prec_limits
  ) +
  scale_y_continuous(
    breaks = br_4marginal,
    limits = c(0, max(br_4marginal) * 1.5)
  ) +
  theme_void() +
  theme(panel.grid.major.y = element_line(
    colour = "grey50",
    linetype = "dashed"
  ))

ggplot() +
  geom_col(
    data = marg_y,
    aes(y, avg, fill = avg),
    color = NA,
    show.legend = FALSE
  ) +
  geom_text(
    data = labs, aes(x = for_y, y = y, label = labs),
    nudge_y = 100,
    angle = 270,
    size = 3
  ) +
  scale_fill_gradientn(
    colours = alpha(mypal, 0.9),
    na.value = NA,
    labels = label_comma(),
    limits = prec_limits
  ) +
  scale_y_continuous(
    breaks = br_4marginal,
    limits = c(0, max(br_4marginal) * 1.2)
  ) +
  coord_flip() +
  theme_void() +
  theme(panel.grid.major.x = element_line(
    colour = "grey50",
    linetype = "dashed"
  ))

Putting all the pieces together

Finally, we would use cowplot::axis_canvas() to create the marginal plots as we want:

# Last step: We combine plots

# Marginal plots
plot_x <- axis_canvas(plot_main, axis = "x") +
  geom_col(
    data = marg_x,
    aes(x, avg, fill = avg),
    color = NA,
    show.legend = FALSE
  ) +
  geom_text(
    data = labs, aes(x = for_x, y = y, label = labs),
    # Adjust the position of the labels
    nudge_y = 300,
    family = "serif",
    fontface = "italic",
    size = base_text_size * 0.2
  ) +
  scale_fill_gradientn(
    colours = alpha(mypal, 0.9),
    na.value = NA,
    labels = label_comma(),
    limits = prec_limits
  ) +
  scale_y_continuous(
    breaks = br_4marginal,
    limits = c(0, max(br_4marginal) * 1.5)
  ) +
  theme_void() +
  theme(panel.grid.major.y = element_line(
    colour = "grey50",
    linetype = "dashed",
    linewidth = 0.1
  ))

plot_x

plot_y <- axis_canvas(plot_main, axis = "y", coord_flip = TRUE) +
  geom_col(
    data = marg_y,
    aes(y, avg, fill = avg),
    color = NA,
    show.legend = FALSE
  ) +
  geom_text(
    data = labs, aes(x = for_y, y = y, label = labs),
    # Adjust the position of the labels
    nudge_y = 300,
    angle = 270,
    family = "serif",
    fontface = "italic",
    size = base_text_size * 0.2
  ) +
  scale_fill_gradientn(
    limits = prec_limits,
    colours = alpha(mypal, 0.9),
    na.value = NA,
    labels = label_comma()
  ) +
  scale_y_continuous(
    breaks = br_4marginal,
    limits = c(0, max(br_4marginal) * 1.5)
  ) +
  coord_flip() +
  theme_void() +
  theme(panel.grid.major.x = element_line(
    colour = "grey50",
    linetype = "dashed",
    linewidth = 0.1
  ))
plot_y

And insert everything in the main plot. See the final result:

# Combine all plots into one
sizes_axis <- grid::unit(.3, "null")

plot_final <- insert_xaxis_grob(plot_main, plot_x,
  position = "top",
  height = sizes_axis
)
plot_final <- insert_yaxis_grob(plot_final, plot_y,
  position = "right",
  width = sizes_axis * 1.25
)

gg_final <- ggdraw(plot_final)
gg_final

And with a bit of effort we got it.

Recap

Much of the code we have created relates with the theming and labels of the plot. Here you can find a simplified version:

Simplified version

Hillshade, colors and marginal plots with tidyterra (I)

Mon, 17 Oct 2022 00:00:00 +0200

How to overlay SpatRasters

8 min.

This is the first post of a series of two, showing how to overlay a SpatRaster on top of a Hillshade background. Next post would show how to add marginal plots including information of the values of the raster by longitude and latitude. See the second post here.

Using shadow effects on relief mappings is a very common technique, that allows to produce informative yet beautiful maps. If you are interested on this topic and you work with R, you would have probably seen this map:

The production of this map by Timo Grossenbacher has been a reference for years. However, last developments on the R package ecosystem (terra, sf and support of both classes on ggplot2, development of ggnewscale, etc.) can make even easier the task of producing such type of maps.

In fact, Dominic Royé recently wrote a very detailed post on creating shadow effects on map reliefs. On this first post of the series I would replicate that technique with a slight variation (e.g. not making use of ggnewscale) and I would discuss a bit on the potential choice of a color palette for this kind of maps.

Libraries

I would use the following libraries:

## Libraries

library(terra)
library(tidyterra)
library(ggplot2)
library(dplyr)
library(scales)

# Get the data
library(geodata)

Get the data

First step is to get the altitude data. I use here the package geodata for simplicity, but you can use as well elevatr that is much more complete. However elevatr produces the result as RasterLayers, so you would need to convert the object to SpatRaster with terra::rast().

# Cache map data
mydir <- "~/R/mapslib/misc"

r_init <- elevation_30s("ROU", path = mydir)

r_init
#> class       : SpatRaster 
#> dimensions  : 588, 1176, 1  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : 20.1, 29.9, 43.5, 48.4  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source      : ROU_elv_msk.tif 
#> name        : ROU_elv_msk 
#> min value   :          -4 
#> max value   :        2481

# For better handling we set here the names
names(r_init) <- "alt"

# We don't want values lower than 0
r <- r_init %>%
  mutate(alt = pmax(0, alt))

r
#> class       : SpatRaster 
#> dimensions  : 588, 1176, 1  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : 20.1, 29.9, 43.5, 48.4  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source      : memory 
#> name        :  alt 
#> min value   :    0 
#> max value   : 2481

We can now have a quick look to the plot with tidyterra::autoplot():

# Quick look
autoplot(r) +
  theme_minimal()

Hillshading

Next step is to calculate the hillshade. Royé has a very detailed discussion here, so I would not go into details. Basically what we want to create is a layer that approximates the potential “texture” of the surface based on the elevation and the sun position. This is straightforward with terra::terrain() and terra::shade() functions:

## Create hillshade effect

slope <- terrain(r, "slope", unit = "radians")
aspect <- terrain(r, "aspect", unit = "radians")
hill <- shade(slope, aspect, 30, 270)

# normalize names
names(hill) <- "shades"

# Hillshading, but we need a palette
pal_greys <- hcl.colors(1000, "Grays")

ggplot() +
  geom_spatraster(data = hill) +
  scale_fill_gradientn(colors = pal_greys, na.value = NA)
#> SpatRaster resampled to ncells = 501501

We can also do the following hack to avoid the use of a scale_fill_* (via ggplot2 or via ggnewscale::new_scale_fill()):

Select a vector of colors (in this post pal_greys).
Extract the values of the raster and reescale them to the length of the palette (c(1, 1000)).
Round those rescaled values to the nearest integer. So we would have a index indicating which value of pal_greys should be mapped to each cell.
Now use the parameter fill on the geom_ instead of using the scale.

An additional note is that geom_spatraster() has a parameter maxcell that would perform a spatial resampling if the raster has more cells than maxcell. This is for optimization (note that terra::plot() has the same setup and that the users often forgot about it), but we can force to plot all the cells by using maxcell = Inf. On this approach for using fill the value maxcell needs to be effectively set to Inf to ensure that the number of color values and the number of cells is the same.

# Use a vector of colors


index <- hill %>%
  mutate(index_col = rescale(shades, to = c(1, length(pal_greys)))) %>%
  mutate(index_col = round(index_col)) %>%
  pull(index_col)


# Get cols
vector_cols <- pal_greys[index]

# Need to avoid resampling
# and dont use aes

hill_plot <- ggplot() +
  geom_spatraster(
    data = hill, fill = vector_cols, maxcell = Inf,
    alpha = 1
  )

hill_plot

Selecting colors

The selection of colors for elevation maps is a key aspect when designing this kind of visualization since colors can be confused with environmental phenomena (Patterson and Jenny, 2011). For example, by convention green colors are associated to low elevations while orange, browns and whites are associared to high elevations on some of the most common elevation palettes (aka hypsometric tints). See for example the Wikipedia Topographic maps conventions.

This is not ideal, since greens can be confused with forests, for example, so an elevation map of desertic areas would not be appropiated with a green-brown-white color scheme.

There is an additional point to take into account when designing color palettes for maps. A regular gradient would just interpolate colors assuming that the distance among colors is the same:

# Regular gradient
grad <- hypso.colors(10, "dem_poster")

autoplot(r) +
  scale_fill_gradientn(colours = grad, na.value = NA)

For that reason, tidyterra provides additional gradients whose colors are placed unevenly with the goal of providing a better understanding of the maps:

# Hypso gradient
grad_hypso <- hypso.colors2(10, "dem_poster")


autoplot(r) +
  scale_fill_gradientn(colours = grad_hypso, na.value = NA)

Can you notice the difference? In the first map greens are the dominant color. However greens are representing a wide range of elevations (0-750 meters) that correspond with most of the territory. In terms of perception, we won’t be clearly spotting elevation differences in the center of the country, while with the uneven gradient greens only correspond to the range (0 - 250 meters) and the overall perception of elevation improves. Note that the only difference between plots is exclusively the color palette.

For producing our map we are going to assess visually the result of a selection of palettes provided by tidyterra. We use here the version tidyterra::scale_fill_hypso_tint_c() instead of tidyterra::scale_fill_hypso_c() for taking advantage of the uneven color gradients.

A downside of using this scales is that we need also to adjust the limits argument of the functions to make ggplot2 aware of the limits of the value of the raster. This is easily achieved with terra::minmax() but I added an extra touch rounding up and down the range of values to the nearest 500.

# Try some options, but we need to be aware of the values of our raster

r_limits <- minmax(r) %>% as.vector()

# Rounded to lower and upper 500
r_limits <- c(floor(r_limits[1] / 500), ceiling(r_limits[2] / 500)) * 500

# And making min value to 0.
r_limits <- pmax(r_limits, 0)

# Compare
minmax(r) %>% as.vector()
#> [1]    0 2481
r_limits
#> [1]    0 2500


# Now lets have some fun with scales from tidyterra

elevt_test <- ggplot() +
  geom_spatraster(data = r)

# Create a helper function

plot_pal_test <- function(pal) {
  elevt_test +
    scale_fill_hypso_tint_c(
      limits = r_limits,
      palette = pal
    ) +
    ggtitle(pal) +
    theme_minimal()
}

plot_pal_test("etopo1_hypso")
plot_pal_test("dem_poster")
plot_pal_test("spain")
plot_pal_test("pakistan")
plot_pal_test("utah_1")
plot_pal_test("wiki-2.0_hypso")

I finally selected for my plot the "dem_poster" palette, but this is completely a personal choice. You should select the palette you feel more comfortable with. See the full range of color palettes provided by tidyterra here.

Final plot

So now it is time to blend both the hillshade layer and the altitude layer using some level of alpha on the upper layer.

base_plot <- hill_plot +
  # Avoid resampling with maxcell
  geom_spatraster(data = r, maxcell = Inf) +
  scale_fill_hypso_tint_c(
    limits = r_limits,
    palette = "dem_poster",
    alpha = 0.4,
    labels = label_comma(),
    # For the legend I use custom breaks
    breaks = c(
      seq(0, 500, 100),
      seq(750, 1500, 250),
      2000
    )
  )

base_plot

And with a bit of trickery and theming we can have our final map. First we load a font from Google with a custom function:

myload_fonts <- function(fontname, family,
                         fontdir = tempdir()) {
  fontname_url <- utils::URLencode(fontname)
  fontzip <- tempfile(fileext = ".zip")
  download.file(paste0("https://fonts.google.com/download?family=", fontname_url),
    fontzip,
    quiet = TRUE,
    mode = "wb"
  )
  unzip(fontzip,
    exdir = fontdir,
    junkpaths = TRUE
  )

  # Load fonts
  paths <- list(
    regular = "Regular.ttf",
    bold = "Bold.ttf",
    italic = "Italic.ttf",
    bolditalic = "BoldItalic.ttf"
  )


  namefile <- gsub(" ", "", fontname)
  paths_end <- file.path(
    fontdir,
    paste(namefile, paths, sep = "-")
  )


  names(paths_end) <- names(paths)

  sysfonts::font_add(family,
    regular = paths_end["regular"],
    bold = paths_end["bold"],
    italic = paths_end["italic"],
    bolditalic = paths_end["bolditalic"]
  )

  return(invisible())
}

And now we theme it:

# Theming
myload_fonts("Noto Serif", "notoserif", "~/R/googlefonts")
showtext::showtext_auto()

# Adjust text size
base_text_size <- 30

base_plot +
  # Change guide
  guides(fill = guide_legend(
    title = "   m.",
    direction = "horizontal",
    nrow = 1,
    keywidth = 1.75,
    keyheight = 0.5,
    label.position = "bottom",
    title.position = "right",
    override.aes = list(alpha = 1)
  )) +
  labs(
    title = "Elevation of Romania",
    subtitle = "Hillshade and hypsometric tint blend",
    caption = paste0(
      "@dhernangomez using tidyterra, ggplot2, geodata R packages.",
      " Data: Shuttle Radar Topography Mission (SRTM)"
    )
  ) +
  theme_minimal(base_family = "notoserif") +
  theme(
    plot.background = element_rect("grey97", colour = NA),
    plot.margin = margin(20, 20, 20, 20),
    plot.caption = element_text(size = base_text_size * 0.5),
    plot.title = element_text(face = "bold", size = base_text_size * 1.4),
    plot.subtitle = element_text(
      margin = margin(b = 10),
      size = base_text_size
    ),
    axis.text = element_text(size = base_text_size * 0.7),
    legend.position = "bottom",
    legend.title = element_text(size = base_text_size * 0.8),
    legend.text = element_text(size = base_text_size * 0.8),
    legend.key = element_rect("grey50"),
    legend.spacing.x = unit(0, "pt")
  )

References

Patterson T, Jenny B (2011). “The Development and Rationale of Cross-blended Hypsometric Tints.” Cartographic Perspectives, 31–46. https://doi.org/10.14714/CP69.20

Grossenbacher T (2016). “Beautiful thematic maps with ggplot2 (only).” https://timogrossenbacher.ch/bivariate-maps-with-ggplot2-and-sf/.

Royé D (2022). “Hillshade effects.” https://dominicroye.github.io/en/2022/hillshade-effects/.

Hernangómez D (2022). tidyterra: tidyverse Methods and ggplot2 Helpers for terra Objects. https://doi.org/10.5281/zenodo.6572471.

Introducing tidyterra

Wed, 25 May 2022 00:00:00 +0200

Easily work and ggplot SpatRasters

4 min.

If you have been playing around with R for a while, probably you are familiarized with the volcano dataset:

data("volcano")
image(volcano, col = terrain.colors(256, rev = TRUE))

This represents the topographic information of one of the volcanoes of Auckland (New Zealand), specifically Maungawhau / Mount Eden. But do you know that this map is flipped?

On this post I introduce the tidyterra package, recently added to CRAN and I would show you how to geotag the volcano dataset. We would produce also ggplot2 maps using the functions of tidyterra.

# Libraries
library(terra)
library(ggplot2)
library(tidyterra)
library(maptiles)
library(sf)

Wait, `volcano` is flipped?

