org.af.jhlir.tools
Class RCmdBatch

java.lang.Object
  org.af.jhlir.tools.RCmdBatch

public class RCmdBatch
extends Object

Execute R in batch mode. Use this to query R for information / set up stuff / install packages, before you can properly connect to it through jhlir. Don't rely on this class too much and try to connect to R properly as aerly as possibly as error recognition and handling is shaky, as one can only use the textual output of the R batch script. Only prerequisite to invoke this class is knowledge of the path to R_HOME.

Field Summary

static String[]

R_ARGS

Constructor Summary

RCmdBatch(File rHome)
Constructor

RCmdBatch(String rHome)
Constructor

Method Summary

List<String>	exec(List<String> input) Excecute a list of R commands in batch mode.
List<String>	getInstalledPackages() Retrieves all installed R packages on the library paths.
RPackage	getInstalledPackInfo(String pack) Retrieve information about an installed R package on the current library paths.
String	getLibPaths() Get the R lib paths, separated by the path separator of your platform.
String	getRVersion() Get R version as a String.
RPackage	installCranPackage(String pack) Installs an R package from CRAN into the defaullt library directory.
RPackage	installCranPackage(String pack, File where) Installs an R package from CRAN.
RPackage	installRForgePackage(String pack) Installs an R package from R-Forge into the defaullt library directory.
RPackage	installRForgePackage(String pack, File where) Installs an R package from R-Forge.
boolean	isInstalled(String pack) Check whether an R package was installed on the current library paths.
Map<String,String>	retrieveInfo(List<String> input, List<String> vars) Excecute a list of R commands in batch mode and return the contents of R variables as strings.
String	retrieveInfo(List<String> input, String var) Excecute a list of R commands in batch mode and return the content of a R variable as a string.
void	retrieveRInfo() Collects information of the used R engine and stores it in this object.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

R_ARGS

public static final String[] R_ARGS

Constructor Detail

RCmdBatch

public RCmdBatch(File rHome)

Constructor

Parameters:

rHome - R Home directory.

RCmdBatch

public RCmdBatch(String rHome)

Constructor

Parameters:

rHome - Absolute Path to R Home directory.

Method Detail

exec

public List<String> exec(List<String> input)
                  throws RCmdBatchException

Excecute a list of R commands in batch mode. R CMD BATCH will write an output file, whose lines are returned as strings.

Parameters:

input - List of R commonds

Returns:

Contents of output file.

Throws:

RCmdBatchException - In case of IO errors or general errors with the R CMD BATCH process. Underlying exceptions are encapsulated as causing exceptions.

retrieveInfo

public String retrieveInfo(List<String> input,
                           String var)
                    throws RCmdBatchException

Excecute a list of R commands in batch mode and return the content of a R variable as a string. Uses exec method. !! Don't use this for too complicated stuff. At the moment the R variable must only generate a one-line string when printed!!

Parameters:

input - List of R commands

var - R variable you want to retrieve.

Returns:

Contents R variable as string when printed in R.

Throws:

RCmdBatchException - In case of IO errors or general errors with the R CMD BATCH process. Underlying exceptions are encapsulated as causing exceptions.

retrieveInfo

public Map<String,String> retrieveInfo(List<String> input,
                                       List<String> vars)
                                throws RCmdBatchException

Excecute a list of R commands in batch mode and return the contents of R variables as strings. Uses exec method. !! Don't use this for too complicated stuff. At the moment the R variables must only generate a one-line string when printed!!

Parameters:

input - List of R commands

vars - R variables you want to retrieve.

Returns:

Contents R variables as strings when printed in R.

Throws:

RCmdBatchException - In case of IO errors or general errors with the R CMD BATCH process. Underlying exceptions are encapsulated as causing exceptions.

getInstalledPackInfo

public RPackage getInstalledPackInfo(String pack)
                              throws RCmdBatchException

Retrieve information about an installed R package on the current library paths. Uses exec method.

Parameters:

pack - R package name.

Returns:

Information about R package or null if package was not found.

Throws:

RCmdBatchException - See exec(java.util.List).

isInstalled

public boolean isInstalled(String pack)
                    throws RCmdBatchException

Check whether an R package was installed on the current library paths. Simply performs getInstalledPackInfo(pack) == null

Parameters:

pack - R package name.

Returns:

True if package was found.

Throws:

RCmdBatchException - See exec(java.util.List).

getInstalledPackages

public List<String> getInstalledPackages()
                                  throws RCmdBatchException

Retrieves all installed R packages on the library paths. Uses exec method.

Returns:

List of installed R package names.

Throws:

RCmdBatchException - See exec(java.util.List).

installCranPackage

public RPackage installCranPackage(String pack)
                            throws CantFindPackageException,
                                   RCmdBatchException

Installs an R package from CRAN into the defaullt library directory. Uses exec method.

Parameters:

pack - R package to install.

Returns:

Package information after install.

Throws:

CantFindPackageException - If the package is not available on CRAN.

RCmdBatchException - See exec(java.util.List).

installCranPackage

public RPackage installCranPackage(String pack,
                                   File where)
                            throws CantFindPackageException,
                                   RCmdBatchException

Installs an R package from CRAN. Uses exec method.

Parameters:

pack - R package to install.

where - Directory to install the package into.

Returns:

Package information after install.

Throws:

CantFindPackageException - If the package is not available on CRAN.

RCmdBatchException - See exec(java.util.List).

installRForgePackage

public RPackage installRForgePackage(String pack)
                              throws CantFindPackageException,
                                     RCmdBatchException

Installs an R package from R-Forge into the defaullt library directory. Uses exec method.

Parameters:

pack - R package to install.

Returns:

Package information after install.

Throws:

CantFindPackageException - If the package is not available on R-Forge.

RCmdBatchException - See exec(java.util.List).

installRForgePackage

public RPackage installRForgePackage(String pack,
                                     File where)
                              throws CantFindPackageException,
                                     RCmdBatchException

Installs an R package from R-Forge. Uses exec method.

Parameters:

pack - R package to install.

where - Directory to install the package into.

Returns:

Package information after install.

Throws:

CantFindPackageException - If the package is not available on R-Forge.

RCmdBatchException - See exec(java.util.List).

retrieveRInfo

public void retrieveRInfo()
                   throws RCmdBatchException

Collects information of the used R engine and stores it in this object.

Throws:

RCmdBatchException

See Also:

this.getRVersion, this.getLibPaths

getRVersion

public String getRVersion()

Get R version as a String. Call retrieveRInfo() before this.

Returns:

R version.

getLibPaths

public String getLibPaths()

Get the R lib paths, separated by the path separator of your platform. Call retrieveRInfo() before this.

Returns:

R lib paths.