AbstractRClient (baseCode 1.1.11 API)

java.lang.Object
- ubic.basecode.util.r.AbstractRClient

All Implemented Interfaces:

RClient

Direct Known Subclasses:

JRIClient, RServeClient
```
public abstract class AbstractRClient
extends Object
implements RClient
```
Base class for RClients

Author:

Paul

Field Summary

Fields
Modifier and Type Field and Description

protected static org.slf4j.Logger log

Fields
Modifier and Type	Field and Description
`protected static org.slf4j.Logger`	`log`

Constructor Summary

Constructors
Constructor and Description

AbstractRClient()

Constructors
Constructor and Description
`AbstractRClient()`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`assignFactor(List<String> strings)`
`String`	`assignFactor(String factorName, List<String> list)`
`String`	`assignMatrix(double[][] matrix)` Assign a 2-d matrix.
`String`	`assignMatrix(DoubleMatrix<?,?> matrix)` Assign a 2-d matrix.
`String`	`assignMatrix(DoubleMatrix<?,?> matrix, org.apache.commons.collections4.Transformer rowNameExtractor)` Assign a 2-d matrix.
`String`	`assignStringList(List<?> strings)` Define a variable corresponding to a character array in the R context, given a List of Strings.
`boolean`	`booleanDoubleArrayEval(String command, String argName, double[] arg)` Run a command that takes a double array as an argument and returns a boolean.
`String`	`dataFrame(ObjectMatrix<String,String,Object> matrix)` Convert an object matrix into an R data frame.
`ObjectMatrix<String,String,Object>`	`dataFrameEval(String command)` Evaluate a command that returns a dataFrame
`abstract void`	`disconnect()`
`double[]`	`doubleArrayDoubleArrayEval(String command, String argName, double[] arg)` Run a command that has a single double array parameter, and returns a double array.
`double[]`	`doubleArrayEval(String command)` Run a command that returns a double array with no arguments.
`double[]`	`doubleArrayTwoDoubleArrayEval(String command, String argName, double[] arg, String argName2, double[] arg2)` Run a command that takes two double array arguments and returns a double array.
`double`	`doubleTwoDoubleArrayEval(String command, String argName, double[] arg, String argName2, double[] arg2)` Run a command that takes two double arrays as arguments and returns a double value.
`int[]`	`intArrayEval(String command)`
`LinearModelSummary`	`linearModel(double[] data, Map<String,List<?>> factors)` Lower level access to linear model.
`LinearModelSummary`	`linearModel(double[] data, ObjectMatrix<String,String,Object> d)`
`List<?>`	`listEval(Class<?> listEntryType, String command)` FIXME only partly implemented, possibly not going to stay.
`boolean`	`loadLibrary(String libraryName)`
`protected void`	`loadScript(InputStream is)` There is a pretty annoying limitation of this.
`OneWayAnovaResult`	`oneWayAnova(double[] data, List<String> factor)` Lower-level access to a simple one-way ANOVA
`Map<String,OneWayAnovaResult>`	`oneWayAnovaEval(String command)`
`void`	`remove(String variableName)` Remove a variable from the R namespace
`Map<String,LinearModelSummary>`	`rowApplyLinearModel(String dataMatrixVarName, String modelFormula, String[] factorNames)` Run lm with anova on all the rows of a matrix
`String`	`stringEval(String command)` Evaluate any command and return a string
`List<String>`	`stringListEval(String command)`
`TwoWayAnovaResult`	`twoWayAnova(double[] data, List<String> factor1, List<String> factor2, boolean includeInteraction)` Lower-level access to two-way ANOVA
`Map<String,TwoWayAnovaResult>`	`twoWayAnovaEval(String command, boolean withInteractions)` Evaluates two way anova commands of the form apply(matrix,1,function(x){anova(aov(x~farea+ftreat))} and apply(matrix,1,function(x){anova(aov(x~farea+ftreat+farea*ftreat))} where farea and ftreat have already been transposed and had factor called on them.
`static String`	`variableIdentityNumber(Object ob)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.basecode.util.r.RClient
assign, assign, assign, assign, eval, getLastError, isConnected, retrieveMatrix, voidEval

- Field Detail
  - log
```
protected static org.slf4j.Logger log
```
- Constructor Detail
  - AbstractRClient
```
public AbstractRClient()
```
- Method Detail
  - variableIdentityNumber
```
public static String variableIdentityNumber(Object ob)
```
    Parameters:
    
    ob -
    
    Returns:
  - assignFactor
```
public String assignFactor(List<String> strings)
```
    Specified by:
    
    assignFactor in interface RClient
    
    Returns:
    
    the name of the factor generated.
  - assignFactor
```
public String assignFactor(String factorName,
                           List<String> list)
```
    Specified by:
    
    assignFactor in interface RClient
    
    Returns:
    
    the factor name
  - assignMatrix
```
public String assignMatrix(double[][] matrix)
```
    Description copied from interface: RClient
    
    Assign a 2-d matrix.
    
