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https://github.com/hypertidy/geodist
Ultra lightweight, ultra fast calculation of geo distances
https://github.com/hypertidy/geodist
Last synced: 18 days ago
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Ultra lightweight, ultra fast calculation of geo distances
- Host: GitHub
- URL: https://github.com/hypertidy/geodist
- Owner: hypertidy
- License: other
- Created: 2018-06-06T09:01:47.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2024-05-23T14:49:50.000Z (6 months ago)
- Last Synced: 2024-10-04T07:48:55.169Z (about 1 month ago)
- Language: C
- Homepage: https://hypertidy.github.io/geodist/
- Size: 579 KB
- Stars: 93
- Watchers: 6
- Forks: 7
- Open Issues: 8
-
Metadata Files:
- Readme: README.Rmd
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Codemeta: codemeta.json
Awesome Lists containing this project
- jimsghstars - hypertidy/geodist - Ultra lightweight, ultra fast calculation of geo distances (C)
README
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set (
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
[](https://github.com/hypertidy/geodist/actions?query=workflow%3AR-CMD-check)
[](https://github.com/hypertidy/geodist/actions?query=workflow%3Apkgcheck)
[](http://www.repostatus.org/#active)
[](https://codecov.io/gh/hypertidy/geodist)
[](http://cran.r-project.org/web/packages/geodist)
# geodist
An ultra-lightweight, zero-dependency package for very fast calculation of
geodesic distances. Main eponymous function, `geodist()`, accepts only one or
two primary arguments, which must be rectangular objects with unambiguously
labelled longitude and latitude columns (that is, some variant of `lon`/`lat`,
or `x`/`y`).
```{r, eval = FALSE}
n <- 50
x <- cbind (-10 + 20 * runif (n), -10 + 20 * runif (n))
y <- cbind (-10 + 20 * runif (2 * n), -10 + 20 * runif (2 * n))
colnames (x) <- colnames (y) <- c ("x", "y")
d0 <- geodist (x) # A 50-by-50 matrix
d1 <- geodist (x, y) # A 50-by-100 matrix
d2 <- geodist (x, sequential = TRUE) # Vector of length 49
d2 <- geodist (x, sequential = TRUE, pad = TRUE) # Vector of length 50
```
## Installation
You can install latest stable version of `geodist` from CRAN with:
```{r cran-installation, eval = FALSE}
install.packages ("geodist") # current CRAN version
```
Alternatively, current development versions can be installed using any of the
following options:
```{r gh-installation, eval = FALSE}
# install.packages("remotes")
remotes::install_git ("https://git.sr.ht/~mpadge/geodist")
remotes::install_git ("https://codeberg.org/hypertidy/geodist")
remotes::install_bitbucket ("hypertidy/geodist")
remotes::install_gitlab ("hypertidy/geodist")
remotes::install_github ("hypertidy/geodist")
```
Then load with
```{r library}
library (geodist)
packageVersion ("geodist")
```
## Detailed Usage
Input(s) to the `geodist()` function can be in arbitrary rectangular format.
```{r}
n <- 1e1
x <- tibble::tibble (
x = -180 + 360 * runif (n),
y = -90 + 180 * runif (n)
)
dim (geodist (x))
y <- tibble::tibble (
x = -180 + 360 * runif (2 * n),
y = -90 + 180 * runif (2 * n)
)
dim (geodist (x, y))
x <- cbind (
-180 + 360 * runif (n),
-90 + 100 * runif (n),
seq (n), runif (n)
)
colnames (x) <- c ("lon", "lat", "a", "b")
dim (geodist (x))
```
All outputs are distances in metres, calculated with a variety of spherical and
elliptical distance measures. Distance measures currently implemented are
Haversine, Vincenty (spherical and elliptical)), the very fast [mapbox cheap
ruler](https://github.com/mapbox/cheap-ruler-cpp/blob/master/include/mapbox/cheap_ruler.hpp)
(see their [blog
post](https://blog.mapbox.com/fast-geodesic-approximations-with-cheap-ruler-106f229ad016)),
and the "reference" implementation of [Karney
(2013)](https://link.springer.com/content/pdf/10.1007/s00190-012-0578-z.pdf), as
implemented in the package [`sf`](https://cran.r-project.org/package=sf). (Note
that `geodist` does not accept
[`sf`](https://cran.r-project.org/package=sf)-format objects; the
[`sf`](https://cran.r-project.org/package=sf) package itself should be used for
that.) The [mapbox cheap ruler
algorithm](https://github.com/mapbox/cheap-ruler-cpp) is intended to provide
approximate yet very fast distance calculations within small areas (tens to a few
hundred kilometres across).
### Benchmarks of geodesic accuracy
The `geodist_benchmark()` function - the only other function provided by the
`geodist` package - compares the accuracy of the different metrics to the
nanometre-accuracy standard of [Karney
(2013)](https://link.springer.com/content/pdf/10.1007/s00190-012-0578-z.pdf).
```{r}
geodist_benchmark (lat = 30, d = 1000)
```
All distances (`d)` are in metres, and all measures are accurate to within 1m
over distances out to several km (at the chosen latitude of 30 degrees). The
following plots compare the absolute and relative accuracies of the different
distance measures implemented here. The mapbox cheap ruler algorithm is the
most accurate for distances out to around 100km, beyond which it becomes
extremely inaccurate. Average relative errors of Vincenty distances remain
generally constant at around 0.2%, while relative errors of cheap-ruler
distances out to 100km are around 0.16%.
