3. stars tidyverse methods
Edzer Pebesma
For a better version of the stars vignettes see https://r-spatial.github.io/stars/articles/
This vignette shows how some of the tidyverse verbs can be used on stars objects.
The stars and tidyverse packages are loaded by
library(stars)
library(dplyr)
Methods now available for class stars are
methods(class = "stars")
## [1] $<- %in% Math Ops
## [5] [ [<- [[<- adrop
## [9] aggregate aperm as.POSIXct as.data.frame
## [13] as.tbl_cube as_tibble c coerce
## [17] contour cut dim dimnames
## [21] dimnames<- drop_units droplevels expand_dimensions
## [25] filter hist image initialize
## [29] is.na merge mutate plot
## [33] prcomp predict print pull
## [37] rename select show slice
## [41] slotsFromS3 split st_apply st_area
## [45] st_as_sf st_as_sfc st_as_stars st_bbox
## [49] st_coordinates st_crop st_crs st_crs<-
## [53] st_dimensions st_dimensions<- st_downsample st_extract
## [57] st_geometry st_geotransform st_geotransform<- st_interpolate_aw
## [61] st_intersects st_join st_mosaic st_normalize
## [65] st_redimension st_rotate st_sample st_set_bbox
## [69] st_transform st_write time transmute
## [73] write_stars
## see '?methods' for accessing help and source code
We will work with a three-band section of a landsat image:
system.file("tif/L7_ETMs.tif", package = "stars") %>%
read_stars -> x
x
## stars object with 3 dimensions and 1 attribute
## attribute(s):
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## L7_ETMs.tif 1 54 69 68.91242 86 255
## dimension(s):
## from to offset delta refsys point x/y
## x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
## y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
## band 1 6 NA NA NA NA
slice
slice slices a sub-array out of the cube; this is done by specifying the dimension on which to act, and the slice number.
x %>% slice(band, 6) -> x6
x6
## stars object with 2 dimensions and 1 attribute
## attribute(s):
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## L7_ETMs.tif 1 32 60 59.97521 88 255
## dimension(s):
## from to offset delta refsys point x/y
## x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
## y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
It returns a lower-dimensional array if a single element is selected along the slice dimension.
filter
Similar to slice, filter selects on dimensions but evaluates their values rather than their index: in
x %>% filter(x > 289000, x < 291000, band > 3) -> x7
x7
## stars object with 3 dimensions and 1 attribute
## attribute(s):
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## L7_ETMs.tif 5 54 70 71.79194 88 252
## dimension(s):
## from to offset delta refsys point x/y
## x 1 70 289004 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
## y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
## band 1 3 4 1 NA NA
the subarray is created based on the x coordinate values.
Note that filter converts the object to a tbl_cube, and uses the dplyr filter method for tbl_cube objects. This has the limitation that stars objects with rectilinear, curvilinear or simple feature geometries cannot be handled. For such objects, using regular [ selection or using st_crop may be an alternative.
pull
pull pulls out an array from a stars object:
x %>% pull(1) -> x8
class(x8)
## [1] "array"
dim(x8)
## x y band
## 349 352 6
mutate
x %>% mutate(band2 = 2 * L7_ETMs.tif) -> x2
x2
## stars object with 3 dimensions and 2 attributes
## attribute(s):
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## L7_ETMs.tif 1 54 69 68.91242 86 255
## band2 2 108 138 137.82484 172 510
## dimension(s):
## from to offset delta refsys point x/y
## x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
## y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
## band 1 6 NA NA NA NA
select
select selects an attribute, or a set of attributes:
x2 %>% select(band2) -> x9
x9
## stars object with 3 dimensions and 1 attribute
## attribute(s):
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## band2 2 108 138 137.8248 172 510
## dimension(s):
## from to offset delta refsys point x/y
## x 1 349 288776 28.5 SIRGAS 2000 / UTM zone 25S FALSE [x]
## y 1 352 9120761 -28.5 SIRGAS 2000 / UTM zone 25S FALSE [y]
## band 1 6 NA NA NA NA
geom_stars
geom_raster is a ggplot2 geom function that accepts stars objects as its data argument and
- sets up the raster or vector spatial coordinates as plot dimensions, and the first attribute as the fill variable
- allows for downsampling (without choosing a suitable downsampling level)
- chooses between using
geom_raster, geom_rect and geom_sf depending on whether the geometry is regular, rectilinear or has vector geometries
An example use is
library(ggplot2)
library(viridis)
ggplot() +
geom_stars(data = x) +
coord_equal() +
facet_wrap(~band) +
theme_void() +
scale_fill_viridis() +
scale_x_discrete(expand = c(0, 0)) +
scale_y_discrete(expand = c(0, 0))