    Specified by:
    
    assignMatrix in interface RClient
    
    Returns:
    
    the name of the variable by which the R matrix can be referred.
  - assignMatrix
```
public String assignMatrix(DoubleMatrix<?,?> matrix)
```
    Description copied from interface: RClient
    
    Assign a 2-d matrix.
    
    Specified by:
    
    assignMatrix in interface RClient
    
    Returns:
    
    the name of the variable by which the R matrix can be referred.
  - assignMatrix
```
public String assignMatrix(DoubleMatrix<?,?> matrix,
                           org.apache.commons.collections4.Transformer rowNameExtractor)
```
    Description copied from interface: RClient
    
    Assign a 2-d matrix.
    
    Specified by:
    
    assignMatrix in interface RClient
    
    Returns:
    
    the name of the variable by which the R matrix can be referred.
  - assignStringList
```
public String assignStringList(List<?> strings)
```
    Description copied from interface: RClient
    
    Define a variable corresponding to a character array in the R context, given a List of Strings.
    
    Specified by:
    
    assignStringList in interface RClient
    
    Returns:
    
    the name of the variable in the R context.
  - booleanDoubleArrayEval
```
public boolean booleanDoubleArrayEval(String command,
                                      String argName,
                                      double[] arg)
```
    Description copied from interface: RClient
    
    Run a command that takes a double array as an argument and returns a boolean.
    
    Specified by:
    
    booleanDoubleArrayEval in interface RClient
    
    Returns:
  - dataFrame
```
public String dataFrame(ObjectMatrix<String,String,Object> matrix)
```
    Description copied from interface: RClient
    
    Convert an object matrix into an R data frame. Columns that look numeric are treated as numbers. Booleans and Strings are treated as factors.
    
    Specified by:
    
    dataFrame in interface RClient
    
    Returns:
    
    variable name in R-land.
  - dataFrameEval
```
public ObjectMatrix<String,String,Object> dataFrameEval(String command)
```
    Description copied from interface: RClient
    
    Evaluate a command that returns a dataFrame
    
    Specified by:
    
    dataFrameEval in interface RClient
    
    Returns:
    
    an ObjectMatrix representation of the data frame.
  - disconnect
```
public abstract void disconnect()
```
  - doubleArrayDoubleArrayEval
```
public double[] doubleArrayDoubleArrayEval(String command,
                                           String argName,
                                           double[] arg)
```
    Description copied from interface: RClient
    
    Run a command that has a single double array parameter, and returns a double array.
    
    Specified by:
    
    doubleArrayDoubleArrayEval in interface RClient
    
    Returns:
  - doubleArrayEval
```
public double[] doubleArrayEval(String command)
```
    Description copied from interface: RClient
    
    Run a command that returns a double array with no arguments.
    
    Specified by:
    
    doubleArrayEval in interface RClient
    
    Returns:
  - doubleArrayTwoDoubleArrayEval
```
public double[] doubleArrayTwoDoubleArrayEval(String command,
                                              String argName,
                                              double[] arg,
                                              String argName2,
                                              double[] arg2)
```
    Description copied from interface: RClient
    
    Run a command that takes two double array arguments and returns a double array.
    
    Specified by:
    
    doubleArrayTwoDoubleArrayEval in interface RClient
    
    Returns:
  - doubleTwoDoubleArrayEval
```
public double doubleTwoDoubleArrayEval(String command,
                                       String argName,
                                       double[] arg,
                                       String argName2,
                                       double[] arg2)
```
    Description copied from interface: RClient
    
    Run a command that takes two double arrays as arguments and returns a double value.
    
    Specified by:
    
    doubleTwoDoubleArrayEval in interface RClient
    
    Returns:
  - intArrayEval
```
public int[] intArrayEval(String command)
```
    Specified by:
    
    intArrayEval in interface RClient
  - linearModel
```
public LinearModelSummary linearModel(double[] data,
                                      Map<String,List<?>> factors)
```
    Description copied from interface: RClient
    
    Lower level access to linear model. Fairly simple. Factors are assigned in turn.
    