Let’s check it out. Thanks to the package maptiles we can have a glimpse of the location of Maungawhau using map tiles (as Google Maps uses). We would use tidyterra for displaying the map tile:

# location of Maungawhau

box <- c(
  174.7611552780,
  -36.8799200525,
  174.7682380109,
  -36.8719519780
)
class(box) <- "bbox"
box <- st_as_sfc(box)
st_crs(box) <- 4326

box <- box %>%
  # To crs for NZGD49
  st_transform(27200)

tile <- get_tiles(box, crop = TRUE, zoom = 16)


ggtile <- ggplot() +
  geom_spatraster_rgb(data = tile)

ggtile

So well, here you go. A neat and crisp RGB tile of Maungawhau. Now, the next question is, how to match the volcano dataset (a matrix) with this tile (a geo-tagged map tile)? Let’s check it out

Working with SpatRasters

Thanks to the terra package we can start converting volcano into a SpatRaster:

volcano_rast <- rast(volcano)

terra::plot(volcano_rast)

# Wait, it is flipped!
volcano_rast_ok <- rast(volcano[
  seq(nrow(volcano), 1, -1),
  seq(ncol(volcano), 1, -1)
])

# Much better!
terra::plot(volcano_rast_ok)

volcano_rast_ok
#> class       : SpatRaster 
#> dimensions  : 87, 61, 1  (nrow, ncol, nlyr)
#> resolution  : 1, 1  (x, y)
#> extent      : 0, 61, 0, 87  (xmin, xmax, ymin, ymax)
#> coord. ref. :  
#> source      : memory 
#> name        : lyr.1 
#> min value   :    94 
#> max value   :   195

Nice! Now we have a raster of volcano, but still without geotagged information. Thanks to this article of Tomislav Hengl (\@tom_hengl) we can check the basic geographic parameters of volcano (see Volcano Maungawhau), that are:

CRS: EPSG:27200
xllcorner: 2667400
yllcorner: 6478700
cellsize: 10 m
ncols: 61
nrows: 87

And we can translate that easily to an empty SpatRaster:

# Extra length for proper handling extent
xrange <- range(seq(from = 2667400, length.out = 62, by = 10))
yrange <- range(seq(from = 6478700, length.out = 88, by = 10))

template <- rast(
  crs = "EPSG:27200",
  xmin = xrange[1],
  xmax = xrange[2],
  ymin = yrange[1],
  ymax = yrange[2],
  resolution = 10
)
template
#> class       : SpatRaster 
#> dimensions  : 87, 61, 1  (nrow, ncol, nlyr)
#> resolution  : 10, 10  (x, y)
#> extent      : 2667400, 2668010, 6478700, 6479570  (xmin, xmax, ymin, ymax)
#> coord. ref. : NZGD49 / New Zealand Map Grid (EPSG:27200)

So now we only need to transfer the values from volcano_rast_ok to our template:

# Use tidyterra for pull the values of one raster
# and create a new layer

volcano2 <- template %>%
  mutate(elevation = pull(volcano_rast_ok, lyr.1)) %>%
  select(elevation)

volcano2
#> class       : SpatRaster 
#> dimensions  : 87, 61, 1  (nrow, ncol, nlyr)
#> resolution  : 10, 10  (x, y)
#> extent      : 2667400, 2668010, 6478700, 6479570  (xmin, xmax, ymin, ymax)
#> coord. ref. : NZGD49 / New Zealand Map Grid (EPSG:27200) 
#> source      : memory 
#> name        : elevation 
#> min value   :        94 
#> max value   :       195

terra::plot(volcano2)

# And plot it
ggtile +
  geom_spatraster(data = volcano2) +
  scale_fill_terrain_c(alpha = 0.75)

An Easter egg

The volcano dataset may not be completely up to date. As a compliment, tidyterra includes a .tif file with the same dimensions that our volcano2 raster, but with the topographic values extracted from Auckland LiDAR 1m DEM (2013) and resampled to a resolution of 5x5 meters, for package size optimization. See here how to load it and check the plotting tidyterra possibilities:

# Load out Easter Egg

volcano2_easter <- rast(system.file("extdata/volcano2.tif",
  package = "tidyterra"
))

volcano2_easter
#> class       : SpatRaster 
#> dimensions  : 174, 122, 1  (nrow, ncol, nlyr)
#> resolution  : 5, 5  (x, y)
#> extent      : 1756969, 1757579, 5917003, 5917873  (xmin, xmax, ymin, ymax)
#> coord. ref. : NZGD2000 / New Zealand Transverse Mercator 2000 (EPSG:2193) 
#> source      : volcano2.tif 
#> name        : elevation 
#> min value   :  76.26222 
#> max value   :  195.5542
terra::plot(volcano2_easter)

# Only altitudes of more than 130m

volcano_filter <- volcano2_easter %>%
  filter(elevation > 130)


ggtile +
  geom_spatraster(data = volcano_filter) +
  scale_fill_viridis_c(na.value = NA, alpha = 0.7) +
  labs(fill = "Elevation (m)")

# Contour lines

ggtile +
  geom_spatraster_contour(data = volcano2_easter, binwidth = 10)

# Contour lines + contour polygons

ggtile +
  geom_spatraster_contour_filled(
    data = volcano2_easter,
    breaks = seq(70, 210, 20),
    alpha = 0.7
  ) +
  geom_spatraster_contour(
    data = volcano2_easter, binwidth = 2.5,
    alpha = 0.7, size = .2, color = "grey10"
  ) +
  coord_sf(expand = FALSE)

Unknown pleasures with R

Sun, 01 May 2022 00:00:00 +0200

Joyplot elevation maps with ggridges and terra

8 min.

On 1970, Harold D. Craft Jr. published his Ph.D thesis “Radio observations of the pulse profiles and dispersion measures of twelve pulsars”. The thesis (337 pages) includes on pages 214 to 216 the following depictions of successive pulses of some pulsars:

From “Radio Observations of the Pulse Profiles and Dispersion Measures of Twelve Pulsars” by Harold D. Craft, Jr. (September 1970). Original source: https://blogs.scientificamerican.com/sa-visual/pop-culture-pulsar-origin-story-of-joy-division-s-unknown-pleasures-album-cover-video/

Nine years later, a young graphic designer named Peter Saville had a new project. He had to design the cover of the debut album of a young British rock band, named Joy Division. At some point of the process Bernand Summer (lead guitar of Joy Division)¹, found the following image on The Cambridge Encyclopaedia of Astronomy (1977 edition):

Saville presented a black and white version, producing a cover that reaches an iconic status in the ’80s. This cover has been reproduced in the form of tattoos, fashion clothes, merchandising, video games and even 3-D sculptures:

If you are interested on knowing more about this fascinating history of science and design you can find it on Pop Culture Pulsar: Origin Story of Joy Division’s Unknown Pleasures Album Cover by Jen Christiansen.

Since then, this kind of plots have become very popular, being known as ridge plots or joyplots, in honor of Joy Division. On this post, I would produce “joyplots” with R for specific regions of the world using the elevation data for creating the ridges.

Creating joyplot maps with R

This topic has already been covered by other authors, as Daniel Redondo (Spanish) and Travis M. White. However, they both use QGIS, while on this post I would work completely on R.

Some initial considerations we may need to bear in mind:

On this post I will use geom_ridgline() instead of geom_density_ridges(). This would provide us with more control on the final plot, but it has a point of attention: both the coordinates and the elevation should be in the same unit (See why ). Therefore we should project both the raster and the base sf object on a suitable CRS defined in meters (in this case).
Joyplots are much cooler when only a few lines are displayed. This is directly related with the number of rows of our raster. A very detailed raster (e.g. lots of rows) would produce a much detailed plot but it may not suit our needs.

Now, let’s start with the required libraries:

# Libraries

# Spatial
library(sf)
library(terra)
library(giscoR) # Shapes
library(elevatr)

# Data viz and wrangling
library(ggplot2)
library(dplyr)
library(ggridges)

The first step consists on selecting our region of interest (sf object) and extracting the elevation data. We can achieve that with giscoR and elevatr. In this post I would create a joyplot of Andalusia. Note that, given we are creating just a visualization, the resolution of the sf object is not very relevant.

# Select a Spanish Region: Andalucia
region <- gisco_get_nuts(nuts_id = "ES61") %>%
  # And project data
  st_transform(25830)

Now we need to extract the elevation using elevatr. We can also adjust the zoom level as needed. You can find a good guidance on the zoom levels on the OpenStreetMaps wiki.

dem <- get_elev_raster(region, z = 7, clip = "bbox", expand = 10000) %>%
  # And convert to terra
  rast() %>%
  # Mask to the shape
  mask(vect(region))

# Rename layer for further manipulation
names(dem) <- "elev"

nrow(dem)
#> [1] 698

terra::plot(dem)

We already have our elevation raster. Now the next step is to adjust the number of rows of our raster to a lower number. We can then aggregate the raster (i.e. reduce the number of cells or increasing the size of the cells) using a scaling factor that would reduce the number of rows to our desired target (in this case 90 rows):

# Approx
factor <- round(nrow(dem) / 90)

dem_agg <- aggregate(dem, factor)

nrow(dem_agg)
#> [1] 88

terra::plot(dem_agg)

We can check how the number of rows have decreased. Also, the plot shows that we have now less cells.

Now, we may need to perform additional manipulations on the values of the raster:

We need to ensure that all the valid values are equal or greater than zero.
We would replace the NAs produced when masking the raster to zero. We would use this later to decide whether to remove or not some parts of the plot.

After that, we would create a data frame with the information needed for creating the joyplot.

dem_agg[dem_agg < 0] <- 0
dem_agg[is.na(dem_agg)] <- 0

dem_df <- as.data.frame(dem_agg, xy = TRUE, na.rm = FALSE)

as_tibble(dem_df)
#> # A tibble: 12,848 x 3
#>          x        y  elev
#>           
#>  1  77184. 4306315.     0
#>  2  81049. 4306315.     0
#>  3  84914. 4306315.     0
#>  4  88779. 4306315.     0
#>  5  92644. 4306315.     0
#>  6  96510. 4306315.     0
#>  7 100375. 4306315.     0
#>  8 104240. 4306315.     0
#>  9 108105. 4306315.     0
#> 10 111970. 4306315.     0
#> # ... with 12,838 more rows

Now is a good moment to adjust the units of the coordinates and the elevation if needed. In this case both are in meters, but I would show you how to perform those adjustment with the units package:

library(units)

# Units of DEM projection
units_crs <- st_crs(dem_agg)$units

units_crs
#> [1] "m"

# Example, convert to miles
# Adjust as needed

dem_miles <- dem_df %>%
  mutate(
    x = set_units(x, "m"),
    x_mile = set_units(x, "mi"),
    y = set_units(y, "m"),
    y_mile = set_units(y, "mi"),
    elev = set_units(elev, "m"),
    elev_mile = set_units(elev, "mi")
  )

as_tibble(dem_miles)
#> # A tibble: 12,848 x 6
#>          x        y elev x_mile y_mile elev_mile
#>        [m]      [m]  [m]   [mi]   [mi]      [mi]
#>  1  77184. 4306315.    0   48.0  2676.         0
#>  2  81049. 4306315.    0   50.4  2676.         0
#>  3  84914. 4306315.    0   52.8  2676.         0
#>  4  88779. 4306315.    0   55.2  2676.         0
#>  5  92644. 4306315.    0   57.6  2676.         0
#>  6  96510. 4306315.    0   60.0  2676.         0
#>  7 100375. 4306315.    0   62.4  2676.         0
#>  8 104240. 4306315.    0   64.8  2676.         0
#>  9 108105. 4306315.    0   67.2  2676.         0
#> 10 111970. 4306315.    0   69.6  2676.         0
#> # ... with 12,838 more rows

Finally, we can create our joyplot. Note that we can “train” the scales of our ggplot to an spatial object automatically if we pass our region object into the plot. The relative height of the ridges is controlled via the scale parameter:

ggplot() +
  # Just for the scales, pass with NA arguments so it is not shown
  geom_sf(data = region, color = NA, fill = NA) +
  geom_ridgeline(
    data = dem_df, aes(
      x = x, y = y,
      group = y,
      height = elev
    ),
    scale = 25
  ) +
  theme_ridges()

The last step is to provide a black theme, resembling the cover of the album:

ggplot() +
  geom_sf(data = region, color = NA, fill = NA) +
  geom_ridgeline(
    data = dem_df, aes(
      x = x, y = y,
      group = y,
      height = elev
    ),
    scale = 25,
    fill = "black",
    color = "white",
    size = .25
  ) +
  theme_void() +
  theme(plot.background = element_rect(fill = "black"))

Variations

We can produce some variations of the same map using several parameters and other artifacts.

Using `geom_density_ridges()`

We can use geom_density_ridges() with stat="identity" instead of geom_ridgeline() for creating a similar map:

ggplot() +
  geom_sf(data = region, color = NA, fill = NA) +
  geom_density_ridges(
    data = dem_df, aes(
      x = x, y = y,
      group = y,
      height = elev
    ),
    stat = "identity",
    scale = 25,
    fill = "black",
    color = "white",
    size = .25
  ) +
  theme_void() +
  theme(plot.background = element_rect(fill = "black"))

Land only

If we use geom_ridgeline() it is quite easy to remove some parts of the lines, as the parameter min_height allow us to control the minimum height to be plotted. I found this much more difficult when using geom_density_ridges(), where the equivalent parameter rel_min_height is relative to the overall maximum height.

This is the main reason why we replaced the NA values with zeros, so those parts of the string can be easily removed.

ggplot() +
  geom_sf(data = region, color = NA, fill = NA) +
  geom_ridgeline(
    data = dem_df, aes(
      x = x, y = y,
      group = y,
      height = elev
    ),
    scale = 25,
    fill = "black",
    color = "white",
    size = .25,
    min_height = 0.1
  ) +
  theme_void() +
  theme(plot.background = element_rect(fill = "black"))

With colors

We can apply different colors to the plot. Note that ggridges only accepts different aes by row, and not by column:

# Classify on three different bands

dem_df <- dem_df %>%
  mutate(class = cut_number(y, n = 3))

ggplot() +
  geom_sf(data = region, color = NA, fill = NA) +
  geom_ridgeline(
    data = dem_df, aes(
      x = x, y = y,
      group = y,
      height = elev,
      color = class
    ),
    scale = 25,
    fill = "black",
    size = .5,
    show.legend = FALSE
  ) +
  theme_void() +
  theme(plot.background = element_rect(fill = "black")) +
  scale_color_manual(values = alpha(
    c(
      "#007A33",
      "white",
      "#007A33"
    ),
    .95
  ))

Combine with another objects

Like using a sf object:

highres <- gisco_get_nuts(
  nuts_id = "ES61",
  resolution = 1
) %>%
  # And project data
  st_transform(25830) %>%
  st_buffer(-5000)

ggplot() +
  geom_sf(data = highres, color = NA, fill = "#007A33", alpha = 0.95) +
  geom_ridgeline(
    data = dem_df, aes(
      x = x, y = y,
      group = y,
      height = elev
    ),
    scale = 25,
    fill = "black",
    color = "white",
    size = .25,
    min_height = 0.1
  ) +
  theme_void() +
  theme(plot.background = element_rect(fill = "black"))

Or maybe adding a frame to the plot

frame <- as.polygons(dem_agg, extent = TRUE) %>%
  st_as_sf()

ggplot() +
  geom_sf(data = frame, color = "lightblue", fill = NA, size = 2) +
  geom_ridgeline(
    data = dem_df, aes(
      x = x, y = y,
      group = y,
      height = elev
    ),
    scale = 25,
    fill = "black",
    color = "white",
    size = .25
  ) +
  theme_void() +
  theme(plot.background = element_rect(fill = "black"))

References

Craft Jr, H. D. (1970). Radio observations of the pulse profiles and dispersion measures of twelve pulsars. Cornell University.

Mitton, Simon (1977). The Cambridge encyclopaedia of astronomy. Prentice-Hall of Canada.

Lipez, Zachary (2019, June 14). “How Joy Division’s ‘Unknown Pleasures`’ image went from underground album cover to a piece of cultural ubiquity” The Washington Post. https://wapo.st/3K6Chsc

White, T. M. (2019). Cartographic Pleasures: Maps Inspired by Joy Division’s Unknown Pleasures Album Art. Cartographic Perspectives, (92), 65–78. https://doi.org/10.14714/CP92.1536

Redondo, Daniel (2020, January 25). “Mapas estilo Joy Division con QGIS y R.” https://danielredondo.com/blog/2020-01-25-joy_division/

Other versions of the story credit drummer Stephen Morris for finding it. ↑

Corona timelapse

Mon, 14 Mar 2022 00:00:00 +0100

Travel restrictions amidst the COVID crisis across time - A German perspective

1 min.

Project discontinued

In April 2021, my brother Diego and I saw the need for a friendly and automated interface to the meticulous and ever-changing restrictions that the German authorities imposed to travels abroad amid the COVID crisis.

Despite the drastic variations in this regard that most foreign countries have experienced during last year, the mild character of the currently predominant Omicron variant has finally led Germany to lift all COVID-related obstacles to international travel. The long-awaited contemplation of an all-green world map has filled us with joy, but, to be honest, it has also rendered our website quite boring, no matter how many languages we have translated it into (6 as of now 🇩🇪 🇬🇧 🇪🇸 🇫🇷 🇵🇱 🇹🇷).

To compensate for this, we have put all the pieces together to produce a chronology of the COVID crisis through the lenses of the Robert Koch Institut (RKI), the German entity that was responsible for COVID risk assessment of international areas. Most of the effort was already made, since we have been scraping RKI’s information (via scrapy) for almost one year. To complete the puzzle, we only needed to apply our method to the old risk assesment reports that had been issued before we started the project. That is, we have just combined our already developed scraping muscle with the Archive.org Wayback Machine as provided by Evan Sangaline, and we have of course worked around the inconsistencies of German bureaucracy.

After all, we hope that corona-atlas remains boring and that our world map remains green. Now it is finally time for quite some Wanderlust!

Insets with ggplot2 and tmap - and mapsf!

Thu, 03 Mar 2022 00:00:00 +0100

A map on a map

3 min.

This post is dedicated to Dominic Royé, AKA \@dr_xeo

A common challenge when creating maps is how to include an inset map on your visualization. An inset map is nothing more than a smaller map usually included on a corner that may provide additional context to the overall map. It is also useful for representing spatial units that may form part of a country but its geographical location would imply an imperfect visualization, or even to include small units that otherwise won’t be shown on the map.

