Package ubic.basecode.util.r

Interface RClient

All Known Implementing Classes:
AbstractRClient, JRIClient, RServeClient
public interface RClient
Abstraction of a connection to R
Author:
Paul

  • Method Details

    • 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)