```{r plot, eval = FALSE, echo = FALSE}
lat <- 30
d <- 10^(1:35 / 5) # 1m to 100 km
y <- lapply (d, function (i) geodist_benchmark (lat = lat, d = i))
# yabs <- do.call (rbind, lapply (y, function (i) i [1, ])) [, c (1, 2, 4)]
# yrel <- 100 * do.call (rbind, lapply (y, function (i) i [2, ])) [, c (1, 2, 4)]
yabs <- do.call (rbind, lapply (y, function (i) i [1, ]))
yrel <- 100 * do.call (rbind, lapply (y, function (i) i [2, ]))
yvals <- list (yabs, yrel)
cols <- c ("skyblue", "lawngreen", "tomato")
par (mfrow = c (1, 2))
ylabs <- c ("Absolute error (m)", "Relative error (%)")
ylims <- list (range (yvals [[1]]), c (min (yvals [[2]]), 1))
for (i in 1:2)
{
plot (NULL, NULL,
xlim = range (d / 1000), ylim = ylims [[i]],
bty = "l", log = "xy", xaxt = "n", yaxt = "n",
xlab = "distance (km)", ylab = ylabs [i]
)
axis (d / 1000,
side = 1, at = c (0.001, 0.1, 10, 1e3, 1e4),
labels = c ("0.001", "0.1", "10", "1000", "")
)
if (i == 1) {
yl <- 10^(-3:5)
axis (yvals [[i]],
side = 2, at = c (0.001, 0.1, 10, 100, 10000),
labels = c ("0.001", "0.1", "10", "100", "1000")
)
} else {
yl <- c (0.1, 0.2, 0.3, 0.4, 0.5, 1, 2)
axis (yvals [[i]],
side = 2, at = yl,
labels = c ("0.1", "0.2", "0.3", "0.4", "0.5", "1", "2")
)
}
junk <- sapply (yl, function (j) {
lines (range (d / 1000), rep (j, 2),
col = "grey", lty = 2
)
})
xl <- 10^(-3:6)
junk <- sapply (xl, function (j) {
lines (rep (j, 2), range (yvals [[i]]),
col = "grey", lty = 2
)
})
for (j in (1:ncol (yabs)) [-1]) {
lines (d / 1000, yvals [[i]] [, j], col = cols [j])
}
legend ("topleft",
lwd = 1, col = cols, bty = "n",
legend = colnames (yvals [[i]])
)
}
```
### Performance comparison
The following code demonstrates the relative speed advantages of the different
distance measures implemented in the `geodist` package.
```{r benchmark2}
n <- 1e3
dx <- dy <- 0.01
x <- cbind (-100 + dx * runif (n), 20 + dy * runif (n))
y <- cbind (-100 + dx * runif (2 * n), 20 + dy * runif (2 * n))
colnames (x) <- colnames (y) <- c ("x", "y")
rbenchmark::benchmark (
replications = 10, order = "test",
d1 <- geodist (x, measure = "cheap"),
d2 <- geodist (x, measure = "haversine"),
d3 <- geodist (x, measure = "vincenty"),
d4 <- geodist (x, measure = "geodesic")
) [, 1:4]
```
Geodesic distance calculation is available in the [`sf`
package](https://cran.r-project.org/package=sf). Comparing computation speeds
requires conversion of sets of numeric lon-lat points to `sf` form with the
following code:
```{r x_to_sf, message = FALSE}
require (magrittr)
x_to_sf <- function (x) {
sapply (seq (nrow (x)), function (i) {
sf::st_point (x [i, ]) %>%
sf::st_sfc ()
}) %>%
sf::st_sfc (crs = 4326)
}
```
```{r benchmark}
n <- 1e2
x <- cbind (-180 + 360 * runif (n), -90 + 180 * runif (n))
colnames (x) <- c ("x", "y")
xsf <- x_to_sf (x)
sf_dist <- function (xsf) sf::st_distance (xsf, xsf)
geo_dist <- function (x) geodist (x, measure = "geodesic")
rbenchmark::benchmark (
replications = 10, order = "test",
sf_dist (xsf),
geo_dist (x)
) [, 1:4]
```
Confirm that the two give almost identical results:
```{r}
ds <- matrix (as.numeric (sf_dist (xsf)), nrow = length (xsf))
dg <- geodist (x, measure = "geodesic")
formatC (max (abs (ds - dg)), format = "e")
```
All results are in metres, so the two differ by only around 10 nanometres.
The [`geosphere` package](https://cran.r-project.org/package=geosphere) also
offers sequential calculation which is benchmarked with the following code:
```{r, echo = FALSE}
n <- 1e4
x <- cbind (-180 + 360 * runif (n), -90 + 180 * runif (n))
colnames (x) <- c ("x", "y")
```
```{r sequential}
fgeodist <- function () geodist (x, measure = "vincenty", sequential = TRUE)
fgeosph <- function () geosphere::distVincentySphere (x)
rbenchmark::benchmark (
replications = 10, order = "test",
fgeodist (),
fgeosph ()
) [, 1:4]
```
`geodist` is thus around 3 times faster than `sf` for highly accurate geodesic
distance calculations, and around twice as fast as `geosphere` for calculation
of sequential distances.
### Test Results
```{r load-testthat, message = FALSE}
require (devtools)
require (testthat)
```
```{r tests, eval = TRUE}
date ()
devtools::test ("tests/")
```
## Contributors
All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropenscilabs/allcontributors) following the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome!
### Code
### Issues