I have already covered this using the base plot() function, but this time I would show how to produce these insets using the ggplot2 and the tmap packages. In short: use cowplot package.

Test case: Canary Island as an inset

On this example, I would create a map of Spain using mapSpain and creating an inset for the Canary Islands.

The “true” map of Spain is:

library(mapSpain)
library(sf)
library(ggplot2)
library(dplyr)

regions <- esp_get_ccaa(moveCAN = FALSE)

ggplot(regions) +
  geom_sf()

I would use a different CRS for each part of Spain. In the case of mainland Spain I would use ETRS89 / UTM 30N (EPSG:25830) and for the Canary Islands I would use REGCAN95 / UTM 28N (EPSG:4083)

main <- regions %>%
  filter(ccaa.shortname.es != "Canarias") %>%
  st_transform(25830)

ggplot(main) +
  geom_sf()

island <- regions %>%
  filter(ccaa.shortname.es == "Canarias") %>%
  st_transform(4083)

ggplot(island) +
  geom_sf()

So that was easy! Just a couple of maps using ggplot2. Let’s start mixing and matching!

On `ggplot2`

We have already created two quick maps on ggplot2. Now, to produce our map with insets we would:

Produce two plots: The main plot and the sub plot providing a minimal style. We would store them as ggplot2 objects.
We would combine both objects with cowplot.

# Main plot
main_gg <- ggplot(main) +
  geom_sf() +
  theme_void() +
  theme(
    plot.background = element_rect(fill = "grey85", colour = NA),
    # Add a bit of margin on the bottom left
    # We would place the inset there
    plot.margin = margin(l = 80, b = 80)
  )

# Sub plot
sub_gg <- ggplot(island) +
  geom_sf() +
  theme_void() +
  # Add a border to the inset
  theme(
    panel.border = element_rect(fill = NA, colour = "black"),
    plot.background = element_rect(fill = "grey95")
  )

We have our objects in place, and now is when the magic happens! With cowplot we can combine both maps on a single one. You may need to play a bit with the parameters x, y hjust and vjust of the sub plot to improve the placement:

library(cowplot)

ggdraw() +
  draw_plot(main_gg) +
  draw_plot(sub_gg,
    height = 0.2,
    x = -0.25,
    y = 0.08
  )

Note also that this approach is valid not only for maps, but for all type of plot produced by ggplot2, since this package is not specific for map objects:

# Combining non-spatial plots
library(palmerpenguins)

mass_flipper <- ggplot(
  data = penguins,
  aes(
    x = flipper_length_mm,
    y = body_mass_g
  )
) +
  geom_point(aes(
    color = species,
    shape = species
  ),
  size = 3,
  alpha = 0.8
  ) +
  theme_minimal() +
  scale_color_manual(values = c("darkorange", "purple", "cyan4"))

flipper_hist <- ggplot(data = penguins, aes(x = flipper_length_mm)) +
  geom_histogram(aes(fill = species),
    alpha = 0.5,
    position = "identity",
    show.legend = FALSE
  ) +
  scale_fill_manual(values = c("darkorange", "purple", "cyan4")) +
  theme_void() +
  theme(plot.background = element_rect(fill = "white"))


# Non-sense plot!
ggdraw() +
  draw_plot(mass_flipper) +
  draw_plot(flipper_hist,
    scale = 0.25,
    y = 0.3,
    x = -0.2
  )

On `tmap`

We can follow a similar approach on tmap. On versions v3.x.x (there is a new revamped version on development) we can use tmap_grob() to convert the tmap objects to the objects that cowplot can handle.

library(tmap)

main_tmap <- tm_shape(main) +
  tm_polygons() +
  tm_layout(
    inner.margins = c(.3, .3, 0, 0),
    frame = FALSE
  )


main_tmap <- tmap_grob(main_tmap)

sub_tmap <- tm_shape(island) +
  tm_polygons()

sub_tmap <- tmap_grob(sub_tmap)

Once that we have these new “grobs”, we can use the same approach than we applied to ggplot2 objects.

ggdraw() +
  draw_plot(main_tmap) +
  draw_plot(sub_tmap,
    height = 0.3,
    x = -0.2
  )

Update: On `mapsf`

Timotheé Giraud (AKA \@rgeomatic), the developer of mapsf, shared also how to create inset maps using that package:

library(mapsf)

mf_map(main)
mf_inset_on(island, pos = "bottomright", cex = .3)
mf_map(island)
box(lwd = .5)
mf_inset_off()

Beautiful Maps with R (IV): Fun with flags revisited

Fri, 28 Jan 2022 00:00:00 +0100

Any picture as a basemap

2 min.

On 27 Jan. 2022 my package rasterpic was accepted on CRAN (Hooray!!). This package allows to geotag images, using an spatial object (from sf or terra) as a geographic reference.

I tweeted about that, and it seems to have a good feedback from the #rspatial community:

#rspatial Do we need a package for using our own pictures as base maps? I don’t know, but anyway we have it! {rasterpic} 📦 is now on CRAN, and we can convert our pngs to spatial rasters like this https://t.co/fpoollARoN pic.twitter.com/l9o7rQwdgX
— dieghernan ن (@dhernangomez) January 27, 2022

I received also an interesting reply to this from Hefin Ioan Rhys @HRJ21:

Ooh I think a map with countries filled with their own flag would be poppin'.
— Hefin Ioan Rhys (@HRJ21) January 28, 2022

That remembers me to a previous post that I wrote when I added some new functions to the cartography package, now replaced by the mapsf package.

With rasterpic we have now an alternative tool for creating maps using images, and this quick post would show you how to do it.

I would replicate the Africa map presented on my previous plot, but this time I would use newer packages, as giscoR package, and the development version of ggspatial (not released yet), that adds support to SpatRaster object on ggplot2. The flags would be extracted from the GitHub repository https://github.com/hampusborgos/country-flags.

# Development version of ggspatial
# devtools::install_github("paleolimbot/ggspatial")
library(ggspatial)
library(ggplot2)
library(giscoR)
library(dplyr)
library(rasterpic)

# For country names
library(countrycode)

world <- gisco_get_countries(epsg = 3857)
africa <- gisco_get_countries(region = "Africa", epsg = 3857)

# Base map of Africa
plot <- ggplot(world) +
  geom_sf(fill = "grey90") +
  theme_minimal() +
  theme(panel.background = element_rect(fill = "lightblue"))

plot +
  # Zoom on Africa
  coord_sf(
    xlim = c(-2000000, 6000000),
    ylim = c(-4000000, 5000000)
  )

Now, let’s add the flags with a loop:

# We paste the ISO2 code to each african country
africa$iso2 <- countrycode(africa$ISO3_CODE, "iso3c", "iso2c")

# Get flags from repo - low quality to speed up the code
flagrepo <- "https://raw.githubusercontent.com/hjnilsson/country-flags/master/png250px/"

# Loop and add
for (iso in africa$iso2) {
  # Download pic and plot
  imgurl <- paste0(flagrepo, tolower(iso), ".png")
  tmpfile <- tempfile(fileext = ".png")
  download.file(imgurl, tmpfile, quiet = TRUE, mode = "wb")

  # Raster
  x <- africa %>% filter(iso2 == iso)
  x_rast <- rasterpic_img(x, tmpfile, crop = TRUE, mask = TRUE)
  plot <- plot + layer_spatial(x_rast)
}

plot +
  geom_sf(data = africa, fill = NA) +
  # Zoom on Africa
  coord_sf(
    xlim = c(-2000000, 6000000),
    ylim = c(-4000000, 5000000)
  )

Corona Atlas

Fri, 30 Apr 2021 00:00:00 +0200

Interactive map of the international COVID-19 risk areas as designated by the German authorities.

1 min.

Project discontinued

Visit https://dieghernan.github.io/corona-atlas.de/

Interactive map of the international COVID-19 risk areas as designated by the German authorities.

The data is updated periodically from the website of the Robert Koch Institute.

Data scraping is performed on Python with scrapy. The scraper also uses pandas and pycountry.

For the prototype version, map visualization was created with R and generated a map via {rmarkdown} using {leaflet}, {giscoR} and some packages included on the tidyverse. For the deployment, map logic has moved to Javascript to escalate with multiple languages.

spain-munic-bot

Fri, 29 Jan 2021 00:00:00 +0100

A twitter bot written in R.

1 min.

Project discontinued

🤖 Twitter bot: random municipalities of Spain 🇪🇸 with {mapSpain} posted with {rtweet} via a GitHub Action

Hi! I am a bot 🤖 that tweets a random map of a Spanish municipality with its name, province, and autonomous community (and a inset map of Spain showing the region and the community). I run 🏃‍♀️ every 20 minutes.

I have a website!!

Tweets by spainmunic

📦 R packages

Core packages used in the project are:

{mapSpain} for the location of the municipalities, base polygons and coordinates and imagery,
{osmdata} for the streets,
{tmap} for plotting,
{rtweet} for posting,

Other packages used are {sf}, {dplyr} and another common supporting packages.

Leaflet-providersESP

Mon, 26 Oct 2020 00:00:00 +0100

Plugin for Leaflet.js

1 min.

Leaflet-providersESP is a plugin for Leaflet that contains configurations for various tile layers provided by public organisms of Spain.

Demo

Full docs and examples on https://dieghernan.github.io/leaflet-providersESP/

This code would generate a leaflet map with a layer provided by Leaflet-providersESP.

	</span>Minimal page | leaflet-providersESP<span class="nt">
	 charset="utf-8" />
	 name="viewport" content="width=device-width, initial-scale=1.0">
	
	 rel="stylesheet" href="https://unpkg.com/[email protected]/dist/leaflet.css" />
	
	 id="mapid">

All providers

Head/Tails breaks on the classInt package.

Sun, 05 Apr 2020 00:00:00 +0200

11 min.

There are far more ordinary people (say, 80 percent) than extraordinary people (say, 20 percent); this is often characterized by the 80/20 principle, based on the observation made by the Italian economist Vilfredo Pareto in 1906 that 80% of land in Italy was owned by 20% of the population. A histogram of the data values for these phenomena would reveal a right-skewed or heavy-tailed distribution. How to map the data with the heavy-tailed distribution?

Jiang (2013)

Abstract

This vignette discusses the implementation of the “Head/tail breaks” style (Jiang (2013)) on the classIntervals function of the classInt package. A step-by-step example is presented in order to clarify the method. A case study using spData::afcon is also included, making use of other additional packages as sf.

Introduction

The Head/tail breaks, sometimes referred as ht-index (Jiang and Yin (2013)), is a classification scheme introduced by Jiang (2013) in order to find groupings or hierarchy for data with a heavy-tailed distribution.

Heavy-tailed distributions are heavily right skewed, with a minority of large values in the head and a majority of small values in the tail. This imbalance between the head and tail, or between many small values and a few large values, can be expressed as “far more small things than large things”.

Heavy tailed distributions are commonly characterized by a power law, a lognormal or an exponential function. Nature, society, finance (Vasicek (2002)) and our daily lives are full of rare and extreme events, which are termed “black swan events” (Taleb (2008)). This line of thinking provides a good reason to reverse our thinking by focusing on low-frequency events.

library(classInt)

# 1. Characterization of heavy-tail distributions----
set.seed(1234)
# Pareto distribution a=1 b=1.161 n=1000
sample_par <- 1 / (1 - runif(1000))^(1 / 1.161)
opar <- par(no.readonly = TRUE)
par(mar = c(2, 4, 3, 1), cex = 0.8)
plot(
  sort(sample_par, decreasing = TRUE),
  type = "l",
  ylab = "F(x)",
  xlab = "",
  main = "80/20 principle"
)
abline(
  h = quantile(sample_par, .8),
  lty = 2,
  col = "red3"
)
abline(
  v = 0.2 * length(sample_par),
  lty = 2,
  col = "darkblue"
)
legend(
  "topleft",
  legend = c("F(x): p80", "x: Top 20%"),
  col = c("red3", "darkblue"),
  lty = 2,
  cex = 0.8
)

hist(
  sample_par,
  n = 100,
  xlab = "",
  main = "Histogram",
  col = "grey50",
  border = NA,
  probability = TRUE
)
par(opar)

Breaking method

The method itself consists on a four-step process performed recursively until a stopping condition is satisfied. Given a vector of values \(v = (a_1, a_2, ..., a_n)\) the process can be described as follows:

On each iteration, compute \(\mu = \sum_{i=1}^{n} a_i \:\:\: \forall \: a_i \in v\).
Break \(v\) into the \(tail\) and the \(head\): \(tail = \{ a_x \in v | a_x \lt \mu \}\) \(head = \{ a_x \in v | a_x \gt \mu \}\).
Assess if the proportion of \(head\) over \(v\) is lower or equal than a given threshold: \(\frac{|head|}{|v|} \le thresold\)
If 3 is TRUE, repeat 1 to 3 until the condition is FALSE or no more partitions are possible (i.e. \(head\) has less than two elements).

It is important to note that, at the beginning of a new iteration, \(v\) is replaced by \(head\). The underlying hypothesis is to create partitions until the head and the tail are balanced in terms of distribution.So the stopping criteria is satisfied when the last head and the last tail are evenly balanced.

In terms of threshold, Jiang, Liu, and Jia (2013) set 40% as a good approximation, meaning that if the \(head\) contains more than 40% of the observations the distribution is not considered heavy-tailed.

The final breaks are the vector of consecutive \(\mu\):

[breaks = (\mu_1, \mu_2, \mu_3, …, \mu_n )]

Step by step example

We reproduce here the pseudo-code¹ as per Jiang (2019):

Recursive function Head/tail Breaks:
 Rank the input data from the largest to the smallest
 Break the data into the head and the tail around the mean;
 // the head for those above the mean
 // the tail for those below the mean
 While (head <= 40%):
 Head/tail Breaks (head);
End Function

A step-by-step example in R (for illustrative purposes) has been developed:

opar <- par(no.readonly = TRUE)
par(mar = c(2, 2, 3, 1), cex = 0.8)
var <- sample_par
thr <- .4
brks <- c(min(var), max(var)) # Initialise with min and max

sum_table <- data.frame(
  iter = 0,
  mu = NA,
  prop = NA,
  n_var = NA,
  n_head = NA
)
# Pars for chart
limchart <- brks
# Iteration
for (i in 1:10) {
  mu <- mean(var)
  brks <- sort(c(brks, mu))
  head <- var[var > mu]
  prop <- length(head) / length(var)
  stopit <- prop < thr & length(head) > 1
  sum_table <- rbind(
    sum_table,
    c(i, mu, prop, length(var), length(head))
  )
  hist(
    var,
    main = paste0("Iter ", i),
    breaks = 50,
    col = "grey50",
    border = NA,
    xlab = "",
    xlim = limchart
  )
  abline(v = mu, col = "red3", lty = 2)
  ylabel <- max(hist(var, breaks = 50, plot = FALSE)$counts)
  labelplot <- paste0("PropHead: ", round(prop * 100, 2), "%")
  text(
    x = mu,
    y = ylabel,
    labels = labelplot,
    cex = 0.8,
    pos = 4
  )
  legend(
    "right",
    legend = paste0("mu", i),
    col = c("red3"),
    lty = 2,
    cex = 0.8
  )
  if (isFALSE(stopit)) {
    break
  }
  var <- head
}
par(opar)

As it can be seen, in each iteration the resulting head gradually loses the high-tail property, until the stopping condition is met.

iter	mu	prop	n_var	n_head
1	5.6755	14.5%	1000	145
2	27.2369	21.38%	145	31
3	85.1766	19.35%	31	6
4	264.7126	50%	6	3

The resulting breaks are then defined as breaks = c(min(var), mu1, mu2, ..., mu_n, max(var)).

Implementation on `classInt` package

The implementation in the classIntervals function should replicate the results:

ht_sample_par <- classIntervals(sample_par, style = "headtails")
brks == ht_sample_par$brks

## [1] TRUE TRUE TRUE TRUE TRUE TRUE

As stated in Jiang (2013), the number of breaks is naturally determined, however the thr parameter could help to adjust the final number. A lower value on thr would provide less breaks while a larger thr would increase the number, if the underlying distribution follows the “far more small things than large things” principle.

opar <- par(no.readonly = TRUE)
par(mar = c(2, 2, 2, 1), cex = 0.8)

pal1 <- c("wheat1", "wheat2", "red3")
# Minimum: single break
print(paste("number of breaks", length(classIntervals(sample_par, style = "headtails", thr = 0)$brks - 1)))
plot(
  classIntervals(sample_par, style = "headtails", thr = 0),
  pal = pal1,
  main = "thr = 0"
)

# Two breaks
print(paste("number of breaks", length(classIntervals(sample_par, style = "headtails", thr = 0.2)$brks - 1)))
plot(
  classIntervals(sample_par, style = "headtails", thr = 0.2),
  pal = pal1,
  main = "thr = 0.2"
)

# Default breaks: 0.4
print(paste("number of breaks", length(classIntervals(sample_par, style = "headtails")$brks - 1)))
plot(classIntervals(sample_par, style = "headtails"),
  pal = pal1,
  main = "thr = Default"
)

# Maximum breaks
print(paste("number of breaks", length(classIntervals(sample_par, style = "headtails", thr = 1)$brks - 1)))
plot(
  classIntervals(sample_par, style = "headtails", thr = 1),
  pal = pal1,
  main = "thr = 1"
)
par(opar)

The method always returns at least one break, corresponding to mean(var).

