Package ubic.basecode.math.linearmodels

Interface LinearModelSummary

    • Method Detail

      • 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|)"}

      • 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()

      • 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