# Biochemically Intuitive Generalized Loewe Model

## Documentation for package ‘BIGL’ version 1.9.3

- 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