Case study

Jiang (2013) states that "the new classification scheme is more natural than the natural breaks in finding the groupings or hierarchy for data with a heavy-tailed distribution." (p. 482), referring to Jenks’ natural breaks method. In this case study we would compare headtails vs. fisher, that is the alias for the Fisher-Jenks algorithm and it is always preferred to the jenks style (see ?classIntervals). For this example we will use the afcon dataset from spData package, plus some additional spatial information in order to create the data visualization.

library(spData)
data(afcon, package = "spData")

Let’s have a look to the Top 10 values and the distribution of the variable totcon (index of total conflict 1966-78):

# Top10
knitr::kable(head(afcon[order(afcon$totcon, decreasing = TRUE), c("name", "totcon")], 10))

opar <- par(no.readonly = TRUE)
par(mar = c(4, 4, 3, 1), cex = 0.8)
hist(afcon$totcon,
  n = 20,
  main = "Histogram",
  xlab = "totcon",
  col = "grey50",
  border = NA,
)
plot(
  density(afcon$totcon),
  main = "Distribution",
  xlab = "totcon",
)
par(opar)

The data shows that EG and SU data present a clear hierarchy over the rest of values. As per the histogram, we can confirm a heavy-tailed distribution and therefore the “far more small things than large things” principle.

As a testing proof, on top of headtails and fisher we would use also quantile to have a broader view on the different breaking styles. As quantile is a position-based metric, it doesn’t account for the magnitude of F(x) (hierarchy), so the breaks are solely defined by the position of x on the distribution.

Applying the three aforementioned methods to break the data:

brks_ht <- classIntervals(afcon$totcon, style = "headtails")
print(brks_ht)
# Same number of classes for "fisher"
nclass <- length(brks_ht$brks) - 1
brks_fisher <- classIntervals(afcon$totcon,
  style = "fisher",
  n = nclass
)
print(brks_fisher)

brks_quantile <- classIntervals(afcon$totcon,
  style = "quantile",
  n = nclass
)
print(brks_quantile)

pal1 <- c("wheat1", "wheat2", "red3")
opar <- par(no.readonly = TRUE)
par(mar = c(2, 2, 2, 1), cex = 0.8)
plot(brks_ht, pal = pal1, main = "headtails")
plot(brks_fisher, pal = pal1, main = "fisher")
plot(brks_quantile, pal = pal1, main = "quantile")
par(opar)

It is observed that the top three classes of headtails enclose 5 observations, whereas fisher includes 13 observations. In terms of classification, headtails breaks focuses more on extreme values.

The next plot compares a continuous distribution of totcon re-escalated to a range of [1,nclass] versus the distribution across breaks for each style. The continuous distribution has been offset by -0.5 in order to align the continuous and the discrete distributions.

# Helper function to reescale values
help_reescale <- function(x, min = 1, max = 10) {
  r <- (x - min(x)) / (max(x) - min(x))
  r <- r * (max - min) + min
  return(r)
}
afcon$ecdf_class <- help_reescale(afcon$totcon,
  min = 1 - 0.5,
  max = nclass - 0.5
)
afcon$ht_breaks <- cut(afcon$totcon,
  brks_ht$brks,
  labels = FALSE,
  include.lowest = TRUE
)

afcon$fisher_breaks <- cut(afcon$totcon,
  brks_fisher$brks,
  labels = FALSE,
  include.lowest = TRUE
)

afcon$quantile_break <- cut(afcon$totcon,
  brks_quantile$brks,
  labels = FALSE,
  include.lowest = TRUE
)

opar <- par(no.readonly = TRUE)
par(mar = c(4, 4, 1, 1), cex = 0.8)
plot(
  density(afcon$ecdf_class),
  ylim = c(0, 0.8),
  lwd = 2,
  main = "",
  xlab = "class"
)
lines(density(afcon$ht_breaks), col = "darkblue", lty = 2)
lines(density(afcon$fisher_breaks), col = "limegreen", lty = 2)
lines(density(afcon$quantile_break),
  col = "red3",
  lty = 2
)
legend("topright",
  legend = c(
    "Continuous", "headtails",
    "fisher", "quantile"
  ),
  col = c("black", "darkblue", "limegreen", "red3"),
  lwd = c(2, 1, 1, 1),
  lty = c(1, 2, 2, 2),
  cex = 0.8
)
par(opar)

It can be observed that the distribution of headtails breaks is also heavy-tailed, and closer to the original distribution. On the other extreme, “quantile” provides a quasi-uniform distribution, ignoring the totcon hierarchy

In terms of data visualization, we compare here the final map using the techniques mentioned above. On this plotting exercise, a choropleth map would be created.

Additionally, a high-granularity choropleth map is created with a greater number of classes, in order to compare and contrast the actual grouping options against a more granular approach.

library(sf)
library(giscoR)
library(cartography)

opar <- par(no.readonly = TRUE)

par(
  mfrow = c(2, 2),
  mar = c(1, 1, 1, 1),
  bg = "white"
)
africa <- gisco_get_countries(resolution = 60, region = "Africa", epsg = 3857)

afcon.sf <- st_as_sf(afcon, crs = 4326, coords = c("x", "y"))
afcon.sf <- st_transform(afcon.sf, st_crs(africa))
# afcon.sf <- st_join(africa[, "admin"], afcon.sf)
afcon.sf <- afcon.sf[order(afcon.sf$totcon), ]



# High granularity map
plot(st_geometry(africa), col = "grey80", border = NA)
propSymbolsLayer(
  afcon.sf,
  var = "totcon",
  inches = 0.2,
  col = adjustcolor("grey10", alpha.f = 0.5),
  border = NA
)
title(main = "High granularity map")

# Quantile

pal <- hcl.colors(5, palette = "inferno", alpha = 0.6)
plot(st_geometry(africa), col = "grey80", border = NA)
propSymbolsTypoLayer(
  afcon.sf,
  var = "totcon",
  inches = 0.2,
  col = pal,
  border = NA,
  legend.var.pos = "n",
  legend.var2.pos = "bottomleft",
  var2 = "quantile_break"
)
title(main = "Quantile")


# Fisher
plot(st_geometry(africa), col = "grey80", border = NA)
propSymbolsTypoLayer(
  afcon.sf,
  var = "totcon",
  inches = 0.2,
  col = pal,
  border = NA,
  legend.var.pos = "n",
  legend.var2.pos = "bottomleft",
  var2 = "fisher_breaks"
)
title(main = "Fisher")

# Head Tails
plot(st_geometry(africa), col = "grey80", border = NA)
propSymbolsTypoLayer(
  afcon.sf,
  var = "totcon",
  inches = 0.2,
  col = pal,
  border = NA,
  legend.var.pos = "n",
  legend.var2.pos = "bottomleft",
  var2 = "ht_breaks"
)
title(main = "Head Tails")
par(opar)

As per the results, headtails seems to provide a better understanding of the most extreme values when the result is compared against the high-granularity plot. The quantile style, as expected, just provides a clustering without taking into account the real hierarchy. The fisher plot is in-between of these two interpretations.

It is also important to note that headtails and fisher reveal different information that can be useful depending of the context. While headtails highlights the outliers, it fails on providing a good clustering on the tail, while fisher seems to reflect better these patterns. This can be observed on the values of Western Africa and the Niger River Basin, where headtails doesn’t highlight any special cluster of conflicts, fisher suggests a potential cluster, aligned with the high-granularity plot. This can be confirmed on the histogram generated previously, where a concentration of totcon around 1,000 is visible.

References

Jiang, Bin. 2013. "Head/Tail Breaks: A New Classification Scheme for Data with a Heavy-Tailed Distribution." The Professional Geographer 65 (3): 482–94. DOI.

———. 2019. "A Recursive Definition of Goodness of Space for Bridging the Concepts of Space and Place for Sustainability." Sustainability 11 (15): 4091. DOI.

Jiang, Bin, Xintao Liu, and Tao Jia. 2013. "Scaling of Geographic Space as a Universal Rule for Map Generalization." Annals of the Association of American Geographers 103 (4): 844–55. DOI.

Jiang, Bin, and Junjun Yin. 2013. "Ht-Index for Quantifying the Fractal or Scaling Structure of Geographic Features." Annals of the Association of American Geographers 104 (3): 530–40. DOI.

Taleb, Nassim Nicholas. 2008. The Black Swan: The Impact of the Highly Improbable. 1st ed. London: Random House.

Vasicek, Oldrich. 2002. "Loan Portfolio Value." Risk, December, 160–62.

The method implemented on classInt corresponds to head/tails 1.0 as named on this article. ↑

COVID19 Microsite

Sat, 04 Apr 2020 00:00:00 +0200

Tracking the outbreak in Spain by region

1 min.

Project discontinued

Visit the microsite with maps and official data on the impact of COVID19 in Spain.

https://dieghernan.github.io/COVID19 [In Spanish]

Overall deceases in Spain by COVID19 - Evolution

New features on cartography package

Mon, 17 Feb 2020 00:00:00 +0100

Vignette of the package expansion

6 min.

Introduction

The aim of this document is to describe the new features added to cartography on version 2.4.0 by dieghernan and already available on CRAN.

Those new features are:

hatchedLayer and legendHatched functions.
pngLayer and getPngLayer functions.
wordcloudLayer function.

These functions don’t handle sp objects on purpose, favoring sf instead.

Installation

#install.packages("cartography")
library(cartography)
packageVersion("cartography")
## [1] '3.0.0'

Hatched Map

Version of typology/choropleth maps using a hatched filling. This is particularly useful for those maps that needs to be printed on black and white, as academic papers. These maps also are useful for representing overlapping dimensions.

Example 1

library(sf)
library(jsonlite)
library(dplyr)

#Shape
cntries = st_read("https://ec.europa.eu/eurostat/cache/GISCO/distribution/v2/countries/geojson/CNTR_RG_20M_2016_3035.geojson",
                  stringsAsFactors = FALSE)
## Reading layer `CNTR_RG_20M_2016_3035' from data source `https://ec.europa.eu/eurostat/cache/GISCO/distribution/v2/countries/geojson/CNTR_RG_20M_2016_3035.geojson' using driver `GeoJSON'
## Simple feature collection with 257 features and 6 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -7142317 ymin: -9160665 xmax: 16932290 ymax: 15428010
## Projected CRS: ETRS89-extended / LAEA Europe

# Include trade blocks
df <- fromJSON("https://raw.githubusercontent.com/dieghernan/Country-Codes-and-International-Organizations/master/outputs/Countrycodesfull.json")
ISO_memcol <- function(df,
                       orgtosearch) {
  ind <- match(orgtosearch, unlist(df[1, "org_id"]))
  or <- lapply(1:nrow(df), function(x)
    unlist(df[x, "org_member"])[ind])
  or <- data.frame(matrix(unlist(or)), stringsAsFactors = F)
  names(or) <- orgtosearch
  df2 <- as.data.frame(cbind(df, or, stringsAsFactors = F))
  return(df2)
}
df <- ISO_memcol(df, "EU")
df <- ISO_memcol(df, "EFTA")
df <- ISO_memcol(df, "EuroArea")


cntries = merge(cntries,
                df,
                by.x = "ISO3_CODE",
                by.y = "ISO_3166_3",
                all.x = TRUE)

library(cartography)


#Limits EU
#Plot base map
plot(
  st_geometry(cntries),
  xlim = c(2200000, 7150000),
  ylim = c(1380000, 5500000),
)
plot(st_geometry(cntries), add = TRUE)
plot(st_geometry(cntries[!is.na(cntries$EU),]), col = "grey60", add = TRUE)
plot(st_geometry(cntries[!is.na(cntries$EFTA),]), col = "black", add = TRUE)
#Add hatching
hatchedLayer(
  cntries[!is.na(cntries$EuroArea),],
  pattern = "right2left",
  col = "white",
  density = 3,
  add = TRUE
)
legendTypo(
  "topright",
  title.txt = "",
  categ = c("EU", "EFTA"),
  col = c("grey60", "black"),
  nodata = FALSE
)

legendHatched(
  "right",
  title.txt = "Within EU",
  categ = "Euro\nArea",
  patterns = "right2left",
  frame = TRUE
)
layoutLayer(
  title = "European Trade Blocks",
  theme = "grey.pal",
  sources = "© EuroGeographics for the administrative boundaries.",
  author =  paste0("cartography ", packageVersion("cartography")),
  scale = 500,
  frame = TRUE
)

Example 2

library(sf)
library(cartography)

# Plot World
plot(
  cntries$geometry,
  col = "white",
  xlim = c(2200000, 7150000),
  ylim = c(1380000, 5500000),
)
#Add layers for non european area - left2right
NOEUR = subset(cntries, CONTINENT.EN != "Europe" | is.na(CONTINENT.EN))
hatchedLayer(
  NOEUR,
  pattern = "left2right",
  add = TRUE,
  #Basic usage
  density = 2,
  #Densify default grid
  lwd = 1.2,
  lty = 3,
  col = "grey50"
)            #Formatting

#Extract Europe Regions
EUR = subset(cntries, CONTINENT.EN == "Europe" & SUBREGION.EN != "Western Asia")[, "SUBREGION.EN"]
levels <- sort(unique(EUR$SUBREGION.EN))


#Plot Regions
# First element with zigzag
hatchedLayer(EUR[EUR$SUBREGION.EN == levels[1], ],
             add = TRUE,
             density = 4,
             pattern = "zigzag")

#dot with parms
hatchedLayer(
  EUR[EUR$SUBREGION.EN == levels[2], ],
  add = TRUE,
  pattern = "dot",
  pch = 4,
  cex = 0.5,
  density = 3.5)

#vertical
hatchedLayer(EUR[EUR$SUBREGION.EN == levels[3], ],
             add = TRUE,
             pattern = "vertical",
             density = 3)

#another dot
hatchedLayer(EUR[EUR$SUBREGION.EN == levels[4], ],
             add = TRUE,
             pattern = "dot",
             pch= 15,
             density = 3.5)

#create legend
legendHatched(
  pos = "topright",
  title.txt = "",
  title.cex = 0.1,
  categ = c(levels, "Others"),
  patterns = c("zigzag",
               "dot",
               "vertical",
               "dot",
               "left2right"),
  pch = c(4,15),
  lty = c(1, 1, 3),
  col = c(rep("black", length(levels)), "grey50"),
  frame = TRUE
)

layoutLayer(
  title = "Regions of Europe (United Nations)",
  theme = "grey.pal",
  sources = "© EuroGeographics for the administrative boundaries.",
  author =  paste0("cartography ", packageVersion("cartography")),
  scale = 500,
  frame = TRUE
) 

legendHatched honors the order on the parameters. In this case, two dot patterns are presents, so pch = c(4,15) takes care of that. Note that three line-type patterns are also plotted, as and in the previous case, lty = c(1, 1, 3) respect that order.

Example 3

hatchedLayer also could be useful for plotting several dimensions on the same map, in combination with another functions of the package.

library(sf)
library(cartography)



#Warsaw Pact - roughly mapped via UN Region
wp <- subset(cntries, SUBREGION.EN == "Eastern Europe")

#European Union - after Brexit
eu <- subset(cntries, !is.na(EU))

#Euro Area
ea <- subset(cntries, !is.na(EuroArea))

#Flags for plotting
flag = ifelse(cntries$ISO3_CODE %in% eu$ISO3_CODE,
              "European Union",
              cntries$CONTINENT.EN)


flag = ifelse(!flag %in% c("Europe", "European Union"), "Other",
              flag)
cntries$flag <- flag



#Plot lims
plot(
  st_geometry(cntries),
  xlim = c(2200000, 7150000),
  ylim = c(1380000, 5500000)
)


#Combine with typoLayer
typoLayer(
  x = cntries,
  var = "flag",
  legend.pos = "n",
  legend.values.order = c("European Union",
                          "Europe",
                          "Other"),
  col = c("#A6BDDB",
          "#FEFEE9",
          "#E0E0E0"),
  add = TRUE
)

#hatching
hatchedLayer(
  x = ea,
  pattern = "left2right",
  cellsize = 100000,
  add = TRUE
)

hatchedLayer(
  x = wp,
  pattern = "vertical",
  col="red",
  cellsize = 75000,
  add = TRUE
)

#Legend
legendHatched(
  pos = "right",
  title.txt = "Economic Region",
  categ = c(
    "Euro Area",
    "Former \nWarsaw Pact",
    "European Union",
    "Europe",
    "Other"
  ),
  patterns = c("left2right", "vertical"),
  col = c("black", "red", "#A6BDDB",
          "#FEFEE9",
          "#E0E0E0"),
  ptrn.bg = c("white", "white", "#A6BDDB",
              "#FEFEE9",
              "#E0E0E0"),
  frame = TRUE
)

layoutLayer(
  title = "European Countries - Blocks",
  theme = "blue.pal",
  sources = "© EuroGeographics for the administrative boundaries.",
  author =  paste0("cartography ", packageVersion("cartography")),
  scale = 500,
  frame = TRUE
)

`png` Layer

This new capability geotags a .png file, effectively converting the image into a tile. This allows the user to create visual maps by masking an image to the shape of a POLYGON/MULTIPOLYGON.

