1. 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_geometry       st_interpolate_aw
## [49] st_intersects     st_join           st_mosaic         st_normalize     
## [53] st_redimension    st_sample         st_transform      st_transform_proj
## [57] 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

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))