wthielen/php-r

Provides ability to run R scripts from PHP

php-r

PHPR (or php-r) is a library that provides ability to run R scripts from PHP. Available as a bundle for Symfony2 users. Composer package: kachkaev/php-r.

The idea is based on invoking a command-line version of R and exchanging messages with this external process. Integration with server-based implementation of R can be easily implemented on demand as the library architecture supports that.

It is possible to both run all R code in one batch and interactively exchange commands with R interpreter.

Usage

Option 1: all R code in one batch

use Kachkaev\PHPR\RCore;
use Kachkaev\PHPR\Engine\CommandLineREngine;

$r = new RCore(new CommandLineREngine('/usr/bin/R'));

$result = $r->run(<<<EOF
x = 1
y = 2
x + y
x + z
x - y
EOF
    );

echo $result;

PHP output:

> x = 1
> y = 2
> x + y
[1] 3
> x + z
Error: object 'z' not found 
> x - y
[1] -1

Method run() is always called in a clean scope of R variables, i.e. the following usage will result an R error:

echo $r->run("x = 100")
echo "\n=====\n"
echo $r->run("x * x")

PHP output:

> x = 100
=====
> x * x
Error: object 'x' not found

Option 2: interactive exchange of data

To exchange commands with a single R process interactively, another approach should be used:

use Kachkaev\PHPR\RCore;
use Kachkaev\PHPR\Engine\CommandLineREngine;

$r = new RCore(new CommandLineREngine('/usr/bin/R'));
$rProcess = $r->createInteractiveProcess();
$rProcess->start();
$rProcess->write('x = 100');
// Do something else
$rProcess->write('x * x');

echo $rProcess->getAllResult();

PHP output:

> x = 100
> x * x
[1] 10000

The process is synchronous, i.e. if R code sent to write() implies some complex computations, PHP will wait until they are finished.

Multiple commands can be passed to R inside one write(); they can be multi-line too:

$rProcess->write(<<<EOF
x = 1
y = 10 + (x 
+ x / 2)
z = 42
EOF
    );

It is strictly necessary to keep commands complete. The following example will result a critical error, and R process will be terminated.

$rProcess->write('x = 1 + (');
// IncompleteRCommandException

Separate access to input / output / errors for each R command

To avoid manual splitting of a mix of R input, output and errors, the result of script execution can be accessed separately:

$rProcess = $r->createInteractiveProcess();
$rProcess->start();
$rProcess->write(<<<EOF
x = 1
y = 2
x
y
EOF
    );
    
$rProcess->write(<<<EOF
x + 41
x + xxx
x + y
EOF
    );
    
echo $rProcess->getLastWriteInput();
// x + 41
// x + xxx
// x + y

echo $rProcess->getLastWriteOutput();
// 42
// 
// [1] 3

echo $rProcess->hasLastWriteErrors();
// true

echo $rProcess->getLastWriteErrorCount();
// 1

$errors = $rProcess->getLastWriteErrors();
echo $errors[0]->getErrorMessage()
// object 'xxx' not found
echo $errors[0]->getCommand()
// x + xxx

$rProcess->getAllInput();
$rProcess->getAllOutput();
$rProcess->hasErrors();
$rProcess->getErrorCount();
$rProcess->getErrors();

Passing true to get(LastWrite|All)Input/get(LastWrite|All)Output/get(LastWrite|All)Result splits strings into arrays, where each element corresponds to a single command:

$rProcess = $r->createInteractiveProcess();
$rProcess->start();
$rProcess->write(<<<EOF
x = 
1 + 1
y
x
EOF
    );
$inputAsArray = $rProcess->getAllInput(true);
// ['x ={newline}1 + 1', 'y', 'x']
$outputAsArray = $rProcess->getAllOutput(true);
// ['', null, '2']
$resultAsArray = $rProcess->getAllResult(true);
// [
//   ['x ={newline}1 + 1', '', null],
//   ['y', null, 'Error: object \'y\' not found'],
//   ['x', '2', null]
// ]

Sensitivity to R errors

If it is necessary to make sure that a sequence of R commands is running with no errors, and calling hasLastWriteErrors() after each write() is unreasonable, the process can be made sensible to errors. RErrorsException will be thrown on write():

$rProcess->setErrorSensitive(true);
$rProcess->write('x = 1 + missingVariable');
// RErrorsException 

This is the same as:

$rProcess->setErrorSensitive(false);
$rProcess->write('x = 1 + missingVariable');
if ($rProcess->hasLastWriteErrors()) {
    throw new RErrorsException($rProcess->getLastWriteInput(true), $rProcess->getLastWriteOutput(true), $rProcess->getLastWriteErrors());
}

R-related errors and the exception thrown are not critical; the same instance of R process can be still used after they occur. If last input contains multiple commands, and several of them cause errors, RErrorsException will have the complete list. In any case all commands passed to write() will be attempted by R interpreter.

$allErrors = $rErrorsException->getErrors();
if (count ($allErrors) > 1) {
    $secondError = $allErrors[1];
    echo $secondError->getErrorMessage();
}

Parsing R output

To ease parsing of R output, ROutputParser can be used:

use Kachkaev\PHPR\ROutputParser;

$rOutputParser = new ROutputParser();
$rProcess->write('21 + 21');
var_dump($rProcess->getLastWriteOutput());
// string(6) "[1] 42"
var_dump($rOutputParser->singleNumber($rProcess->getLastWriteOutput()));
// int(42)

See PHPdoc annotations to classes for more details.

License

MIT. See LICENSE.