Package ubic.basecode.math.linearmodels

Interface LinearModelSummary

All Superinterfaces:
Serializable
public interface LinearModelSummary extends Serializable

  • Field Details

  • Method Details

    • getAnova

      @Nullable GenericAnovaResult getAnova()
      Returns:
      may be null if ANOVA was not run.

    • getCoefficients

      double[] getCoefficients()

    • getContrastCoefficients

      DoubleMatrix<String,String> getContrastCoefficients()
      Returns:
      The contrast coefficients and associated statistics for all tested contrasts.

      Row names are the contrasts, for example for a model with one factor "f" with two levels "a" and "b": {"(Intercept)", "fb"}. columns are always {"Estimate" ,"Std. Error", "t value", "Pr(>|t|)"}

    • getContrastCoefficients

      Map<String,Double> getContrastCoefficients(String factorName)

    • getContrastCoefficientStderr

      Map<String,Double> getContrastCoefficientStderr(String factorName)
      For the requested factor, return the standard errors associated with the contrast coefficient estimates.

    • getContrastPValues

      Map<String,Double> getContrastPValues(String factorName)
      Returns:
      Map of pvalues for the given factor. For continuous factors or factors with only one level, there will be just one value. For factors with N>2 levels, there will be N-1 values, one for each contrast (since we compute treatment contrasts to the baseline)

    • getContrastTStats

      Map<String,Double> getContrastTStats(String factorName)
      Returns:
      Map of T statistics for the given factor. For continuous factors or factors with only one level, there will be just one value. For factors with N>2 levels, there will be N-1 values, one for each contrast (since we compute treatment contrasts to the baseline)

    • getEffects

      double[] getEffects()

    • getFStat

      double getFStat()
      Returns:
      F statistic for overall model fit.

    • getFactorNames

      List<String> getFactorNames()
      Returns:
      the factorNames

    • getInterceptCoefficient

      double getInterceptCoefficient()

    • getInterceptPValue

      double getInterceptPValue()

    • getInterceptTStat

      double getInterceptTStat()

    • getKey

      String getKey()

    • getNumeratorDof

      double getNumeratorDof()

    • getOverallPValue

      double getOverallPValue()
      Overall p value for F stat of model fit (upper tail probability)
      Returns:
      value or NaN if it can't be computed for some reason

    • getPriorDof

      double getPriorDof()
      Returns:
      the priorDof

    • getResidualsDof

      double getResidualsDof()

    • getResiduals

      double[] getResiduals()
      Returns:
      the residuals

    • getRSquared

      double getRSquared()
      Returns:
      the rSquared

    • getAdjRSquared

      double getAdjRSquared()
      Returns:
      the adjRSquared

    • getSigma

      double getSigma()
      Residual standard deviation

    • getStdevUnscaled

      double[] getStdevUnscaled()
      Unscaled standard deviations for the coefficient estimators in same order as coefficients. The standard errors are given by stdev.unscaled * sigma (a la limma)

    • isBaseline

      boolean isBaseline(String factorValueName)

    • isShrunken

      boolean isShrunken()
      Whether this is the result of emprical bayes shrinkage of variance estimates