--- title: "geodist" author: "Mark Padgham" date: "`r Sys.Date()`" output: html_document: toc: true toc_float: true number_sections: false theme: flatly vignette: > %\VignetteIndexEntry{geodist} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ```{r pkg-load, echo = FALSE, message = FALSE, eval = FALSE} devtools::load_all (".", export_all = FALSE) ``` # 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 intro, 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 ``` ## Detailed Usage Input(s) to the `geodist()` function can be in arbitrary rectangular format. ```{r tibble, eval = FALSE} n <- 1e1 x <- tibble::tibble ( x = -180 + 360 * runif (n), y = -90 + 180 * runif (n) ) dim (geodist (x)) #> [1] 10 10 y <- tibble::tibble ( x = -180 + 360 * runif (2 * n), y = -90 + 180 * runif (2 * n) ) dim (geodist (x, y)) #> [1] 10 20 x <- cbind ( -180 + 360 * runif (n), -90 + 100 * runif (n), seq (n), runif (n) ) colnames (x) <- c ("lon", "lat", "a", "b") dim (geodist (x)) #> [1] 10 10 ``` All outputs are distances in metres, calculated with a variety of spherical and elliptical distance measures. Distance measures currently implemented are Haversine, Vincenty (spherical), 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.) Note 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 (typically the size of single cities or study sites). ### 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, eval = FALSE} geodist_benchmark (lat = 30, d = 1000) #> haversine vincenty cheap #> absolute 0.836551561 0.836551562 0.594188257 #> relative 0.002155514 0.002155514 0.001616718 ``` All distances (`d)` are in metres, so that result indicates that all measures are accurate to within 1m over distances out to several km. 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, ])) 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 1:3) { lines (d / 1000, yvals [[i]] [, j], col = cols [j]) } legend ("topleft", lwd = 1, col = cols, bty = "n", legend = colnames (yvals [[i]]) ) } ``` ![](./fig1.png) ### Performance comparison The following code demonstrates the relative speed advantages of the different distance measures implemented in the `geodist` package. ```{r benchmark-measures, eval = FALSE} 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] #> test replications elapsed relative #> 1 d1 <- geodist(x, measure = "cheap") 10 0.058 1.000 #> 2 d2 <- geodist(x, measure = "haversine") 10 0.185 3.190 #> 3 d3 <- geodist(x, measure = "vincenty") 10 0.276 4.759 #> 4 d4 <- geodist(x, measure = "geodesic") 10 3.106 53.552 ``` 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, eval = 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-sf, eval = FALSE} 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 (x) sf::st_distance (x, x) geo_dist <- function (x) geodist (x, measure = "geodesic") rbenchmark::benchmark ( replications = 10, order = "test", sf_dist (xsf), geo_dist (x) ) [, 1:4] #> Linking to GEOS 3.6.2, GDAL 2.3.0, proj.4 5.0.1 #> test replications elapsed relative #> 2 geo_dist(x) 10 0.066 1.000 #> 1 sf_dist(xsf) 10 0.210 3.182 ``` Confirm that the two give almost identical results: ```{r benchmark-sf-accuracy, eval = FALSE} ds <- matrix (as.numeric (sf_dist (xsf)), nrow = length (xsf)) dg <- geodist (x, measure = "geodesic") formatC (max (abs (ds - dg)), format = "e") #> [1] "7.4506e-09" ``` 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, eval = FALSE} fgeodist <- function () geodist (x, measure = "vincenty", sequential = TRUE) fgeosph <- function () geosphere::distVincentySphere (x) rbenchmark::benchmark ( replications = 10, order = "test", fgeodist (), fgeosph () ) [, 1:4] #> test replications elapsed relative #> 1 fgeodist() 10 0.022 1.000 #> 2 fgeosph() 10 0.048 2.182 ```