stars package: how to define additional dimensions based on an attribute (filename)? - r

Question

I have a set of raster files (in this case downloaded from http://www.paleoclim.org/) that I am reading into R using the stars package.
library("tidyverse")
library("fs")
library("stars")
data_path <- "./paleoclim"
(data_files <- list.files(data_path, pattern = "*.tif"))
#> [1] "BA_v1_2_5m_bio_1_badia.tif"
#> [2] "BA_v1_2_5m_bio_10_badia.tif"
#> [3] "BA_v1_2_5m_bio_11_badia.tif"
#> [...]
#> [39] "EH_v1_2_5m_bio_1_badia.tif"
#> [40] "EH_v1_2_5m_bio_10_badia.tif"
#> [41] "EH_v1_2_5m_bio_11_badia.tif"
#> [...]
#> [58] "HS1_v1_2_5m_bio_1_badia.tif"
#> [59] "HS1_v1_2_5m_bio_10_badia.tif"
#> [60] "HS1_v1_2_5m_bio_11_badia.tif"
#> [...]
(paleoclim <- read_stars(path(data_path, data_files)))
#> stars object with 2 dimensions and 133 attributes
#> attribute(s):
#> BA_v1_2_5m_bio_1_badia.tif BA_v1_2_5m_bio_10_badia.tif
#> Min. :101.0 Min. :213.0
#> 1st Qu.:166.0 1st Qu.:278.0
#> Median :173.0 Median :298.0
#> Mean :171.8 Mean :290.3
#> 3rd Qu.:180.0 3rd Qu.:304.0
#> Max. :200.0 Max. :325.0
#> [...]
#> dimension(s):
#> from to offset delta refsys point values
#> x 1 72 36 0.0416667 WGS 84 FALSE NULL [x]
#> y 1 48 33 -0.0416667 WGS 84 FALSE NULL [y]
Created on 2020-12-07 by the reprex package (v0.3.0)
The filenames contain two pieces of information that I would like to represent as dimensions of the stars object, e.g. HS1_v1_2_5m_bio_1_badia.tif refers to period "HS1" and bioclimatic variable "bio_1".
I've got as far as using st_redimension() to create the new dimensions and levels:
periods <- str_extract(names(paleoclim), "[^_]+")
biovars <- str_extract(names(paleoclim), "bio_[0-9]+")
paleoclim %>%
merge() %>%
st_redimension(
new_dims = st_dimensions(x = 1:72, y = 1:48,
period = unique(periods),
biovar = unique(biovars))
)
#> stars object with 4 dimensions and 1 attribute
#> attribute(s):
#> X
#> Min. : -91.0
#> 1st Qu.: 26.0
#> Median : 78.0
#> Mean : 588.2
#> 3rd Qu.: 256.0
#> Max. :11275.0
#> dimension(s):
#> from to offset delta refsys point values
#> x 1 72 1 1 NA FALSE NULL [x]
#> y 1 48 1 1 NA FALSE NULL [y]
#> period 1 7 NA NA NA FALSE BA,...,YDS
#> biovar 1 19 NA NA NA FALSE bio_1,...,bio_9
But this doesn't actually map the values of the attributes (filenames) to the levels of the new dimensions. Also, most of the information (e.g. CRS) about the original x and y dimensions are lost because I have to recreate them manually.
How do you properly define new dimensions of a stars object based on another dimension or attribute?

Answer 1

Don't see a straightforward way to split one dimension into two after all files have been read into a three-dimensional stars object. An alternative approach you could use is:
read one folder at a time, where all files of that folder go into the variable third dimension, stored as separate stars objects in a list,
then combine the resulting stars objects, where the stars objects go into the period fourth dimension.
For this example, I downloaded the following two products and unzipped into two separate folders:
http://sdmtoolbox.org/paleoclim.org/data/BA/BA_v1_10m.zip
http://sdmtoolbox.org/paleoclim.org/data/HS1/HS1_v1_10m.zip
Here is the code:
library(stars)
# Directories with GeoTIFF files
paths = c(
"/home/michael/Downloads/BA_v1_10m",
"/home/michael/Downloads/HS1_v1_10m"
)
# Read the files and set 3rd dimension
r = list()
for(i in paths) {
files = list.files(path = i, pattern = "\\.tif$", full.names = TRUE)
r[[i]] = read_stars(files)
names(r[[i]]) = basename(files)
r[[i]] = st_redimension(r[[i]])
}
# Combine the list
r = do.call(c, r)
# Attributes to 4th dimension
names(r) = basename(paths)
r = st_redimension(r)
# Clean dimension names
r = st_set_dimensions(r, names = c("x", "y", "variable", "period"))
r
and the printout of the result:
## stars object with 4 dimensions and 1 attribute
## attribute(s), summary of first 1e+05 cells:
## BA_v1_10m.HS1_v1_10m
## Min. :-344.0
## 1st Qu.:-290.0
## Median :-274.0
## Mean :-264.8
## 3rd Qu.:-252.0
## Max. :-128.0
## NA's :94073
## dimension(s):
## from to offset delta refsys point values x/y
## x 1 2160 -180 0.166667 WGS 84 FALSE NULL [x]
## y 1 1072 88.6667 -0.166667 WGS 84 FALSE NULL [y]
## variable 1 19 NA NA NA NA bio_1.tif,...,bio_9.tif
## period 1 2 NA NA NA NA BA_v1_10m , HS1_v1_10m
The result is a stars object with four dimensions, including x, y, variable, and period.
Here are plots, separately for each of the two levels in the period dimension:
plot(r[,,,,1,drop=TRUE])
plot(r[,,,,2,drop=TRUE])