Biochemically Intuitive Generalized Loewe Model

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Documentation for package ‘BIGL’ version 1.9.1

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addResids Add residuals by adding to mean effects
backscaleResids Backscale residuals
Blissindependence Bliss Independence Model
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' Summarize data by factor
getCP Estimate CP matrix from bootstraps
getd1d2 A function to get the d1d2 identifier
getR Helper functions for the test statistics
GetStartGuess Estimate initial values for dose-response curve fit
getTransformations Return a list with transformation functions
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
L4 4-parameter logistic dose-response function
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.effect-size Plot of effect-size object
plot.MarginalFit Plot monotherapy curve estimates
plot.maxR Plot of maxR object
plot.meanR Plot bootstrapped cumulative distribution function of meanR null distribution
plot.ResponseSurface Method for plotting response surface objects
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.maxR Print summary of maxR object
print.summary.meanR Print summary of meanR object
print.summary.ResponseSurface Print method for the summary function of 'ResponseSurface' 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.maxR Summary of maxR object
summary.meanR Summary of meanR object
summary.ResponseSurface Summary of 'ResponseSurface' 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