Biochemically Intuitive Generalized Loewe Model

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Documentation for package ‘BIGL’ version 1.9.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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'
get.summ.data	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