For high-quality png maps, it is recommended to plot your map on a .svg device.

Example 1

library(sf)
library(cartography)

cntries2 = st_read("https://ec.europa.eu/eurostat/cache/GISCO/distribution/v2/countries/geojson/CNTR_RG_20M_2016_3857.geojson",
                  stringsAsFactors = FALSE)
## Reading layer `CNTR_RG_20M_2016_3857' from data source `https://ec.europa.eu/eurostat/cache/GISCO/distribution/v2/countries/geojson/CNTR_RG_20M_2016_3857.geojson' using driver `GeoJSON'
## Simple feature collection with 257 features and 6 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -20037510 ymin: -30240970 xmax: 20037510 ymax: 18446790
## Projected CRS: WGS 84 / Pseudo-Mercator

cntries2 = merge(cntries2,
                df,
                by.x = "ISO3_CODE",
                by.y = "ISO_3166_3",
                all.x = TRUE)

africa=subset(cntries2, CONTINENT.EN =="Africa") %>%
  arrange(desc(area_km2))


#Get bigger countries

plot(st_geometry(africa[1:20,]), bg="lightblue")


plot(st_geometry(cntries2), col="grey90", add=TRUE)

#Iterate for Africa
#Get flags from repo - low quality to speed up the vignette
flagrepo = "https://raw.githubusercontent.com/hjnilsson/country-flags/master/png250px/"


for (i in 1:nrow(africa)) {
  cntry <- as.character(st_drop_geometry(africa[i, "ISO_3166_2"]))
  a = getPngLayer(africa[i,],
                  paste(flagrepo, tolower(cntry), ".png", sep = ""))
  pngLayer(a, add = TRUE)
}
#Add borders
plot(st_geometry(cntries2), add = TRUE, col = NA, lwd=0.4)

layoutLayer(
  title = "Flags of Africa",
  theme = "green.pal",
  sources = "© EuroGeographics for the administrative boundaries.",
  author =  paste0("cartography ", packageVersion("cartography")),
  scale = 500,
  frame = TRUE
) 

Example 2

library(sf)
library(cartography)

box <- c(xmin=2200000, xmax=7150000,ymin=1380000, ymax=5500000)
nuts0 <-  st_crop(cntries, box)

UK = nuts0 %>% filter(id == "UK")
url = "https://upload.wikimedia.org/wikipedia/commons/thumb/b/b7/Flag_of_Europe.svg/800px-Flag_of_Europe.svg.png"


EU=getPngLayer(nuts0,url, mask=FALSE)
pngLayer(EU, alpha=100)
urluk=flagrepo = "https://raw.githubusercontent.com/hjnilsson/country-flags/master/png250px/gb.png"

UKpng=getPngLayer(UK,urluk)

pngLayer(UKpng, add=TRUE)

wordcloudLayer

A word cloud (or tag cloud) is a visual representation of text data. On a mapping context, this representation is useful for including several information at a glance.

Wordcloud layers fitted into a map shape provide a good trade-off between physical location, scale and labels. Size and colors of the words are also based on the frequency of the factor to be plotted, highlighting the most frequent terms over the rest.

Example 1

eu$dens=eu$pop/eu$area_km2

wordcloudLayer(eu,txt="NAME.EN",freq="dens",
               fittopol = TRUE,
               nclass=7,
               cex.maxmin = c(3,1) )
br=getBreaks(eu$dens, nclass=7)

legendChoro(breaks=br, title.txt="Pop Density",col=carto.pal("blue.pal",7))
layoutLayer(
  title = "Population Density in Europe",
  theme = "blue.pal",
  sources = "© EuroGeographics for the administrative boundaries.",
  author =  paste0("cartography ", packageVersion("cartography")),
  scale = 500,
  frame = TRUE
) 

Example 2

# Genres from MB--
#Import genres
collected = read.csv("./assets/data/US_MB.csv", stringsAsFactors = F)
collected=collected[-1,] %>% arrange(desc(n))

set.seed(1234)

library(rnaturalearth)
shape = ne_countries(country="united states of america", returnclass = "sf") %>% st_transform(3857)
#Get main polygon
shape = shape %>% st_union %>% st_cast("POLYGON")
areas = st_area(shape)
shape = shape[areas == max(areas)]

set.seed(1234)
points = 100
#Sample regular
points = st_sample(shape, points + 5, type = "regular")

#Center points

centr=st_centroid(shape, of_largest_polygon = TRUE)
f=st_distance(points,centr)
dfpoints=st_sf(dist=f,
               geometry=points) %>%
  arrange((dist))


#Create df
points=st_sf(collected[1:100,],
             geometry=st_geometry(dfpoints)[1:100])

plot(shape, col="grey95", border = NA)
wordcloudLayer(points,
               txt="genre",
               freq="n",
               cex.maxmin =  c(3, 0.6),
               col=c("#ba478f", "#eb743b"),
               nclass=7,
               add=TRUE)
layoutLayer(title="Most frequent genres on US",
            sources="Musicbrainz",
              author =  paste0("cartography ", packageVersion("cartography")),
            theme="orange.pal")

We’ll miss you, UK

Thu, 06 Feb 2020 00:00:00 +0100

Brexit and the consequences

1 min.

This is just a super-quick post regarding Brexit. Leaving apart economical, political and social considerations, there is another consequence, now we are one less in the EU.

We will miss you, UK, we wish you the best.

library(cartography)
library(sf)
library(giscoR)


#EU
eu <- giscoR::gisco_countrycode %>% filter(eu)

# Download maps
NUTS1 <- gisco_get_nuts(epsg = 3035, country = eu$ISO3_CODE, nuts_level = 1)


UK <- gisco_get_countries(country =  "GBR", epsg = 3035)

noplot = c("FRY", "ES7", "PT2", "PT3")
NUTS1_Clean = NUTS1 %>% subset(!NUTS_ID %in% noplot) %>%
  group_by(CNTR_CODE) %>% summarise(a=dplyr::n())

# Flag image
url = "https://upload.wikimedia.org/wikipedia/commons/thumb/b/b7/Flag_of_Europe.svg/800px-Flag_of_Europe.svg.png"

#Mask UK
flagcut = getPngLayer(NUTS1_Clean,
                       url)
# Full extent
flag = getPngLayer(NUTS1_Clean,
                       url, mask = FALSE)


par(mar = c(0, 0, 0, 0))
tilesLayer(flag, alpha = 150)
tilesLayer(flagcut, bgalpha = 0, add = T)
plot(st_geometry(UK),
     col = "white",
     border = NA,
     add = TRUE)

Beautiful Maps with R (III): Patterns and hatched maps

Thu, 12 Dec 2019 00:00:00 +0100

A solution for b/w and academic maps.

2 min.

Updated 17 february 2020: All these pieces of work are already available on cartography >v.2.4.0 on functions hatchedLayer and legendHatched. Just install it via install.packages("cartography"). A dedicated blog post with examples on this link.

On this post I would show how to produce different filling patterns that could be added over your shapefiles with the cartography package.

Required R packages

library(sf)
library(dplyr)
library(giscoR)
library(cartography)

DE <- gisco_get_countries(country = "Germany", epsg = 3857)

Let’s see how it works.

par(
  mfrow = c(3, 4),
  mar = c(1, 1, 1, 1),
  cex = 0.5
)
hatchedLayer(DE, "dot")
title("dot")
hatchedLayer(DE, "text", txt = "Y")
title("text")
hatchedLayer(DE, "diamond", density = 0.5)
title("diamond")
hatchedLayer(DE, "grid", lwd = 1.5)
title("grid")
hatchedLayer(DE, "hexagon", col = "blue")
title("hexagon")
hatchedLayer(DE, "horizontal", lty = 5)
title("horizontal")
hatchedLayer(DE, "vertical")
title("vertical")
hatchedLayer(DE, "left2right")
title("left2right")
hatchedLayer(DE, "right2left")
title("right2left")
hatchedLayer(DE, "zigzag")
title("zigzag")
hatchedLayer(DE, "circle")
title("circle")

Let’s play a little bit more with some of the additional features of the function:

par(mar = c(1, 1, 1, 1), mfrow = c(2, 3))
plot(st_geometry(DE))
hatchedLayer(
  DE,
  "dot",
  pch = 10,
  density = 0.5,
  cex = 2,
  col = "darkblue",
  add = T
)
plot(st_geometry(DE))
hatchedLayer(
  DE,
  "dot",
  pch = 21,
  col = "red",
  bg = "green",
  cex = 1.25,
  add = T
)
plot(st_geometry(DE), col = "grey")
hatchedLayer(
  DE,
  "text",
  txt = "DE",
  density = 1.1,
  col = "white",
  add = T
)
plot(st_geometry(DE), col = "blue")
hatchedLayer(
  DE,
  "horizontal",
  lty = 3,
  cellsize = 150 * 1000,
  add = T
)
hatchedLayer(DE, "zigzag", lwd = 2, col = "red")
plot(st_geometry(DE), border = "orange", lwd = 2)
hatchedLayer(DE,
  "left2right",
  density = 2,
  col = "orange",
  add = T
)

Adding legends: the `legendHatched` function

As a complementary function, there is also the legendHatched. Main parameters are:

pos, title.txt, title.cex, values.cex,categ, cex and frame: See ?cartography::legendTypo.
patterns: vector of patterns to be created for each element on categ.
ptrn.bg: Background of the legend box for each categ.
ptrn.text: Text to be used for each categ="text", as a single value or a vector.
dot.cex: cex of each categ="dot", as a single value or a vector.
text.cex: text size of each categ="text", as a single value or a vector.
As in the case of the hatchedLayerfunction, different graphical parameters can be passed (lty, lwd, pch, bg on points).

Note that is also possible to create solid legends, by setting col and ptrn.bg to the same color. Parameters would respect the order of the categ variable.

par(mar = c(0, 0, 0, 0), mfrow = c(1, 1))
plot(st_geometry(DE)) # Null geometry
legendHatched(
  title.txt = "Example 1",
  categ = c("a", "b"),
  patterns = "dot",
  pch = c(16, 23),
  frame = T
)
legendHatched(
  pos = "left",
  title.txt = "Example 2",
  categ = c("c", "d", "other text"),
  patterns = c("text", "zigzag"),
  ptrn.text = c("s", "pp"),
  ptrn.bg = "grey80",
  col = c("red", "blue")
)

legendHatched(
  pos = "topright",
  title.txt = "Example 3",
  categ = c("e", "f", "solid"),
  patterns = c("circle", "left2right"),
  ptrn.bg = c("orange", "yellow", "green"),
  col = c("white", "white", "green"),
  lty = c(2, 4),
  lwd = c(1, 3)
)


legendHatched(
  pos = "bottomright",
  title.txt = "Example 4",
  values.cex = 1.2,
  categ = c("h", "i", "j", "k"),
  patterns = c("grid", "diamond", "horizontal", "dot"),
  cex = 2,
  pch = 22,
  col = "white",
  ptrn.bg = "black",
  bg = "pink"
)

I hope that you find this functions useful. Enjoy and nice mapping!

Quick R: Inset maps

Thu, 07 Nov 2019 00:00:00 +0100

An alternative using plot()

3 min.

How to place an inset map in R? There are many solutions out there using the ggplot2 package (see Drawing beautiful maps programmatically with R, sf and ggplot2 by Mel Moreno and Mathieu Basille). However, I like the old reliable plot function, so the question is: is there another way?

There is. I found inspiration here and I just applied it to a map.

Required R packages

library(sf)
library(dplyr)
library(rnaturalearth)

Mimicking Moreno & Basille

I would present here an alternative version of Drawing beautiful maps programmatically with R, sf and ggplot2, so the bulk of the detail can be found there. I would focus only in the plot()side.

world <- ne_countries(scale = "medium", returnclass = "sf")
USA <- subset(world, admin == "United States of America")

# Plot mainland USA----
par(mar = c(0, 0, 0, 0))
plot(
  st_geometry(world %>%
    st_transform(2163)),
  xlim = c(-2500000, 2500000),
  ylim = c(-2300000, 730000),
  col = "#F6E1B9",
  border = "#646464",
  bg = "#C6ECFF"
)
plot(
  st_geometry(USA) %>% st_transform(2163),
  col = "#FEFEE9",
  border = "black",
  add = T
)

# Plot Alaska----
plot(
  st_geometry(world %>%
    st_transform(3467)),
  xlim = c(-2400000, 1600000),
  ylim = c(200000, 2500000),
  col = "#F6E1B9",
  border = "#646464",
  bg = "#C6ECFF"
)
plot(
  st_geometry(USA) %>% st_transform(3467),
  col = "#FEFEE9",
  border = "black",
  add = T
)

# Plot Hawaii----
plot(
  st_geometry(world %>%
    st_transform(4135)),
  xlim = c(-161, -154),
  ylim = c(18, 23),
  col = "#F6E1B9",
  border = "#646464",
  bg = "#C6ECFF"
)
plot(
  st_geometry(USA) %>% st_transform(4135),
  col = "#FEFEE9",
  border = "black",
  add = T
)

Insetting

From now on, I just focus on the inset part, using the fig() option on par(). Quoting statmethods:

(…) think of the full graph area as going from (0,0) in the lower left corner to (1,1) in the upper right corner. The format of the fig= parameter is a numerical vector of the form c(x1, x2, y1, y2)(…) fig= starts a new plot, so to add to an existing plot use new=TRUE.

So being x1 and y1 the starting points and x2, y2 the final points, we just can set up those parameters and adjust the final placement of the insets. Additionally I added a box around the insets using bbox(). I didn’t mimic Moreno & Basille here and I just worked it by myself.

par(mar = c(0, 0, 0, 0))
plot(
  st_geometry(world %>%
    st_transform(2163)),
  xlim = c(-2500000, 2500000),
  ylim = c(-2300000, 730000),
  col = "#F6E1B9",
  border = "#646464",
  bg = "#C6ECFF"
)
plot(
  st_geometry(USA) %>% st_transform(2163),
  col = "#FEFEE9",
  border = "black",
  add = T
)
# Alaska
par(
  fig = c(0.01, 0.28, 0.01, 0.33),
  new = TRUE
)
plot(
  st_geometry(world %>%
    st_transform(3467)),
  xlim = c(-2400000, 1600000),
  ylim = c(200000, 2500000),
  col = "#F6E1B9",
  border = "#646464",
  bg = "#C6ECFF"
)
plot(
  st_geometry(USA) %>% st_transform(3467),
  col = "#FEFEE9",
  border = "black",
  add = T
)
box(which = "figure", lwd = 1)

# Hawaii
par(
  fig = c(0.29, 0.45, 0.01, 0.15),
  new = TRUE
)
plot(
  st_geometry(world %>%
    st_transform(4135)),
  xlim = c(-161, -154),
  ylim = c(18, 23),
  col = "#F6E1B9",
  border = "#646464",
  bg = "#C6ECFF"
)
plot(
  st_geometry(USA) %>% st_transform(4135),
  col = "#FEFEE9",
  border = "black",
  add = T
)

box(which = "figure", lwd = 1)

Results may vary depending of the size of the original plot (Mainland USA) and your plotting device and output. However with a bit of trial-and-error it is quite easy to adjust the final result.

As an example, see one of my contributions to Wikimedia Commons that represents a map of the NUTS3 regions of the European Union. Several countries (France, Portugal, Spain) have overseas territories so I made a few insets on the right side.

Wikipedia Maps (I): Organ donor rates

Wed, 16 Oct 2019 00:00:00 +0200

A choropleth map with R

2 min.

This is a quick post on how to create a map as per the Wikipedia conventions. In this case I have chosen to plot the international organ donor rates, retrieved on 2019-02-10 although the data refers to 2017 (Source: IRODaT).

