---
title: "qs2"
output:
html_vignette:
keep_md: no
rmarkdown::github_document: default
vignette: >
%\VignetteIndexEntry{qs2}
\usepackage[utf8]{inputenc}
%\VignetteEngine{knitr::rmarkdown}
---
```{r, setup, echo=FALSE}
knitr::knit_engines$set(cpp = function(options) {
options$engine <- "Rcpp"
knitr::engine_output(options, options$code, out = "")
})
IS_GITHUB <- Sys.getenv("IS_GITHUB") != ""
```
```{r results='asis', echo=FALSE, eval=IS_GITHUB}
cat('
[](https://github.com/qsbase/qs2/actions)
[](https://cran.r-project.org/package=qs2)
[](https://cran.r-project.org/package=qs2)
[](https://cran.r-project.org/package=qs2)
')
```
*qs2: a framework for efficient serialization*
`qs2` is the successor to the `qs` package that introduces two new formats: `qs2` and `qdata`. The goal is to have reliable and fast performance for saving and loading objects in R.
The `qs2` format directly uses R serialization (via the `R_Serialize`/`R_Unserialize` C API) while improving underlying compression and disk IO patterns.
If you are familiar with the `qs` package, the benefits and usage are the same.
```{r eval=FALSE}
qs_save(data, "myfile.qs2")
data <- qs_read("myfile.qs2")
```
Use the file extension `qs2` to distinguish it from the original `qs` package. It is not compatible with the original `qs` format.
## Installation
```{r eval=FALSE}
install.packages("qs2")
```
On x64 Mac or Linux (x86 only), you can gain a little more performance with the following configure flag:
```{r eval=FALSE}
remotes::install_cran("qs2", type = "source", configure.args = "--with-simd=AVX2")
```
Multi-threading in `qs2` uses the `Intel Thread Building Blocks` framework via the `RcppParallel` package.
## Converting qs2 to RDS
Because the `qs2` format directly uses R serialization, you can convert it to RDS and vice versa.
```{r eval=FALSE}
file_qs2 <- tempfile(fileext = ".qs2")
file_rds <- tempfile(fileext = ".RDS")
x <- runif(1e6)
# save `x` with qs_save
qs_save(x, file_qs2)
# convert the file to RDS
qs_to_rds(input_file = file_qs2, output_file = file_rds)
# read `x` back in with `readRDS`
xrds <- readRDS(file_rds)
stopifnot(identical(x, xrds))
```
## Validating file integrity
The `qs2` format saves an internal checksum. This can be used to test for file corruption before deserialization via the `validate_checksum` parameter, but has a minor performance penalty.
```{r eval=FALSE}
qs_save(data, "myfile.qs2")
data <- qs_read("myfile.qs2", validate_checksum = TRUE)
```
# Bindings to ZSTD compression library
The package exposes the ZSTD compression library for both in memory data and
file workflows.
## In memory compression and decompression
Use these functions when you already have raw vectors in memory and want
direct control of compression.
```{r eval=FALSE}
x <- serialize(mtcars, connection = NULL)
xz <- zstd_compress_raw(x, compress_level = 3)
x2 <- zstd_decompress_raw(xz)
stopifnot(identical(x, x2))
```
## File compression
These functions mirror typical file compression tools and keep the workflow
simple when you want explicit input and output files.
```{r eval=FALSE}
infile <- tempfile()
writeBin(as.raw(1:5), infile)
zfile <- tempfile(fileext = ".zst")
zstd_compress_file(infile, zfile, compress_level = 1)
outfile <- tempfile()
zstd_decompress_file(zfile, outfile)
stopifnot(identical(readBin(infile, "raw", 5), readBin(outfile, "raw", 5)))
```
## zstd_in and zstd_out
These generic wrappers substitute a zstd compressed file for a normal file
path, so you can add zstd compression support to existing functions for reading and writing data.
```{r eval=FALSE}
# library(data.table)
save_file <- tempfile(fileext = ".csv.zst")
# write out zstd compressed table
zstd_out(data.table::fwrite, mtcars, file = save_file)
# read in zstd compressed table
dt <- zstd_in(data.table::fread, file = save_file)
```
# The qdata format
The package also introduces the `qdata` format which has its own serialization layout and works with only data types (vectors, lists, data frames, matrices).
