Blissindependence       Bliss Independence Model
GetStartGuess           Estimate initial values for dose-response curve
                        fit
L4                      4-parameter logistic dose-response function
addResids               Add residuals by adding to mean effects
backscaleResids         Backscale residuals
bootConfInt             Obtain confidence intervals for the raw effect
                        sizes on every off-axis point and overall
boxcox.transformation   Apply two-parameter Box-Cox transformation
coef.MarginalFit        Coefficients from marginal model estimation
col2hex                 R color to RGB (red/green/blue) conversion.
constructFormula        Construct a model formula from parameter
                        constraint matrix
contour.ResponseSurface
                        Method for plotting of contours based on maxR
                        statistics
df.residual.MarginalFit
                        Residual degrees of freedom in marginal model
                        estimation
directAntivirals        Partial data with combination experiments of
                        direct-acting antivirals
directAntivirals_ALL    Full data with combination experiments of
                        direct-acting antivirals
fitMarginals            Fit two 4-parameter log-logistic functions for
                        a synergy experiment
fitSurface              Fit response surface model and compute meanR
                        and maxR statistics
fitted.MarginalFit      Compute fitted values from monotherapy
                        estimation
fitted.ResponseSurface
                        Predicted values of the response surface
                        according to the given null model
generalizedLoewe        Compute combined predicted response from drug
                        doses according to standard or generalized
                        Loewe model.
generateData            Generate data from parameters of marginal
                        monotherapy model
get.abs_tval            Return absolute t-value, used in optimization
                        call in 'optim.boxcox'
get.summ.data           Summarize data by factor
getCP                   Estimate CP matrix from bootstraps
getR                    Helper functions for the test statistics
getTransformations      Return a list with transformation functions
getd1d2                 A function to get the d1d2 identifier
harbronLoewe            Alternative Loewe generalization
hsa                     Highest Single Agent model
initialMarginal         Estimate initial values for fitting marginal
                        dose-response curves
isobologram             Isobologram of the response surface predicted
                        by the null model
marginalNLS             Fit two 4-parameter log-logistic functions with
                        non-linear least squares
marginalOptim           Fit two 4-parameter log-logistic functions with
                        common baseline
maxR                    Compute maxR statistic for each off-axis dose
                        combination
meanR                   Compute meanR statistic for the estimated model
modelVar                Calculate model variance, assuming variance
                        increases linearly with mean
optim.boxcox            Find optimal Box-Cox transformation parameters
outsidePoints           List non-additive points
plot.BIGLconfInt        Plot confidence intervals in a contour plot
plot.MarginalFit        Plot monotherapy curve estimates
plot.ResponseSurface    Method for plotting response surface objects
plot.effect-size        Plot of effect-size object
plot.maxR               Plot of maxR object
plot.meanR              Plot bootstrapped cumulative distribution
                        function of meanR null distribution
plotConfInt             Plot confidence intervals from BIGL object in a
                        contour plot
plotMeanVarFit          Make a mean-variance plot
plotResponseSurface     Plot response surface
predict.MarginalFit     Predict values on the dose-response curve
predictOffAxis          Compute off-axis predictions
predictResponseSurface
                        Predict the entire response surface, so
                        including on-axis points, and return the result
                        as a matrix. For plotting purposes.
predictVar              Predict variance
print.summary.BIGLconfInt
                        Print summary of BIGLconfInt object
print.summary.MarginalFit
                        Print method for summary of 'MarginalFit'
                        object
print.summary.ResponseSurface
                        Print method for the summary function of
                        'ResponseSurface' object
print.summary.maxR      Print summary of maxR object
print.summary.meanR     Print summary of meanR object
residuals.MarginalFit   Residuals from marginal model estimation
runBIGL                 Run the BIGL application for demonstrating
                        response surfaces
sampleResids            Sample residuals according to a new model
scaleResids             Functions for scaling, and rescaling residuals.
                        May lead to unstable behaviour in practice
simulateNull            Simulate data from a given null model and
                        monotherapy coefficients
summary.BIGLconfInt     Summary of confidence intervals object
summary.MarginalFit     Summary of 'MarginalFit' object
summary.ResponseSurface
                        Summary of 'ResponseSurface' object
summary.maxR            Summary of maxR object
summary.meanR           Summary of meanR object
synergy_plot_bycomp     Plot 2D cross section of response surface
vcov.MarginalFit        Estimate of coefficient variance-covariance
                        matrix
wildbootAddResids       Sample residuals according to a new model
