In michaeldorman/starsExtra: Miscellaneous Functions for Working with 'stars' Rasters

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

starsExtra

R package starsExtra provides several miscellaneous functions for working with stars objects, mainly single-band rasters. Currently includes functions for:

• Focal filtering
• Detrending of Digital Elevation Models
• Calculating flow length
• Calculating the Convergence Index
• Calculating topographic aspect and slope

Installation

CRAN version:

install.packages("starsExtra")

GitHub version:

install.packages("remotes")
remotes::install_github("michaeldorman/starsExtra")

Usage

Once installed, the library can be loaded as follows.

library(starsExtra)

Documentation

The complete documentation can be found at https://michaeldorman.github.io/starsExtra/.

Example

The following code applied a 15*15 mean focal filter on a 533*627 stars Digital Elevation Model (DEM):

data(carmel)
carmel_mean15 = focal2(
  x = carmel,             # Input 'stars' raster
  w = matrix(1, 15, 15),  # Weights
  fun = "mean",           # Aggregation function
  na.rm = TRUE,           # 'NA' in neighborhood are removed
  mask = TRUE             # Areas that were 'NA' in 'x' are masked from result
)

data(carmel)
start = Sys.time()
carmel_mean15 = focal2(carmel, w = matrix(1, 15, 15), fun = "mean", na.rm = TRUE, mask = TRUE)
end = Sys.time()
d = end - start

The calculation takes: r format(d).

The original DEM and the filtered DEM can be combined and plotted with the following expressions:

r = c(carmel, carmel_mean15, along = 3)
r = st_set_dimensions(r, 3, values = c("input", "15*15 mean filter"))
plot(r, breaks = "equal", col = terrain.colors(10), key.pos = 4)

Timing

The following code section compares the calculation time of focal2 in the above example with raster::focal (both using C/C++) and the reference method focal2r (using R code only).

library(microbenchmark)
library(starsExtra)
library(raster)

data(carmel)
carmelr = as(carmel, "Raster")

res = microbenchmark(
  focal2 = focal2(carmel, w = matrix(1, 15, 15), fun = "mean", na.rm = FALSE), 
  focal = focal(carmelr, w = matrix(1, 15, 15), fun = mean, na.rm = FALSE),
  focal2r = focal2r(carmel, w = matrix(1, 15, 15), mean),
  times = 10
)
res

```r
boxplot(res)

x = list.files(pattern = "^README-.*\\.png$")
file.copy(x, "docs/", overwrite = TRUE)

michaeldorman/starsExtra documentation built on Jan. 19, 2024, 8:54 a.m.