Webscrapping

First step is to webscrap Wikipedia in order to get the final table. For doing so, I will use the rvest library. You can get the xpath you want to webscrap as explained here.

library(rvest)
library(dplyr)

Base <-
  read_html("https://en.wikipedia.org/wiki/International_organ_donor_rates") %>%
  html_nodes(xpath = '//*[@id="mw-content-text"]/div/table[3]') %>%
  html_table() %>%
  as.data.frame(
    stringsAsFactors = F,
    fix.empty.names = F
  ) %>%
  select(Country,
    RateDonperMill = Number.of.deceased.donors..per.million.of.population
  )

knitr::kable(head(Base, 10), format = "markdown")

Country	RateDonperMill
Argentina	19.60
Armenia	0.00
Australia	21.60
Austria	23.88
Azerbaijan	0.00
Bahrain	4.00
Bangladesh	0.00
Belarus	26.20
Belgium	30.30
Bolivia	0.36

Now we need to choose a good source of maps:

library(sf)
library(giscoR)

# Map import from Eurostat
WorldMap <- gisco_get_countries(resolution = 3, epsg = 3857) %>%
  select(ISO_3166_3 = ISO3_CODE)

Merging all together

Now let’s join and have a look to see what is going on. We use the countrycode package to retrieve the ISO3 codes of our scrapped dataset:

library(countrycode)

Base$ISO_3166_3 <- countrycode(Base$Country, origin = "country.name", destination = "iso3c")


DonorRate <- left_join(
  WorldMap,
  Base
) %>%
  select(
    Country,
    ISO_3166_3,
    RateDonperMill
  )

Make the `.svg` file

As already explained, I would like to follow the Wikipedia conventions, so some things to bear in mind:

Obviously the colors. Wikipedia already provides a good guidance for this. I would make use of the RColorBrewer library, which implements ColorBrewer in R.
In terms of projection, Wikipedia recommends the Equirectangular projection but, as in their own sample of a gradient map, I would choose to use the Robinson projection.
I should produce an .svg file following also the naming convention.

Some libraries then to use: RColorBrewer, rsvg and specially one of my favourites, cartography:

library(RColorBrewer)
library(cartography)
library(rsvg)

# Create bbox of the world
bbox <- st_linestring(rbind(
  c(-180, 90),
  c(180, 90),
  c(180, -90),
  c(-180, -90),
  c(-180, 90)
)) %>%
  st_segmentize(5) %>%
  st_cast("POLYGON") %>%
  st_sfc(crs = 4326) %>%
  st_transform(crs = "+proj=robin")

# Create SVG
svg(
  "Organ donor rate per million by country gradient map (2017).svg",
  pointsize = 90,
  width =  1600 / 90,
  height = 728 / 90
)

par(mar = c(0.5, 0, 0, 0))
choroLayer(
  DonorRate %>% st_transform("+proj=robin"),
  var = "RateDonperMill",
  breaks = c(0, 5, 10, 20, 30, 40, 50),
  col = brewer.pal(6, "PuBu"),
  border = "#646464",
  lwd = 0.1,
  colNA = "#E0E0E0",
  legend.pos = "left",
  legend.title.txt = "",
  legend.values.cex = 0.25
)

# Bounding box
plot(bbox,
  add = T,
  border = "#646464",
  lwd = 0.2
)

dev.off()

And that’s all. Our .svg file is ready to be included in Wikipedia.

Update: The map is already part of the Wikipedia article.

Beautiful Maps with R (II): Fun with flags

Tue, 18 Jun 2019 00:00:00 +0200

Put a picture on your map

3 min.

Updated 29 december 2020: All these pieces of work are already available on cartography >v.2.4.0 on functions getPngLayer. Just install it via install.packages("cartography"). A dedicated blog post with examples on this link.

Updated 25 January 2023 cartography is in maintenance mode. You can use rasterpic + tidyterra to achieve the same result, see link1 and link2.

Want to use a flag (or any *.png file) as a background of your map? You are in the right post. I am aware that there are some R packages out there, but we focus here in the option provided by cartography::getPngLayer(), that basically converts your image into a raster (see also this article of Paul Murrell, “Raster Images in R Graphics” (The R Journal, Volume 3/1, June 2011)).

Required R packages

library(dplyr)
library(sf)
library(cartography)
library(mapSpain)
library(giscoR)

Choosing a good source for our shape

In this post I am going to plot a map of Spain with its autonomous communities (plus 2 autonomous cities), that is the first-level administrative division of the country. Wikipedia shows an initial map identifying also the flag of each territory.

For that, I will use mapSpain, that uses information from giscoR, whose source is the geodata available in Eurostat. I would also use giscoR to get the world around Spain.

Spain <- esp_get_ccaa(epsg = 3857, res = 3)

World <- gisco_get_countries(epsg = 3857, res = 3)

bboxcan <- esp_get_can_box(epsg = 3857)

# Plot
par(mar = c(0, 0, 0, 0))
plot(st_geometry(Spain),
  col = NA,
  border = NA,
  bg = "#C6ECFF"
)
plot(st_geometry(World),
  col = "#E0E0E0",
  bg = "#C6ECFF",
  add = T
)
plot(st_geometry(Spain), col = "#FEFEE9", add = T)
layoutLayer(
  title = "",
  frame = FALSE,
  scale = 500,
  sources = gisco_attributions(),
  author = "dieghernan, 2019",
)
plot(bboxcan, add = TRUE)

Now we have it! A nice map of Spain with a layout based on the Wikipedia convention for location maps.

Loading the flag

As a first example, I chose Asturias to build my code. So the goal here is to create a RasterBrick from the desired *.png file, add the necessary geographical information and use the shape of Asturias to crop the flag.

# 1.Shape---
shp <- Spain %>% filter(ccaa.shortname.es == "Asturias")

# 2.Get flag---

# Masked
url <- "https://upload.wikimedia.org/wikipedia/commons/thumb/3/3e/Flag_of_Asturias.svg/800px-Flag_of_Asturias.svg.png"

flagnomask <- getPngLayer(shp, url, mask = FALSE)

flagmask <- getPngLayer(shp, url, mask = TRUE)

opar <- par(no.readonly = TRUE)
par(mar = c(1, 1, 1, 1), mfrow = c(1, 2))
pngLayer(flagnomask)
plot(st_geometry(Spain), add = T)

# 4.Mask---
pngLayer(flagmask)
plot(st_geometry(Spain), add = T)

par(opar)

Pro tip: Use high-quality *.png, otherwise the plot would look quite poor. Here I show an extreme example.

MURshp <- Spain %>% filter(ccaa.shortname.es == "Murcia")
MURLow <- getPngLayer(
  MURshp,
  "https://upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Flag_of_the_Region_of_Murcia.svg/100px-Flag_of_the_Region_of_Murcia.svg.png"
)
MURHigh <- getPngLayer(
  MURshp,
  "https://upload.wikimedia.org/wikipedia/commons/thumb/a/a5/Flag_of_the_Region_of_Murcia.svg/1200px-Flag_of_the_Region_of_Murcia.svg.png"
)


# Plot and compare
opar <- par(no.readonly = TRUE)
par(mfrow = c(1, 2), mar = c(1, 1, 1, 1))
plot_sf(MURshp, main = "Low")
pngLayer(MURLow, add = TRUE)

plot_sf(MURshp, main = "High")
pngLayer(MURHigh, add = TRUE)

par(opar)

Now, we are ready to have fun with flags. It’s time to make the flag map of the autonomous communities of Spain.

par(mar = c(0, 0, 0, 0), mfrow = c(1, 1))
plot(Spain %>%
  st_geometry(),
col = NA,
border = NA,
bg = "#C6ECFF"
)
plot(st_geometry(World),
  col = "#E0E0E0",
  add = T
)
plot(st_geometry(bboxcan),
  add = T
)
layoutLayer(
  title = "",
  frame = FALSE,
  sources = "© EuroGeographics for the administrative boundaries",
  author = "dieghernan, 2019",
)
# Andalucia
flag <-
  "https://upload.wikimedia.org/wikipedia/commons/thumb/9/9a/Bandera_de_Andalucia.svg/1000px-Bandera_de_Andalucia.svg.png"
shp <- Spain %>% filter(ccaa.shortname.es == "Andalucía")
pngLayer(getPngLayer(shp, flag), add = TRUE)

# ...more flags
# Go to the source code of this post on GitHub for the full code

plot(st_geometry(Spain),
  col = NA,
  lwd = 2,
  add = T
)

We are done now. If you have suggestion you can leave a comment. As always, if you enjoyed the post you can share it on your preferred social network.

Beautiful Maps with R (I): Fishnets, Honeycombs and Pixels

Sun, 02 Jun 2019 00:00:00 +0200

Awesome simplified maps with R

5 min.

Sometimes you want to produce maps with special layouts. I specially like maps with modified geometries, e.g. simplifiying the original shapes to squares or dots. When doing a little search over the web I found the fantastic post Fishnets and Honeycomb: Square vs. Hexagonal Spatial Grids by Matt Strimas-Mackey that was a huge inspiration (by the way, don’t miss his blog, full of very interesting pieces of work).

The only thing I was not completely comfortable with was that the post used the old-fashioned sp package instead of my personal fav, the sf package, (the post was published in 2016, note that author has also moved to the sf package since then). So I decided to explore further options with sf.

The approach is similar (using grids over a map and work with that) but using st_make_grid. I also expanded it by grouping the grids and also producing dots over the geometries. So basically I produced 5 variations of the map:

Type	Replacement	Grouped
Fishnet	Square	No
Puzzle	Square	Yes
Honeycomb	Hexagon	No
Hexbin	Hexagon	Yes
Pixel	Dot	No

Required R packages

library(sf)
library(giscoR)
library(dplyr)
library(RColorBrewer)

Working with square grids

Let’s use the square option of st_make_grid and play a bit with it.

GB <- ne_download(50,
  type = "map_subunits",
  returnclass = "sf",
  destdir = tempdir()
) %>%
  subset(CONTINENT == "Europe") %>%
  subset(ADM0_A3 == "GBR")

# Projecting and cleaning
GB <- st_transform(GB, 3857) %>% select(NAME_EN, ADM0_A3)
initial <- GB
initial$index_target <- 1:nrow(initial)
target <- st_geometry(initial)

# Create my own color palette
mypal <- colorRampPalette(c("#F3F8F8", "#008080"))

Warning: The cellsize should be established in the same unit that the projection (in this case is meters). Pay special attention on this, given that if the parameter is too small (meaning that the grid is too dense) R could crash easily.

grid <- st_make_grid(target,
  50 * 1000,
  # Kms
  crs = st_crs(initial),
  what = "polygons",
  square = TRUE
)

# To sf
grid <- st_sf(index = 1:length(lengths(grid)), grid) # Add index

# We identify the grids that belongs to a entity by assessing the centroid
cent_grid <- st_centroid(grid)
cent_merge <- st_join(cent_grid, initial["index_target"], left = F)
grid_new <- inner_join(grid, st_drop_geometry(cent_merge))

# Fishnet
Fishgeom <- aggregate(grid_new,
  by = list(grid_new$index_target),
  FUN = min,
  do_union = FALSE
)

# Lets add the df
Fishnet <- left_join(
  Fishgeom %>% select(index_target),
  st_drop_geometry(initial)
) %>%
  select(-index_target)

# Now lets create the Puzzle
Puzzlegeom <- aggregate(st_buffer(grid_new, 0.5), # Avoid slivers
  by = list(grid_new$index_target),
  FUN = min,
  do_union = TRUE
) # This changes!!!

Puzzle <- left_join(
  Puzzlegeom %>% select(index_target),
  st_drop_geometry(initial)
) %>%
  select(-index_target)

# Plot
par(mfrow = c(1, 2), mar = c(1, 1, 1, 1), bg = NA)
plot(st_geometry(Fishnet), col = mypal(4), main = "Fishnet")
plot(st_geometry(Puzzle), col = mypal(4), main = "Puzzle")

Going hex

Extremely easy. We just need to change the square parameter of st_make_grid from TRUE to FALSE

grid <- st_make_grid(target,
  50 * 1000, # Kms
  crs = st_crs(initial),
  what = "polygons",
  square = FALSE # This is the only piece that changes!!!
)
# Make sf
grid <- st_sf(index = 1:length(lengths(grid)), grid) # Add index

# We identify the grids that belongs to a entity by assessing the centroid
cent_grid <- st_centroid(grid)
cent_merge <- st_join(cent_grid, initial["index_target"], left = F)
grid_new <- inner_join(grid, st_drop_geometry(cent_merge))

# Honeycomb
Honeygeom <- aggregate(
  grid_new,
  by = list(grid_new$index_target),
  FUN = min,
  do_union = FALSE
)

# Lets add the df
Honeycomb <- left_join(
  Honeygeom %>%
    select(index_target),
  st_drop_geometry(initial)
) %>%
  select(-index_target)

# Now lets create the Hexbin

Hexbingeom <- aggregate(
  st_buffer(grid_new, 0.5), # Avoid slivers
  by = list(grid_new$index_target),
  FUN = min,
  do_union = TRUE
)

Hexbin <- left_join(
  Hexbingeom %>%
    select(index_target),
  st_drop_geometry(initial)
) %>%
  select(-index_target)

# Plot
par(mfrow = c(1, 2), mar = c(1, 1, 1, 1), bg = NA)
plot(st_geometry(Honeycomb), col = mypal(4), main = "Honeycomb")
plot(st_geometry(Hexbin), col = mypal(4), main = "Hexbin")

Pixel it!

Also quite easy, just a couple of tweaks more, always using st_make_grid.

grid <- st_make_grid(target,
  50 * 1000, # Kms
  crs = st_crs(initial),
  what = "centers"
)

# Make sf
grid <- st_sf(index = 1:length(lengths(grid)), grid) # Add index

# We identify the grids that belongs to a entity by assessing the centroid
cent_grid <- st_centroid(grid)
cent_merge <- st_join(cent_grid, initial["index_target"], left = F)
grid_new <- st_buffer(cent_merge, 50 * 1000 / 2)
Pixelgeom <- aggregate(
  grid_new,
  by = list(grid_new$index_target),
  FUN = min,
  do_union = FALSE
)
# Lets add the df
Pixel <- left_join(
  Pixelgeom %>%
    select(index_target),
  st_drop_geometry(initial)
) %>%
  select(-index_target)

# Plot
par(mfrow = c(1, 1), mar = c(1, 1, 1, 1), bg = NA)
plot(st_geometry(Pixel), col = mypal(4), main = "Pixel")

Wrap up

So finally I wrapped all that in a function (see the code in my repo), that I named stdh_gridpol:

stdh_gridpol <- function(sf,
                         to = "fishnet",
                         gridsize = as.integer(
                           min(
                             diff(st_bbox(sf)[c(1, 3)]),
                             diff(st_bbox(sf)[c(2, 4)])
                           ) / 40
                         ),
                         sliver = 0.5) {
  if (!unique(st_geometry_type(sf)) %in% c("POLYGON", "MULTIPOLYGON")) {
    stop("Input should be  MULTIPOLYGON or POLYGON")
  }
  if (!to %in% c("fishnet", "puzzle", "honeycomb", "hexbin", "pixel")) {
    stop("'to' should be 'fishnet','puzzle','honeycomb','hexbin' or 'pixel'")
  }

  if (class(sf)[1] == "sf") {
    initial <- sf
    initial$index_target <- 1:nrow(initial)
  } else {
    initial <- st_sf(index_target = 1:length(sf), geom = sf)
  }

  target <- st_geometry(initial)

  if (to %in% c("fishnet", "puzzle")) {
    sq <- T
  } else {
    sq <- F
  }
  if (to == "pixel") {
    grid <- st_make_grid(target,
      gridsize,
      crs = st_crs(initial),
      what = "centers"
    )
  } else {
    grid <- st_make_grid(
      target,
      gridsize,
      crs = st_crs(initial),
      what = "polygons",
      square = sq
    )
  }
  grid <- st_sf(index = 1:length(lengths(grid)), grid) # Add index
  if (to == "pixel") {
    cent_merge <- st_join(grid, initial["index_target"], left = F)
    grid_new <- st_buffer(cent_merge, gridsize / 2)
  } else {
    cent_grid <- st_centroid(grid)
    cent_merge <- st_join(cent_grid, initial["index_target"], left = F)
    grid_new <- inner_join(grid, st_drop_geometry(cent_merge))
  }
  if (to %in% c("fishnet", "honeycomb", "pixel")) {
    geom <- aggregate(
      grid_new,
      by = list(grid_new$index_target),
      FUN = min,
      do_union = FALSE
    )
  } else {
    geom <- aggregate(
      st_buffer(grid_new, sliver),
      by = list(grid_new$index_target),
      FUN = min,
      do_union = TRUE
    )
  }
  if (class(initial)[1] == "sf") {
    fin <- left_join(
      geom %>% select(index_target),
      st_drop_geometry(initial)
    ) %>%
      select(-index_target)
    fin <- st_cast(fin, "MULTIPOLYGON")
    return(fin)
  } else {
    fin <- st_cast(geom, "MULTIPOLYGON")
    return(st_geometry(fin))
  }
}
# End of the function-----

fish <- stdh_gridpol(GB, to = "fishnet", gridsize = 50 * 1000)
puzz <- stdh_gridpol(GB, to = "puzzle", gridsize = 50 * 1000)
hon <- stdh_gridpol(GB, to = "honeycomb", gridsize = 50 * 1000)
hex <- stdh_gridpol(GB, to = "hexbin", gridsize = 50 * 1000)
pix <- stdh_gridpol(GB, to = "pixel", gridsize = 50 * 1000)

And that’s it! The function stdh_gridpol has some alert mechanisms, as accepting only POLYGON or MULTIPOLYGON, and the default value of gridsize is computed in a way that the shortest dimension would have 40 cells.