It will replace internal types (functions, promises, external pointers, environments, objects) with NULL. The `qdata` format differs from
the `qs2` format in that it is *not* general, but is more performant.
Please use `qdata` or `qd` as the file extension.
```{r eval=FALSE}
qd_save(data, "myfile.qdata")
data <- qd_read("myfile.qdata")
```
There is a `use_alt_rep` parameter that is intended to improve performance.
For the upcoming CRAN release, qdata does not use ALTREP but should be restored in the release after.
# Usage in C/C++
Serialization functions can be accessed in compiled code. Below is an example using Rcpp.
```{cpp eval=FALSE}
// [[Rcpp::depends(qs2)]]
#include
#include "qs2_external.h"
using namespace Rcpp;
// [[Rcpp::export]]
SEXP test_qs_serialize(SEXP x) {
SEXP buffer = qs_serialize(x, 10, true, 4);
return qs_deserialize(buffer, false, 4);
}
// [[Rcpp::export]]
SEXP test_qd_serialize(SEXP x) {
SEXP buffer = qd_serialize(x, 10, true, true, 4);
return qd_deserialize(buffer, false, false, 4);
}
// [[Rcpp::export]]
SEXP test_qs_save(SEXP x, const std::string& path) {
qs_save(x, path, 10, true, 4);
return qs_read(path, false, 4);
}
// [[Rcpp::export]]
SEXP test_qd_save(SEXP x, const std::string& path) {
qd_save(x, path, 10, true, true, 4);
return qd_read(path, false, false, 4);
}
/*** R
x <- runif(1e7)
stopifnot(identical(test_qs_serialize(x), x))
stopifnot(identical(test_qd_serialize(x), x))
stopifnot(identical(test_qs_save(x, tempfile(fileext = ".qs2")), x))
stopifnot(identical(test_qd_save(x, tempfile(fileext = ".qd")), x))
*/
```
## qdata-cpp external wrappers
You can serialize and de-serialize qdata format outside the R API. Functions for doing so are exported in `qdata_cpp_external.h`.
You can also compile these independently in `inst/include/qdata-cpp` and include in a standalone C++ project.
```{cpp eval=FALSE}
// [[Rcpp::depends(qs2)]]
#include
#include "qdata_cpp_external.h"
// [[Rcpp::export]]
Rcpp::IntegerVector qdata_ext_roundtrip() {
std::vector x{1, 2, 3, 4};
auto bytes = qdata_ext::serialize(x);
qdata_ext::object out = qdata_ext::deserialize(bytes);
const auto& ints = qdata_ext::get(out).values;
return Rcpp::IntegerVector(ints.begin(), ints.end());
}
// [[Rcpp::export]]
Rcpp::IntegerVector qdata_ext_file_roundtrip(const std::string& path) {
std::vector x{1, 2, 3, 4};
qdata_ext::save(path, x);
qdata_ext::object out = qdata_ext::read(path);
const auto& ints = qdata_ext::get(out).values;
return Rcpp::IntegerVector(ints.begin(), ints.end());
}
/*** R
stopifnot(identical(qdata_ext_roundtrip(), 1:4))
stopifnot(identical(qdata_ext_file_roundtrip(tempfile(fileext = ".qdata")), 1:4))
*/
```
# Global Options for qs2
The following global options control the behavior of the `qs2` functions. These global options can be queried or modified using `qopt` function.
- **compress_level**
The default compression level used when compressing data.
**Default:** `3L`
- **shuffle**
A logical flag indicating whether to allow byte shuffling during compression.
**Default:** `TRUE`
- **nthreads**
The number of threads used for compression and decompression.
**Default:** `1L`
- **validate_checksum**
A logical flag indicating whether to validate the stored checksum when reading data.
**Default:** `FALSE`
- **warn_unsupported_types**
For `qd_save`, a logical flag indicating whether to warn when saving an object with unsupported types.
**Default:** `TRUE`
- **use_alt_rep**
For `qd_read` and `qd_deserialize`, a logical flag requesting ALTREP string reads. This option is temporarily disabled; if `TRUE`, qs2 warns and falls back to ordinary character vectors.
**Default:** `FALSE`
---