    Specified by:
    
    linearModel in interface RClient
    
    factors - Map of factorNames to factors (which can be expressed as Strings or Doubles). If you care about the order the factors are introduced into the model, use a LinkedHashMap.
  - linearModel
```
public LinearModelSummary linearModel(double[] data,
                                      ObjectMatrix<String,String,Object> d)
```
    Specified by:
    
    linearModel in interface RClient
    
    d - which will be converted to factors or continuous covariates depending on whether the columns are booleans, strings or numerical. Names of factors are the column names of the design matrix, and the rows are assumed to be in the same order as the data.
    
    Returns:
  - listEval
```
public List<?> listEval(Class<?> listEntryType,
                        String command)
```
    FIXME only partly implemented, possibly not going to stay.
    
    Specified by:
    
    listEval in interface RClient
    
    Parameters:
    
    listEntryType - a hint about what type of object you want the list to contain. If you set this to be null, the method will try to guess, but caution is advised.
    
    command - R command
    
    Returns:
  - loadLibrary
```
public boolean loadLibrary(String libraryName)
```
    Specified by:
    
    loadLibrary in interface RClient
  - oneWayAnova
```
public OneWayAnovaResult oneWayAnova(double[] data,
                                     List<String> factor)
```
    Description copied from interface: RClient
    
    Lower-level access to a simple one-way ANOVA
    
    Specified by:
    
    oneWayAnova in interface RClient
    
    Returns:
  - oneWayAnovaEval
```
public Map<String,OneWayAnovaResult> oneWayAnovaEval(String command)
```
    Specified by:
    
    oneWayAnovaEval in interface RClient
  - remove
```
public void remove(String variableName)
```
    Description copied from interface: RClient
    
    Remove a variable from the R namespace
    
    Specified by:
    
    remove in interface RClient
  - rowApplyLinearModel
```
public Map<String,LinearModelSummary> rowApplyLinearModel(String dataMatrixVarName,
                                                          String modelFormula,
                                                          String[] factorNames)
```
    Description copied from interface: RClient
    
    Run lm with anova on all the rows of a matrix
    
    Specified by:
    
    rowApplyLinearModel in interface RClient
    
    Parameters:
    
    dataMatrixVarName - from an assignment of a matrix
    
    modelFormula - and other options that will be passed as the argument to 'lm(...)', that refers to factor variables that have already been assigned, using x as the outcome. Example might be x ~ f1 + f2.
    
    Returns:
    
    map of row identifiers to populated LinearModelSummaries.
  - stringEval
```
public String stringEval(String command)
```
    Description copied from interface: RClient
    
    Evaluate any command and return a string
    
    Specified by:
    
    stringEval in interface RClient
    
    Returns:
    
    string
  - stringListEval
```
public List<String> stringListEval(String command)
```
    Specified by:
    
    stringListEval in interface RClient
  - twoWayAnova
```
public TwoWayAnovaResult twoWayAnova(double[] data,
                                     List<String> factor1,
                                     List<String> factor2,
                                     boolean includeInteraction)
```
    Description copied from interface: RClient
    
    Lower-level access to two-way ANOVA
    
    Specified by:
    
    twoWayAnova in interface RClient
    
    Returns:
    
    result with interaction term information null if includeInteraction = false
  - twoWayAnovaEval
```
public Map<String,TwoWayAnovaResult> twoWayAnovaEval(String command,
                                                     boolean withInteractions)
```
    Description copied from interface: RClient
    
    Evaluates two way anova commands of the form
    apply(matrix,1,function(x){anova(aov(x~farea+ftreat))}
    and
    apply(matrix,1,function(x){anova(aov(x~farea+ftreat+farea*ftreat))}
    where farea and ftreat have already been transposed and had factor called on them.
    
    Specified by:
    
    twoWayAnovaEval in interface RClient
    
    Returns:
  - loadScript
```
protected void loadScript(InputStream is)
```
    There is a pretty annoying limitation of this. The file must contain only one statement. You can get around this by using c(x<-1,x<-2). See testScript.R
    
    Parameters:
    
    is -

Class AbstractRClient

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface ubic.basecode.util.r.RClient

Field Detail

log

Constructor Detail

AbstractRClient

Method Detail

variableIdentityNumber

assignFactor

assignFactor

assignMatrix

assignMatrix

assignMatrix

assignStringList

booleanDoubleArrayEval

dataFrame

dataFrameEval

disconnect

doubleArrayDoubleArrayEval

doubleArrayEval

doubleArrayTwoDoubleArrayEval

doubleTwoDoubleArrayEval

intArrayEval

linearModel

linearModel

listEval

loadLibrary

oneWayAnova

oneWayAnovaEval

remove

rowApplyLinearModel

stringEval

stringListEval

twoWayAnova

twoWayAnovaEval

loadScript