Leaflet, R, Markdown, Jekyll and GitHub

Mon, 20 May 2019 00:00:00 +0200

Make it work in 6 steps - a short tutorial

5 min.

Recently I have been struggling when trying to embed a leaflet map created with RStudio on my blog, hosted in GitHub via Jekyll (Spoiler: I succeeded ). In my case, I use the Chulapa remote theme created by myself.

Index

Ready? Let’s go!

The GitHub/Jekyll part

The first step is to install the requested libraries in your GitHub page. As Jekyll basically transforms markdown into html, this step is a matter of what to include and where in your own repository.

1. What to include

This part is not really hard. When having a look to the source code of Leaflet for R site it can be seen this chunk:

  
   name="viewport" content="width=device-width, initial-scale=1" />
   href="libs/bootstrap/css/flatly.min.css" rel="stylesheet" />
  
  ...
  
  ...
  
   href="libs/rstudio_leaflet/rstudio_leaflet.css" rel="stylesheet" />

So now we have it! The only thing to remember is that we need to load the libraries from the leaflet server (https://rstudio.github.io/leaflet), meaning that we have to prepend that url to the libraries in our installation:

  
   name="viewport" content="width=device-width, initial-scale=1" />
   href="https://rstudio.github.io/leaflet/libs/bootstrap/css/flatly.min.css" rel="stylesheet" />
  
  ...
  
  ...
  
       href="https://rstudio.github.io/leaflet/libs/rstudio_leaflet/rstudio_leaflet.css" rel="stylesheet" />

You can have a look of my implementation on ./_includes/leaflet.html.

2.Where to include

This a little bit more complicated, depending on the structure of your Jekyll template. The code chunk should be included in the section of your page, so you would need to find where to put it. In the case of Chulapa it is on ./_includes/custom/custom_head_before_css.html.

So now you just have to paste in the the code that you got on step 1.

Pro tip: For a better performance of the site, include these libraries only when you need it. In my case, I added a custom variable in my YAML front matter for those posts with a leaflet map, leafletmap: true. Go to step 4 for a working example.

The RStudio part

3. Creating the leaflet map

Now it’s time to create a leaflet map with RStudio. I just keep it simple for this post, so I took the first example provided in Leaflet for R - Introduction

library(leaflet)

m <- leaflet() %>%
  addTiles() %>%  # Add default OpenStreetMap map tiles
  addMarkers(lng=174.768, lat=-36.852, popup="The birthplace of R")
m  # Print the map

It is assumed that you are creating a post with RStudio, so the code presented above should be embedded in an .Rmd file.

4. Set up the YAML front matter

Before knitting your .Rmd, you have to set up the YAML front matter. Here it is essential to set up the option always_allow_html: yes, as well as output: github_document. As an example, this post was created with the front matter:

---
title: Leaflet, R, Markdown, Jekyll and GitHub
subtitle: Make it work in 6 steps - a short tutorial
tags: [R,leaflet,Jekyll, html, maps]
header_img: https://dieghernan.github.io/assets/figs/20190520_imgpost.webp
leafletmap: true
always_allow_html: yes
last_modified_at: 2021-05-30
output: 
  md_document:
    variant: gfm
    preserve_yaml: true
---

We are almost there! Now “Knit” your code and get the corresponding .mdfile.

The Markdown part

5. Modifying the `.md` file

Update: This is not needed any more! I still leave it here for info. You can skip to the next section.

Have a look to the .md code that you have just created. Although not displayed in the preview, you can see in the file itself a chunk that looks like this:

Actually that chunk is your leaflet map, created with RStudio. You can’t see it now because you are previewing a markdown file in your local PC, and the libraries installed in step 1 are installed on GitHub, but we would solve it later.

Now you just need to paste this piece of code before that chunk:


 id="htmlwidget-7ab57412f7b1df4d5773" style="width:100%;height:216px;" class="leaflet html-widget">


  

 Warning: Have you checked
the YAML front matter of your .md file? Have another look, specially
if you have followed my Pro tip.

Gallery: Size of a leaflet map 

A note: For a complete understanding of this section it is
recommended to access it on multiple devices, so you can see the
different behavior on different screens. Google Chrome allows you to
simulate different devices (more info
here).

Fixed size

With these examples you can see how to control the absolute size of the
leaflet map. The disadvantage of this method is that the size would be
fixed for all the devices, so maps sized for smartphones or tables
wouldn’t look as nice in laptops, etc. and vice versa.

Example 1: 672x480px

Fixed size in pixels. By default in my machine:

leaflet(options = leafletOptions(minZoom = 1.25, maxZoom = 8)) %>%
  addTiles() %>%
  setMaxBounds(-200, -90, 200, 90) %>%
  setView(-3.56948, 40.49181, zoom = 3)





Example 2: 200x300px

Let’s go narrow and long with html "width:200px;height:300px;":

leaflet(
  options = leafletOptions(minZoom = 1.25, maxZoom = 8),
  width = "200px", height = "300px"
) %>%
  addTiles() %>%
  setMaxBounds(-200, -90, 200, 90) %>%
  setView(-3.56948, 40.49181, zoom = 3)





Responsive size

Recommended option. These maps would adapt to the width of your
screen, no matter what device you are using.

Example 3: 100% width

leaflet(
  options = leafletOptions(minZoom = 1.25, maxZoom = 8),
  width = "100%"
) %>%
  addTiles() %>%
  setMaxBounds(-200, -90, 200, 90) %>%
  setView(-3.56948, 40.49181, zoom = 3)



Where in the world?
Mon, 13 May 2019 00:00:00 +0200
	
 				A leaflet map with the places I have flown
    		1 min.
				This is a very personal post, where I just show the map of all the
places I have traveled by plain







✈️ 251,536.4 kms. flown so far.

Top Cities


  
    
      City
      Country
      N
    
  
  
    
      Bilbao
      Spain
      62
    
    
      London
      United Kingdom
      23
    
    
      Edinburgh
      United Kingdom
      21
    
    
      Barcelona
      Spain
      16
    
    
      Brussels
      Belgium
      8
    
    
      Berlin
      Germany
      6
    
    
      Munich
      Germany
      6
    
    
      Palma de Mallorca
      Spain
      6
    
    
      Amsterdam
      Netherlands
      4
    
    
      Frankfurt
      Germany
      4
    
  


Top Countries


  
    
      Country
      Continent
      N
    
  
  
    
      Spain
      Europe
      97
    
    
      United Kingdom
      Europe
      46
    
    
      Germany
      Europe
      16
    
    
      Belgium
      Europe
      8
    
    
      France
      Europe
      6
    
  


Top Continents


  
    
      Continent
      Region
      N
    
  
  
    
      Europe
      Southern Europe
      101
    
    
      Europe
      Northern Europe
      52
    
    
      Europe
      Western Europe
      36
    
    
      Asia
      Western Asia
      6
    
    
      North America
      Northern America
      6
    
  


				


Cast a line to subsegments in R
Sun, 05 May 2019 00:00:00 +0200
	
 				User-defined function using sf package
    		3 min.
				This post introduces a used-defined function used for casting sf objects of class LINESTRING or POLYGON into sub-strings.

Required R packages

library(sf)
library(rnaturalearth)
library(dplyr)


The problem

The sfpackage includes st_cast, a very powerful function that transforms geometries into other different types of geometries (i.e. LINESTRINGto POLYGON, etc.).

italy <- ne_countries(country = "italy", returnclass = "sf")
italy_pol <- italy %>% st_cast("POLYGON")
italy_lin <- italy_pol %>% st_cast("LINESTRING")
italy_pt <- italy_lin %>% st_cast("POINT")
par(mfrow = c(2, 2), mar = c(1, 1, 1, 1), bg = NA)
plot(st_geometry(italy), col = c("red", "yellow", "blue"), main = "MULTIPOLYGON")
plot(st_geometry(italy_pol), col = c("red", "yellow", "blue"), main = "POLYGON")
plot(st_geometry(italy_lin), col = c("red", "yellow", "blue"), main = "LINE")
plot(st_geometry(italy_pt), col = c("red", "yellow", "blue"), main = "POINT")




What I missed when using st_cast is the possibility to “break” the LINESTRING objects into sub-segments:



An approach

So one possible solution could be to create LINESTRING objects for each consecutive pair of POINT objects across the original geometry. Let’s check it:

par(mfrow = c(1, 2), mar = c(1, 1, 1, 1))
test <- ne_countries(country = "spain", returnclass = "sf") %>%
  st_cast("POLYGON") %>%
  st_cast("LINESTRING")
plot(st_geometry(test), col = c("red", "yellow", "blue"), main = "LINESTRING")

geom <- lapply(
  1:(length(st_coordinates(test)[, 1]) - 1),
  function(i) {
    rbind(
      as.numeric(st_coordinates(test)[i, 1:2]),
      as.numeric(st_coordinates(test)[i + 1, 1:2])
    )
  }
) %>%
  st_multilinestring() %>%
  st_sfc(crs = st_crs(test)) %>%
  st_cast("LINESTRING")
plot(st_geometry(geom), col = c("red", "yellow", "blue"), main = "AFTER FUNCTION")




The function stdh_cast_substring

Finally, I wrapped the solution into a function and extended it a little bit:


  
    When the input is not a LINESTRING or a POLYGON returns an error and stops.
  
  
    The function accepts sf with several rows or sfc objects with several geometries, and returns the same class of input. In the case of sf objects, the input data.frame is added.
  
  
    By default, the output is a MULTILINESTRING geometry. This has the benefit that output has the same number of geometries than the input. This can be modified setting the parameter to as LINESTRING, that in fact only casts the MULTILINESTRING object into LINESTRING.
  


stdh_cast_substring <- function(x, to = "MULTILINESTRING") {
  ggg <- st_geometry(x)

  if (!unique(st_geometry_type(ggg)) %in% c("POLYGON", "LINESTRING")) {
    stop("Input should be  LINESTRING or POLYGON")
  }
  for (k in 1:length(st_geometry(ggg))) {
    sub <- ggg[k]
    geom <- lapply(
      1:(length(st_coordinates(sub)[, 1]) - 1),
      function(i) {
        rbind(
          as.numeric(st_coordinates(sub)[i, 1:2]),
          as.numeric(st_coordinates(sub)[i + 1, 1:2])
        )
      }
    ) %>%
      st_multilinestring() %>%
      st_sfc()

    if (k == 1) {
      endgeom <- geom
    }
    else {
      endgeom <- rbind(endgeom, geom)
    }
  }
  endgeom <- endgeom %>% st_sfc(crs = st_crs(x))
  if (class(x)[1] == "sf") {
    endgeom <- st_set_geometry(x, endgeom)
  }

  if (to == "LINESTRING") {
    endgeom <- endgeom %>% st_cast("LINESTRING")
  }
  return(endgeom)
}

The function could be improved in terms of performance. Given that it works at a coordinate level, for high-resolution objects it has some degree of delay

test100 <- ne_countries(
  continent = "south america",
  returnclass = "sf"
) %>%
  st_cast("POLYGON")

test50 <- ne_countries(50,
  continent = "south america",
  returnclass = "sf"
) %>%
  st_cast("POLYGON")



init <- Sys.time()
t1 <- stdh_cast_substring(test100, "LINESTRING")
end <- Sys.time()
kable(end - init, format = "markdown")



  
    
      x
    
  
  
    
      0.1729319 secs
    
  


init <- Sys.time()
t2 <- stdh_cast_substring(test50, "LINESTRING")
end <- Sys.time()
kable(end - init, format = "markdown")



  
    
      x
    
  
  
    
      2.288558 secs
    
  


par(mfrow = c(1, 1), mar = c(0, 0, 0, 0))
plot(st_geometry(test50), col = NA, bg = "#C6ECFF")
plot(st_geometry(ne_countries(50, returnclass = "sf")), col = "#F6E1B9", border = "#646464", add = T)
plot(st_geometry(test50), col = "#FEFEE9", border = "#646464", add = T)
plot(st_geometry(t2), col = c("red", "yellow", "blue"), add = T, lwd = 0.5)




It can be seen a difference in terms of performance, noting that test100 has 15 polygons decomposed in 914 sub-strings while test50 has 80 polygons to 8,414 sub-strings. In that sense, the original st_cast is much faster, although this solution may work well in most cases.

				


Using CountryCodes database and sf package
Sat, 27 Apr 2019 00:00:00 +0200
	
 				vignette of the CountryCodes project
    		2 min.
				This vignette is an example of use of the database provided in the Github project Country Codes and International Organizations & Groups
  by using the sf package in R.

Required R packages

library(sf)
library(jsonlite)
library(rnaturalearth)
library(dplyr)


Reading the data
The first step consists on reading the database provided (in this example the json file) and extracting one international organization. In this example we will plot the Commonwealth of Nations.

df <- fromJSON("https://raw.githubusercontent.com/dieghernan/Country-Codes-and-International-Organizations/master/outputs/Countrycodesfull.json")
# Identify Commonwealth acronym
orgsdb <- read.csv("https://raw.githubusercontent.com/dieghernan/Country-Codes-and-International-Organizations/master/outputs/CountrycodesOrgs.csv") %>%
  distinct(org_id, org_name)

kable(orgsdb[grep("Common", orgsdb$org_name), ], format = "markdown")



  
    
       
      org_name
      org_id
    
  
  
    
      25
      Commonwealth
      C
    
    
      26
      Central American Common Market
      CACM
    
    
      30
      Caribbean Community and Common Market
      CARICOM
    
    
      42
      Commonwealth of Independent States
      CIS
    
    
      43
      Common Market for Eastern and Southern Africa
      COMESA
    
    
      115
      Southern Cone Common Market
      MERCOSUR
    
  


In our case, the value to search is C. It is provided also a function that extract the membership from the json database:

ISO_memcol <- function(df,
                       orgtosearch) {
  ind <- match(orgtosearch, unlist(df[1, "org_id"]))
  or <- lapply(1:nrow(df), function(x) {
    unlist(df[x, "org_member"])[ind]
  })
  or <- data.frame(matrix(unlist(or)), stringsAsFactors = F)
  names(or) <- orgtosearch
  df2 <- as.data.frame(cbind(df, or, stringsAsFactors = F))
  return(df2)
}
df_org <- ISO_memcol(df, "C")


Now df_org has a new column, named C, containing the membership status of each country.

df_org %>%
  count(C) %>%
  kable(format = "markdown")



  
    
      C
      n
    
  
  
    
      member
      53
    
    
      NA
      222
    
  


df_org %>%
  filter(!is.na(C)) %>%
  select(
    ISO_3166_3,
    NAME.EN,
    C
  ) %>%
  head() %>%
  kable(format = "markdown")



  
    
      ISO_3166_3
      NAME.EN
      C
    
  
  
    
      ATG
      Antigua & Barbuda
      member
    
    
      AUS
      Australia
      member
    
    
      BHS
      Bahamas
      member
    
    
      BGD
      Bangladesh
      member
    
    
      BRB
      Barbados
      member
    
    
      BLZ
      Belize
      member
    
  


Replacing the data on a map.
In this example the rnaturalearth package is used for retrieving an sf object.  The code below replaces the data.frame part of the sfobject.
and replacing the dataframefor the dedicated database.

testmap <- ne_countries(50,
  "countries",
  returnclass = "sf"
) %>%
  select(ISO_3166_3 = adm0_a3) %>%
  full_join(df_org)

# We add also tiny countries
tiny <- ne_countries(50,
  "tiny_countries",
  returnclass = "sf"
) %>%
  select(ISO_3166_3 = adm0_a3) %>%
  full_join(df_org)

# Identify dependencies
ISOCommon <- df_org %>%
  filter(!is.na(C)) %>%
  select(
    ISO_3166_3.sov = ISO_3166_3,
    C_sov = C
  )
tiny <- left_join(tiny, ISOCommon)
tiny$C <- coalesce(tiny$C, tiny$C_sov)


Plotting map: Wikipedia style
Now we would try to plot a map resembling the one presented in the Wikipedia page for the Commonwealth.



The map we will generate is presented under a Robinson projection and the color palette will be based in the Wikipedia convention for Orthographic Maps, since it is the one used in the example.

