RClient (baseCode 1.2-SNAPSHOT API)

All Known Implementing Classes:

AbstractRClient, JRIClient, RServeClient
```
public interface RClient
```
Abstraction of a connection to R

Author:

Paul

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`void`	`assign(String argName, double[] arg)`
`void`	`assign(String arg0, int[] arg1)`
`void`	`assign(String sym, String ct)`
`void`	`assign(String argName, String[] array)`
`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<?> objects)` 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
`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.
`org.rosuda.REngine.REXP`	`eval(String command)` Evaluate the given command
`String`	`getLastError()`
`int[]`	`intArrayEval(String command)`
`boolean`	`isConnected()`
`LinearModelSummary`	`linearModel(double[] data, Map<String,List<?>> factors)` Lower level access to linear model.
`LinearModelSummary`	`linearModel(double[] data, ObjectMatrix<String,String,Object> design)`
`List<?>`	`listEval(Class<?> listEntryType, String command)`
`boolean`	`loadLibrary(String libraryName)`
`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
`DoubleMatrix<String,String>`	`retrieveMatrix(String variableName)` Get a matrix back out of the R context.
`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.
`void`	`voidEval(String command)`

- Method Detail
  - assign
```
void assign(String argName,
            double[] arg)
```
    Parameters:
    
    argName -
    
    arg -
  - assign
```
void assign(String arg0,
            int[] arg1)
```
  - assign
```
void assign(String sym,
            String ct)
```
  - assign
```
void assign(String argName,
            String[] array)
```
  - assignFactor
```
String assignFactor(List<String> strings)
```
    Parameters:
    
    strings -
    
    Returns:
    
    the name of the factor generated.
  - assignFactor
```
String assignFactor(String factorName,
                    List<String> list)
```
    Parameters:
    
    factorName -
    
    list -
    
    Returns:
    
    the factor name
  - assignMatrix
```
String assignMatrix(double[][] matrix)
```
    Assign a 2-d matrix.
    
    Parameters:
    
    matrix -
    
    Returns:
    
    the name of the variable by which the R matrix can be referred.
  - assignMatrix
```
String assignMatrix(DoubleMatrix<?,?> matrix)
```
    Assign a 2-d matrix.
    
    Parameters:
    
    matrix -
    
    Returns:
    
    the name of the variable by which the R matrix can be referred.
  - assignMatrix
```
String assignMatrix(DoubleMatrix<?,?> matrix,
                    org.apache.commons.collections4.Transformer rowNameExtractor)
```
    Assign a 2-d matrix.
    
    Parameters:
    
    matrix -
    
    rowNameExtractor -
    
    Returns:
    
    the name of the variable by which the R matrix can be referred.
  - assignStringList
```
String assignStringList(List<?> objects)
```
    Define a variable corresponding to a character array in the R context, given a List of Strings.
    
    Parameters:
    
    objects, - which will be stringified if they are not strings.
    
    Returns:
    
    the name of the variable in the R context.
  - booleanDoubleArrayEval
```
boolean booleanDoubleArrayEval(String command,
                               String argName,
                               double[] arg)
```
    Run a command that takes a double array as an argument and returns a boolean.
    
    Parameters:
    
    command -
    
    argName -
    
    arg -
    
    Returns:
  - dataFrame
```
String dataFrame(ObjectMatrix<String,String,Object> matrix)
```
    Convert an object matrix into an R data frame. Columns that look numeric are treated as numbers. Booleans and Strings are treated as factors.
    
    Parameters:
    
    matrix -
    
    Returns:
    
    variable name in R-land.
  - dataFrameEval
```
ObjectMatrix<String,String,Object> dataFrameEval(String command)
```
    Evaluate a command that returns a dataFrame
    
    Parameters:
    
    command -
    
    Returns:
    
    an ObjectMatrix representation of the data frame.
  - doubleArrayDoubleArrayEval
```
double[] doubleArrayDoubleArrayEval(String command,
                                    String argName,
                                    double[] arg)
```
    Run a command that has a single double array parameter, and returns a double array.
    
