Crate extendr_api[][src]

Expand description

A safe and user friendly R extension interface.

  • Build rust extensions to R.
  • Convert R packages to Rust crates.

This library aims to provide an interface that will be familiar to first-time users of Rust or indeed any compiled language.

See Robj for much of the content of this crate. Robj provides a safe wrapper for the R object type.

Use attributes and macros to export to R.

use extendr_api::prelude::*;
// Export a function or impl to R.
#[extendr]
fn fred(a: i32) -> i32 {
    a + 1
}

// define exports using extendr_module
extendr_module! {
   mod mymodule;
   fn fred;    
}

In R:

result <- fred(1)

Robj is a wrapper for R objects. The r!() and R!() macros let you build R objects using Rust and R syntax respectively.

use extendr_api::prelude::*;
test! {
    // An R object with a single string "hello"
    let character = r!("hello");
    let character = r!(["hello", "goodbye"]);
    
    // An R integer object with a single number 1L.
    // Note that in Rust, 1 is an integer and 1.0 is a real.
    let integer = r!(1);
    
    // An R real object with a single number 1.
    // Note that in R, 1 is a real and 1L is an integer.
    let real = r!(1.0);
    
    // An R real vector.
    let real_vector = r!([1.0, 2.0]);
    let real_vector = &[1.0, 2.0].iter().collect_robj();
    let real_vector = r!(vec![1.0, 2.0]);
    
    // An R function object.
    let function = R!("function(x, y) { x + y }")?;
    
    // A named list using the list! macro.
    let list = list!(a = 1, b = 2);
    
    // An unnamed list (of R objects) using the List wrapper.
    let list = r!(List::from_values(vec![1, 2, 3]));
    let list = r!(List::from_values(vec!["a", "b", "c"]));
    let list = r!(List::from_values(&[r!("a"), r!(1), r!(2.0)]));

    // A symbol
    let sym = sym!(wombat);

    // A R vector using collect_robj()
    let vector = (0..3).map(|x| x * 10).collect_robj();
}

In Rust, we prefer to use iterators rather than loops.

use extendr_api::prelude::*;
test! {
    // 1 ..= 100 is the same as 1:100
    let res = r!(1 ..= 100);
    assert_eq!(res, R!("1:100")?);
    
    // Rust arrays are zero-indexed so it is more common to use 0 .. 100.
    let res = r!(0 .. 100);
    assert_eq!(res.len(), 100);
    
    // Using map is a super fast way to generate vectors.
    let iter = (0..3).map(|i| format!("fred{}", i));
    let character = iter.collect_robj();
    assert_eq!(character, r!(["fred0", "fred1", "fred2"]));
}

To index a vector, first convert it to a slice and then remember to use 0-based indexing. In Rust, going out of bounds will cause and error (a panic) unlike C++ which may crash.

use extendr_api::prelude::*;
test! {
    let vals = r!([1.0, 2.0]);
    let slice = vals.as_real_slice().ok_or("expected slice")?;
    let one = slice[0];
    let two = slice[1];
    // let error = slice[2];
    assert_eq!(one, 1.0);
    assert_eq!(two, 2.0);
}

Much slower, but more general are these methods:

use extendr_api::prelude::*;
test! {
    let vals = r!([1.0, 2.0, 3.0]);
    
    // one-based indexing [[i]], returns an object.
    assert_eq!(vals.index(1)?, r!(1.0));
    
    // one-based slicing [x], returns an object.
    assert_eq!(vals.slice(1..=2)?, r!([1.0, 2.0]));
    
    // $ operator, returns an object
    let list = list!(a = 1.0, b = "xyz");
    assert_eq!(list.dollar("a")?, r!(1.0));
}

The R! macro lets you embed R code in Rust and takes Rust expressions in {{ }} pairs.

The Rraw! macro will not expand the {{ }} pairs.

use extendr_api::prelude::*;
test! {
    // The text "1 + 1" is parsed as R source code.
    // The result is 1.0 + 1.0 in Rust.
    assert_eq!(R!("1 + 1")?, r!(2.0));

    let a = 1.0;
    assert_eq!(R!("1 + {{a}}")?, r!(2.0));

    assert_eq!(R!(r"
        x <- {{ a }}
        x + 1
    ")?, r!(2.0));

    assert_eq!(R!(r#"
        x <- "hello"
        x
    "#)?, r!("hello"));

    // Use the R meaning of {{ }} and do not expand.
    assert_eq!(Rraw!(r"
        x <- {{ 1 }}
        x + 1
    ")?, r!(2.0));
}