# Projecting the map
testmap_rob <- st_transform(testmap, "+proj=robin")
tiny_rob <- st_transform(tiny, "+proj=robin")

# Bounding box
bbox <- st_linestring(rbind(
  c(-180, 90),
  c(180, 90),
  c(180, -90),
  c(-180, -90),
  c(-180, 90)
)) %>%
  st_segmentize(5) %>%
  st_cast("POLYGON") %>%
  st_sfc(crs = 4326) %>%
  st_transform(crs = "+proj=robin")

# Plotting
par(mar = c(0, 0, 0, 0), bg = NA)
plot(bbox,
  col = "#FFFFFF",
  border = "#AAAAAA",
  lwd = 1.5
)
plot(
  st_geometry(testmap_rob),
  col = "#B9B9B9",
  border = "#FFFFFF",
  lwd = 0.1,
  add = T
)

plot(
  st_geometry(testmap_rob %>%
    filter(!is.na(C))),
  col = "#346733",
  border = "#FFFFFF",
  lwd = 0.1,
  add = T
)

# By last, add tiny countries
# All
plot(
  st_geometry(tiny_rob),
  col = "#000000",
  bg = "#B9B9B9",
  add = T,
  pch = 21
)
# Dependencies
plot(
  st_geometry(tiny_rob %>%
    filter(!is.na(C)) %>%
    filter(!is.na(ISO_3166_3.sov))),
  bg = "#C6DEBD",
  col = "#000000",
  pch = 21,
  add = T
)
# Independent
plot(
  st_geometry(tiny_rob %>%
    filter(!is.na(C)) %>%
    filter(is.na(ISO_3166_3.sov))),
  bg = "#346733",
  col = "#000000",
  pch = 21,
  add = T
)
plot(bbox,
  col = NA,
  border = "#AAAAAA",
  lwd = 1.5,
  add = T
)




				


Country Codes & Organizations
Thu, 11 Apr 2019 00:00:00 +0200
	
 				A database with geocodes
    		2 min.
				Complete database of countries and territories, their different country codes under common standards (ISO-3166, GEC (Formerly FIPS), M49 (UN), STANAG (NATO), NUTS (EU), etc.) and their membership in different international organizations.

^{Note that blanks are presented as "" instead of NA since ISO-3166-ALPHA 2 for Namibia is NA.}

vignette: Using Country Codes

A. Country Codes .csv

Main .csv file (Link) containing:


  Country and regional codes
  Currency, dependency status ans sovereignty info
  Names in english and spanish as provided by Unicode CLDR
  Additional information (demographics, capital, area, etc.)


Codes included


  
    
      Field
      Description
      Source
      Notes
    
  
  
    
      ISO_3166_1
      ISO 3166-1 numeric
      Wikipedia
       
    
    
      ISO_3166_2
      ISO 3166-1 alpha-2
      Wikipedia
       
    
    
      ISO_3166_3
      ISO 3166-1 alpha-3
      Wikipedia
       
    
    
      FIPS_GEC
      Geopolitical Entities and Codes (GEC)
      CIA World Factbook
      Formerly FIPS 1PUB 10-4
    
    
      STANAG
      STANAG 1059 Country Codes
      CIA World Factbook
      Used by NATO
    
    
      M49
      UN Country Code
      UN Stats
       
    
    
      NUTS
      NUTS 0 code
      Wikipedia
      Used by EU
    
    
      geonameId
      geonameId
      geonames
       
    
    
      continentcode
      geonames Continent Code
      geonames
       
    
    
      regioncode
      UN Regional Code
      UN Stats
       
    
    
      interregioncode
      Interregional Code
      UN Stats
       
    
    
      subregioncode
      Subregion Code
      UN Stats
       
    
    
      ISO_3166_3.sov
      Sovereign code
      Wikipedia, Statoids
      If non-independent
    
  


Other information included


  Currency
  Dependency status
  Names in english and spanish: Country, Continents & Regions, capital
  Population, area (km²) and developed region


B. International Organizations .csv

A single .csv file (Link) describing the membership status of each country across 186 international organizations.


  
    
      Field
      Description
    
  
  
    
      ISO_3166_2
      Matches with Countrycodes .csv
    
    
      ISO_3166_3
      Matches with Countrycodes .csv
    
    
      NAME.EN
      Matches with Countrycodes .csv
    
    
      source
      Main data source
    
    
      org_name
      Name of the organization
    
    
      org_id
      Abbreviation or internal ID
    
    
      org_member
      Membership status
    
  


C. Full json file .json

This .json file (Link) combines the previous files:

[
  ...
  {
    "ISO_3166_1": 12,
    "ISO_3166_2": "DZ",
    "ISO_3166_3": "DZA",
    "ISO_Official": true,
    "FIPS_GEC": "AG",
    "STANAG": "DZA",
    "M49": 12,
    "geonameId": 2589581,
    "continentcode": "AF",
    "regioncode": 2,
    "subregioncode": 15,
    "currency": "DZD",
    "independent": true,
    "NAME.EN": "Algeria",
    "CONTINENT.EN": "Africa",
    "REGION.EN": "Africa",
    "SUBREGION.EN": "Northern Africa",
    "CAPITAL.EN": "Algiers",
    "NAME.ES": "Argelia",
    "CONTINENT.ES": "Africa",
    "REGION.ES": "África",
    "SUBREGION.ES": "África septentrional",
    "CAPITAL.ES": "Argel",
    "pop": 34586184,
    "area_km2": 2381740,
    "Developed": "Developing",
    "org_id": ["ABEDA", "ACP", "ADB", "AFDB", "AFESD", "AG", "AL", 
    ...
    ],
    "org_member": ["member", null, null, "member", "member", null,
    "member",
    ...
    ]
  },
  ...
]

A complementary function (intended to be used in R) has been developed:

ISO_memcol = function(df, #Input dataframe
                      orgtosearch #org id
) {
  ind = match(orgtosearch, unlist(df[1, "org_id"]))
  or = lapply(1:nrow(df), function(x)
    unlist(df[x, "org_member"])[ind])
  or = data.frame(matrix(unlist(or)), stringsAsFactors = F)
  names(or) = orgtosearch
  df2 = as.data.frame(cbind(df, or, stringsAsFactors = F))
  return(df2)
}


D. Data sources


  Wikipedia, the free encyclopedia
    
      ISO-3166
      NUTS
    
  
  The World Factbook - CIA
  United Nations Statistical Division
  geonames
  REST COUNTRIES
  Unicode Common Locale Data Repository (CLDR) Project
  http://www.statoids.com/


				


Bzel
Thu, 25 May 2017 00:00:00 +0200
	
 				A Pebble  project
    		1 min.
				Project discontinued due to the shutdown of Pebble.

Bzel intregates the bezel into your watchface. Display minutes as digits, as a moving dot or as a fill in the bezel.




Download from Rebble Appstore


Features


  Clock mode:
    
      Digital: Minute display based on analog movement
      Dot: Moving dot as minute marker
      Bezel: A bar moving around the bezel as minute marker
    
  
  Autodetection of 12h/24h based on your watch settings


Take your pick


  Pebble Health: Display daily steps.
  Date - Get the weekday based on the language set on your Pebble.
  Weather: Current conditions on °c or °f.
  Choose your weather provider:
    
      Yahoo.com No API Key required (at this moment)
      Wunderground
      OpenWeatherMap
    
  
  Implementation of pmkey.xyz
  Location, based on your selected weather provider
  Night theme displayed between sunset and sunrise


Internationalization

Autotranslating of weekday supported for:

  English
  Spanish
  German
  French
  Portuguese
  Italian


Future developments


  Location for weather and loc
  Square support
  New Minute Mode: Bezel
  Steps
  More Health Metrics


Screenshots



        


        


        



Attributions

Fonts


  Weather Icons by Eric Flowers, modified and fitted to regular alphabet, instead of Unicode values.
  Custom font for icons created via Fontastic.
  Gotham Fonts] downloaded from fontsgeek.com


Weather providers













Others

Master Key is a service for Pebble users. Get a unique PIN and add API Keys for your favorite online services. Please check www.pmkey.xyz for more info.

License

Developed under license MIT.

Made in Madrid, Spain ❤️

				


7egment
Wed, 17 May 2017 00:00:00 +0200
	
 				A Pebble  project
    		1 min.
				Project discontinued due to the shutdown of Pebble.

7egment is a customizable watchface based on the classic 7-segment display that adds your location and the current weather information in the language used on your watch and smartphone.




Download from Rebble Appstore


Features


  Autodetection of 12h/24h based on your watch settings
  Internationalization: Autotranslating of weekday supported for:
    
      English
      Spanish
      German
      French
      Portuguese
      Italian
    
  


Options

  Choose background colors, frame and text
  3 Bands design. Make it match your tie!
  Weather: Current conditions on °c or °f.
  Choose your weather provider:
    
      Wunderground
      OpenWeatherMap
    
  
  Implementation of pmkey.xyz
  Location, based on your selected weather provider
  Bluetooth and GPS warnings
  Night theme displayed between sunset and sunrise


Screenshots



        


        


        



Attributions

Fonts:

  DSEG7Modern-Bold by  Keshikan けしかん.
  Digital7-Regular downloaded from fontsgeek.com


Weather providers










Others

Master Key is a service for Pebble users. Get a unique PIN and add API Keys for your favorite online services. Please check www.pmkey.xyz for more info.

License

Developed under license MIT.

Made in Madrid, Spain ❤️

				


Sfera
Tue, 14 Mar 2017 00:00:00 +0100
	
 				A Pebble  project
    		1 min.
				Project discontinued due to the shutdown of Pebble.

Sfera for Pebble Time Round is a highly customizable watchface that gets the most of the smartwatch capabilities. Set your preferences and enjoy this beautifully designed watchface.




Download from Rebble Appstore


Features


  Clock mode:
    
      Analog: Classic analog watchface
      Digital: Centered hour and minute display based on analog movement
      Dual: Analog and Digital all in one
      Mix: Digital Hour and Analogic Minute
    
  
  Autodetection of 12h/24h based on your watch settings


Take your pick


  Date - Get the weekday based on the language set on your Pebble.
  Dots as minute markers - choose your color
  Battery level displayed beautifully as an arc near the bezel. Choose your color and below 20% it turns red!
  Weather: Current conditions on °c or °f.
  Choose your weather provider:
    
      Yahoo.com No API Key required (at this moment)
      Wunderground
      OpenWeatherMap
    
  
  Implementation of pmkey.xyz
  Location, based on your selected weather provider
  Night theme displayed between sunset and sunrise


Internationalization

Autotranslating of weekday supported for:


  English
  Spanish
  German
  French
  Portuguese
  Italian


Future developments

  12/24h mode
  Night theme
  Several weather providers available
  pmkey.xyz implemented for easy managing your API keys


Screenshots



Attributions

Fonts:


  Weather Icons by Eric Flowers, modified and fitted to regular alphabet, instead of Unicode values.
  Custom font for icons created via Fontastic downloaded from fontsgeek.com


Weather providers













Others

Master Key is a service for Pebble users. Get a unique PIN and add API Keys for your favorite online services. Please check www.pmkey.xyz for more info.

License

Developed under license MIT.

Made in Madrid, Spain ❤️

				


TextWatch Clima
Thu, 16 Feb 2017 00:00:00 +0100
	
 				A Pebble  project
    		1 min.
				Project discontinued due to the shutdown of Pebble.

TextWatch Clima upgrades the classic TextWatch watchface adding a bunch of new capabilities.



Available for all the Classic, Time and Pebble 2 models


Download from Rebble Appstore


Features


  Exact hour in natural language
  Autofit to screen




Take your pick


  Date format: Day Month / Month Day
  Fuzzy time option
  Animation on text
  Language
    
      Spanish
      English
      German (thanks to rodher)
      French
      Italian
      Portuguese
      Norwegian
      Danish
      Swedish
      Esperanto
      Dutch
      Catalan
      More at request
    
  
  Battery bar display
  Weather: Current conditions on °c or °f.
  Night theme displayed between sunset and sunrise
  Choose your weather provider:
    
      Yahoo No API Key required (at this moment)
      Wunderground
      OpenWeatherMap
    
  
  Implementation of pmkey.xyz




Next developments

  Fuzzy time
  Battery
  Option for animations
  Option for non pmkey users
  More languages (Swedish, Esperanto…)


Attributions

Fonts


  Weather Icons by Eric Flowers, modified and fitted to regular alphabet, instead of Unicode values.
  Custom font for icons created via Fontastic.
  Gotham Fonts downloaded from fontsgeek.com


Weather providers













Others


  Master Key is a service for Pebble users. Get a unique PIN and add API Keys for your favorite online services. Please check www.pmkey.xyz for more info.
  wackyneighbor project DC TextWatch Deluxe


Screenshots



        


        


        



License

Developed under license MIT.

Made in Madrid, Spain ❤️

Field	Description
`ISO_3166_2`	Matches with Countrycodes `.csv`
`ISO_3166_3`	Matches with Countrycodes `.csv`
`NAME.EN`	Matches with Countrycodes `.csv`
`source`	Main data source
`org_name`	Name of the organization
`org_id`	Abbreviation or internal ID
`org_member`	Membership status

City	Country	N
Bilbao	Spain	62
London	United Kingdom	23
Edinburgh	United Kingdom	21
Barcelona	Spain	16
Brussels	Belgium	8
Berlin	Germany	6
Munich	Germany	6
Palma de Mallorca	Spain	6
Amsterdam	Netherlands	4
Frankfurt	Germany	4

Country	Continent	N
Spain	Europe	97
United Kingdom	Europe	46
Germany	Europe	16
Belgium	Europe	8
France	Europe	6

Continent	Region	N
Europe	Southern Europe	101
Europe	Northern Europe	52
Europe	Western Europe	36
Asia	Western Asia	6
North America	Northern America	6

	org_name	org_id
25	Commonwealth	C
26	Central American Common Market	CACM
30	Caribbean Community and Common Market	CARICOM
42	Commonwealth of Independent States	CIS
43	Common Market for Eastern and Southern Africa	COMESA
115	Southern Cone Common Market	MERCOSUR

ISO_3166_3	NAME.EN	C
ATG	Antigua & Barbuda	member
AUS	Australia	member
BHS	Bahamas	member
BGD	Bangladesh	member
BRB	Barbados	member
BLZ	Belize	member

Field	Description	Source	Notes
`ISO_3166_1`	ISO 3166-1 numeric	Wikipedia
`ISO_3166_2`	ISO 3166-1 alpha-2	Wikipedia
`ISO_3166_3`	ISO 3166-1 alpha-3	Wikipedia
`FIPS_GEC`	Geopolitical Entities and Codes (GEC)	CIA World Factbook	Formerly FIPS 1PUB 10-4
`STANAG`	STANAG 1059 Country Codes	CIA World Factbook	Used by NATO
`M49`	UN Country Code	UN Stats
`NUTS`	NUTS 0 code	Wikipedia	Used by EU
`geonameId`	geonameId	geonames
`continentcode`	geonames Continent Code	geonames
`regioncode`	UN Regional Code	UN Stats
`interregioncode`	Interregional Code	UN Stats
`subregioncode`	Subregion Code	UN Stats
`ISO_3166_3.sov`	Sovereign code	Wikipedia, Statoids	If non-independent

One world | Projects, maps and coding

Introducing geobounds

Installation

Getting administrative levels (ADM)

Global Composite Boundaries (CGAZ)

Understanding the data

Caching

When should you use geobounds?

Related Packages

rnaturalearth

giscoR

osmdata

Bottom line

Mapping Antarctica

Cool maps from the South Pole

Fixing the geometry

Plotting examples

Graham Bartram’s proposal (1996)

Emblem of the Antarctic Treaty

Antarctica Flag Redesigned

Implementing group_by count in Liquid

Alternative group_by with Liquid

Happy Valentine’s Day

Do you know the Bonne projection?

Optimize your images with R and reSmush.it

Introducing the resmush package

What is reSmush.it?

Why the resmush package?

Using the resmush package

With local files

With online files

Other alternatives

Beautiful Maps with R (V): Point densities

Bertin’s dot density maps with R and GHSL

Libraries

Get the data

Data wrangling

Final plot

Alternative hexagonal grid

References

Star Map with R

First things first: The data

Creating a Star Map with R

Helper funs

Celestial Data

Distribution

Data

Hillshade, colors and marginal plots with tidyterra (II)

Libraries

The plain in Spain

The rain in Spain

Creating a modified palette

Marginal plots (finally)

Profiling marginal plots

Putting all the pieces together

Recap

Hillshade, colors and marginal plots with tidyterra (I)

How to overlay SpatRasters

Libraries

Get the data

Hillshading

Selecting colors

Final plot

References

Introducing tidyterra

Easily work and ggplot SpatRasters

Wait, volcano is flipped?

Working with SpatRasters

An Easter egg

Unknown pleasures with R

Joyplot elevation maps with ggridges and terra

Creating joyplot maps with R

Variations

Using geom_density_ridges()

Land only

With colors

Combine with another objects

References

Corona timelapse

Travel restrictions amidst the COVID crisis across time - A German perspective

Alternative `group_by` with Liquid

Wait, `volcano` is flipped?

Using `geom_density_ridges()`

On `ggplot2`

On `tmap`

Update: On `mapsf`

Implementation on `classInt` package

`png` Layer

Adding legends: the `legendHatched` function

Make the `.svg` file