    Parameters:
    
    command -
    
    argName -
    
    arg -
    
    Returns:
  - doubleArrayEval
```
double[] doubleArrayEval(String command)
```
    Run a command that returns a double array with no arguments.
    
    Parameters:
    
    command -
    
    Returns:
  - doubleArrayTwoDoubleArrayEval
```
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.
    
    Parameters:
    
    command -
    
    argName -
    
    arg -
    
    argName2 -
    
    arg2 -
    
    Returns:
  - doubleTwoDoubleArrayEval
```
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.
    
    Parameters:
    
    command -
    
    argName -
    
    arg -
    
    argName2 -
    
    arg2 -
    
    Returns:
  - eval
```
org.rosuda.REngine.REXP eval(String command)
```
    Evaluate the given command
    
    Parameters:
    
    command -
    
    Returns:
  - getLastError
```
String getLastError()
```
  - intArrayEval
```
int[] intArrayEval(String command)
```
  - isConnected
```
boolean isConnected()
```
  - linearModel
```
LinearModelSummary linearModel(double[] data,
                               Map<String,List<?>> factors)
```
    Lower level access to linear model. Fairly simple. Factors are assigned in turn.
    
    Parameters:
    
    data -
    
    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
```
LinearModelSummary linearModel(double[] data,
                               ObjectMatrix<String,String,Object> design)
```
    Parameters:
    
    data -
    
    design - 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
```
List<?> listEval(Class<?> listEntryType,
                 String command)
```
    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
```
boolean loadLibrary(String libraryName)
```
  - oneWayAnova
```
OneWayAnovaResult oneWayAnova(double[] data,
                              List<String> factor)
```
    Lower-level access to a simple one-way ANOVA
    
    Parameters:
    
    data -
    
    factor -
    
    Returns:
  - oneWayAnovaEval
```
Map<String,OneWayAnovaResult> oneWayAnovaEval(String command)
```
  - remove
```
void remove(String variableName)
```
    Remove a variable from the R namespace
    
    Parameters:
    
    variableName -
  - retrieveMatrix
```
DoubleMatrix<String,String> retrieveMatrix(String variableName)
```
    Get a matrix back out of the R context. Row and Column names are filled in for the resulting object, if they are present.
    
    Parameters:
    
    variableName -
    
    Returns:
  - rowApplyLinearModel
```
Map<String,LinearModelSummary> rowApplyLinearModel(String dataMatrixVarName,
                                                   String modelFormula,
                                                   String[] factorNames)
```
    Run lm with anova on all the rows of a matrix
    
    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.
    
    names - of the factors like {"f1", "f2"}.
    
    Returns:
    
    map of row identifiers to populated LinearModelSummaries.
  - stringEval
```
String stringEval(String command)
```
    Evaluate any command and return a string
    
    Parameters:
    
    command -
    
    Returns:
    
    string
  - stringListEval
```
List<String> stringListEval(String command)
```
  - twoWayAnova
```
TwoWayAnovaResult twoWayAnova(double[] data,
                              List<String> factor1,
                              List<String> factor2,
                              boolean includeInteraction)
```
    Lower-level access to two-way ANOVA
    
    Parameters:
    
    data -
    
    factor1 -
    
    factor2 -
    
    includeInteraction -
    
    Returns:
    
    result with interaction term information null if includeInteraction = false
  - twoWayAnovaEval
```
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.
    
    Parameters:
    
    command -
    
    Returns:
  - voidEval
```
void voidEval(String command)
```

Interface RClient

Method Summary

Method Detail

assign

assign

assign

assign

assignFactor

assignFactor

assignMatrix

assignMatrix

assignMatrix

assignStringList

booleanDoubleArrayEval

dataFrame

dataFrameEval

doubleArrayDoubleArrayEval

doubleArrayEval

doubleArrayTwoDoubleArrayEval

doubleTwoDoubleArrayEval

eval

getLastError

intArrayEval

isConnected

linearModel

linearModel

listEval

loadLibrary

oneWayAnova

oneWayAnovaEval

remove

retrieveMatrix

rowApplyLinearModel

stringEval

stringListEval

twoWayAnova

twoWayAnovaEval

voidEval