The r! macro converts a rust object to an R object and takes parameters.

use extendr_api::prelude::*;
test! {
    // The text "1.0+1.0" is parsed as Rust source code.
    let one = 1.0;
    assert_eq!(r!(one+1.0), r!(2.0));
}

You can call R functions and primitives using the call! macro.

use extendr_api::prelude::*;
test! {

    // As one R! macro call
    let confint1 = R!("confint(lm(weight ~ group - 1, PlantGrowth))")?;
    
    // As many parameterized calls.
    let formula = lang!("~", sym!(weight), lang!("-", sym!(group), 1.0)).set_class(["formula"])?;
    let plant_growth = global!(PlantGrowth)?;
    let model = call!("lm", formula, plant_growth)?;
    let confint2 = call!("confint", model)?;
    
    assert_eq!(confint1.as_real_vector(), confint2.as_real_vector());
}

Rust has a concept of “Owned” and “Borrowed” objects.

Owned objects, such as Vec and String allocate memory which is released when the object lifetime ends.

Borrowed objects such as &i32 and &str are just pointers to annother object’s memory and can’t live longer than the object they reference.

Borrowed objects are much faster than owned objects and use less memory but are used only for temporary access.

When we take a slice of an R vector, for example, we need the original R object to be alive or the data will be corrupted.

use extendr_api::prelude::*;
test! {
    // robj is an "Owned" object that controls the memory allocated.
    let robj = r!([1, 2, 3]);
    
    // Here slice is a "borrowed" reference to the bytes in robj.
    // and cannot live longer than robj.
    let slice = robj.as_integer_slice().ok_or("expected slice")?;
    assert_eq!(slice.len(), 3);
}

Re-exports

pub use robj::Robj;
pub use error::*;
pub use functions::*;
pub use lang_macros::*;
pub use logical::*;
pub use na::*;
pub use rmacros::*;
pub use robj::*;
pub use thread_safety::catch_r_error;
pub use thread_safety::handle_panic;
pub use thread_safety::single_threaded;
pub use thread_safety::this_thread_id;
pub use thread_safety::throw_r_error;
pub use wrapper::*;
pub use robj_ndarray::*;
pub use metadata::Metadata;

Modules

Error handling in Rust called from R.

Argument parsing and checking.

Module metadata

Maintain ownership of R objects.

Common exports for extendr-api.

rmacros - a set of macros to call actual R functions in a rusty way.

R object handling.

See https://serde.rs/impl-serializer.html

Provide limited protection for multithreaded access to the R API.

Wrappers are lightweight proxies for references to R datatypes. They do not contain an Robj (see array.rs for an example of this).

Macros

Execute R code by parsing and evaluating tokens.

Execute R code by parsing and evaluating tokens but without expanding parameters.

Call a function or primitive defined by a text expression with arbitrary parameters. This currently works by parsing and evaluating the string in R, but will probably acquire some shortcuts for simple expessions, for example by caching symbols and constant values.

Create a dataframe.

Define a module and export symbols to R Example:

Create a factor.

Get a global variable.

A macro for constructing R langage objects.

Create a list.

Create a Pairlist R object from a list of name-value pairs.

Convert a rust expression to an R object.

Print via the R error stream.

Print with a newline via the R output stream.

Print via the R output stream.

Print with a newline via the R output stream.

The sym! macro install symbols. You should cache your symbols in variables as generating them is costly.

Macro for running tests.

Get a local variable from the calling function or a global variable if no such variable exists.

Structs

Enums

Type of R objects used by Robj::rtype.

Enum use to unpack R objects into their specialist wrappers. Todo: convert all Robj types to wrappers. Note: this only works if the wrappers are all just SEXPs.

Constants

FALSE value eg. r!(FALSE)

NA value for integers eg. r!(NA_INTEGER)

NA value for logical. r!(NA_LOGICAL)

NA value for real values eg. r!(NA_REAL)

NA value for strings. r!(NA_STRING)

NULL value eg. r!(NULL)

TRUE value eg. r!(TRUE)

Traits

Used for immutable dereferencing operations, like *v.

Used for mutable dereferencing operations, like in *v = 1;.

Simple and safe type conversions that may fail in a controlled way under some circumstances. It is the reciprocal of TryInto.

An attempted conversion that consumes self, which may or may not be expensive.

Functions

Convert extendr’s RType to R’s SEXPTYPE. Panics if the type is Unknown.

Convert R’s SEXPTYPE to extendr’s RType.

Attribute Macros