pizzarr

A Zarr implementation for R.

Installation

Installation requires R 4.0.0 or greater.

install.packages("devtools")
devtools::install_github("keller-mark/pizzarr")

Usage

library(pizzarr)

a <- array(data=1:20, dim=c(2, 10))
#      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
# [1,]    1    3    5    7    9   11   13   15   17    19
# [2,]    2    4    6    8   10   12   14   16   18    20
z <- zarr_create(shape=dim(a), dtype="<f4", fill_value=NA)

z$set_item("...", a)

selection <- z$get_item(list(slice(1, 2), slice(1, 5)))

print(selection$data)
#      [,1] [,2] [,3] [,4] [,5]
# [1,]    1    3    5    7    9
# [2,]    2    4    6    8   10

Current status

(This section has been adapted from the Rarr project README).

Stores

Store	Status (reading / writing)
MemoryStore	✔ / ✔
DirectoryStore	✔ / ✔
HttpStore	✔ / ❌

Data types

Zarr Data Type	Status (reading / writing)	Notes
b1 / boolean	✔ / ✔	Converted to logical in R.
i1 / int8	✔ / ✔	Converted to integer in R.
u1 / uint8	✔ / ✔	Converted to integer in R.
i2 / int16	✔ / ✔	Converted to integer in R.
u2 / uint16	✔ / ✔	Converted to integer in R.
i4 / int32	✔ / ✔	Converted to integer in R.
u4 / uint32	✔ / ✔	Converted to integer in R.
i8 / int64	✔ / ✔	Converted to integer in R.
u8 / uint64	✔ / ✔	Converted to integer in R.
f2 / float16	✔ / ✔	Converted to double in R.
f4 / float32	✔ / ✔	Converted to double in R.
f8 / float64	✔ / ✔	Converted to double in R.
complex	❌ / ❌
timedelta	❌ / ❌
datetime	❌ / ❌
string	✔ / ✔	Converted to character in R.
Unicode	✔ / ✔	Converted to character in R.
void *	❌ / ❌
Structured data types	❌ / ❌
Object data type - VLenUTF8	✔ / ✔	Converted to character in R.

Note: no effort is made to assess loss of precision due to conversion.

Compression tools

Data Type	Status (reading / writing)	Notes
zlib / gzip	✔ / ✔	Only system default compression level 6 is enabled for writing.
bzip2	✔ / ✔	Only system default compression level 6 is enabled for writing.
blosc	✔ / ✔	Only system default compression level 5 is enabled for writing.
LZMA	✔ / ✔	Only system default compression level 9 is enabled for writing.
LZ4	✔ / ✔
Zstd	✔ / ✔

Development

setwd("path/to/pizzarr")
install.packages("devtools")
devtools::install()
devtools::load_all()

Testing

Set TESTTHAT_CPUS=# in .Renviron to run tests in parallel

devtools::check()
devtools::test()

Documentation

install.packages("devtools")
install.packages("pkgdown")
devtools::document()
pkgdown::build_site()

Resources

• Discussion of Zarr in R
• Rarr
  • Note: pizzarr has an optional dependency on Rarr for Blosc (de)compression.
• R package development
  • R packages
  • roxygen2 syntax
  • R6
  • R6 roxygen2 syntax
  • pkgdown
• Zarr implementation
  • zarr_implementations
  • zarr-python
  • LZ4 and ZSTD compression in R
  • zarr.js
  • zarrita.js
  • v2 spec