- 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] $<- Math Ops [
## [5] [<- adrop aggregate aperm
## [9] as.data.frame as.tbl_cube as_tibble c
## [13] coerce contour cut dim
## [17] dimnames dimnames<- drop_units droplevels
## [21] filter image initialize is.na
## [25] merge mutate plot predict
## [29] print pull select show
## [33] slice slotsFromS3 split st_apply
## [37] st_area st_as_sf st_as_sfc st_as_stars
## [41] st_bbox st_coordinates st_crop st_crs
## [45] st_crs<- st_dimensions st_dimensions<- st_extract
## [49] st_geometry st_interpolate_aw st_intersects st_join
## [53] st_mosaic st_normalize st_redimension st_sample
## [57] st_transform st_transform_proj 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):
## L7_ETMs.tif
## Min. : 1.00
## 1st Qu.: 54.00
## Median : 69.00
## Mean : 68.91
## 3rd Qu.: 86.00
## Max. :255.00
## dimension(s):
## from to offset delta refsys point values
## x 1 349 288776 28.5 UTM Zone 25, Southern Hem... FALSE NULL [x]
## y 1 352 9120761 -28.5 UTM Zone 25, Southern Hem... FALSE NULL [y]
## band 1 6 NA NA NA NA NULL
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):
## L7_ETMs.tif
## Min. : 1.00
## 1st Qu.: 32.00
## Median : 60.00
## Mean : 59.98
## 3rd Qu.: 88.00
## Max. :255.00
## dimension(s):
## from to offset delta refsys point values
## x 1 349 288776 28.5 UTM Zone 25, Southern Hem... FALSE NULL [x]
## y 1 352 9120761 -28.5 UTM Zone 25, Southern Hem... FALSE NULL [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):
## L7_ETMs.tif
## Min. : 5.00
## 1st Qu.: 54.00
## Median : 70.00
## Mean : 71.79
## 3rd Qu.: 88.00
## Max. :252.00
## dimension(s):
## from to offset delta refsys point values
## x 1 70 289004 28.5 UTM Zone 25, Southern Hem... FALSE NULL [x]
## y 1 352 9120761 -28.5 UTM Zone 25, Southern Hem... FALSE NULL [y]
## band 1 3 4 1 NA NA NULL
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):
## L7_ETMs.tif band2
## Min. : 1.00 Min. : 2.0
## 1st Qu.: 54.00 1st Qu.:108.0
## Median : 69.00 Median :138.0
## Mean : 68.91 Mean :137.8
## 3rd Qu.: 86.00 3rd Qu.:172.0
## Max. :255.00 Max. :510.0
## dimension(s):
## from to offset delta refsys point values
## x 1 349 288776 28.5 UTM Zone 25, Southern Hem... FALSE NULL [x]
## y 1 352 9120761 -28.5 UTM Zone 25, Southern Hem... FALSE NULL [y]
## band 1 6 NA NA NA NA NULL
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):
## band2
## Min. : 2.0
## 1st Qu.:108.0
## Median :138.0
## Mean :137.8
## 3rd Qu.:172.0
## Max. :510.0
## dimension(s):
## from to offset delta refsys point values
## x 1 349 288776 28.5 UTM Zone 25, Southern Hem... FALSE NULL [x]
## y 1 352 9120761 -28.5 UTM Zone 25, Southern Hem... FALSE NULL [y]
## band 1 6 NA NA NA NA NULL
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))
