Biochemically Intuitive Generalized Loewe Model
Plot response surface
Predict values on the dose-response curve
Functions for scaling, and rescaling residuals. May lead to unstable b...
Apply two-parameter Box-Cox transformation
Coefficients from marginal model estimation
R color to RGB (red/green/blue) conversion.
Calculate model variance, assuming variance increases linearly with me...
Add residuals by adding to mean effects
Backscale residuals
Bliss Independence Model
Obtain confidence intervals for the raw effect sizes on every off-axis...
Construct a model formula from parameter constraint matrix
Method for plotting of contours based on maxR statistics
Residual degrees of freedom in marginal model estimation
Fit two 4-parameter log-logistic functions for a synergy experiment
Fit response surface model and compute meanR and maxR statistics
Compute fitted values from monotherapy estimation
Predicted values of the response surface according to the given null m...
Compute combined predicted response from drug doses according to stand...
Generate data from parameters of marginal monotherapy model
Return absolute t-value, used in optimization call in optim.boxcox
Summarize data by factor
Find optimal Box-Cox transformation parameters
Estimate CP matrix from bootstraps
A function to get the d1d2 identifier
Helper functions for the test statistics
Estimate initial values for dose-response curve fit
Return a list with transformation functions
Alternative Loewe generalization
Highest Single Agent model
List non-additive points
Estimate initial values for fitting marginal dose-response curves
Isobologram of the response surface predicted by the null model
4-parameter logistic dose-response function
Fit two 4-parameter log-logistic functions with non-linear least squar...
Fit two 4-parameter log-logistic functions with common baseline
Compute maxR statistic for each off-axis dose combination
Compute meanR statistic for the estimated model
Plot confidence intervals in a contour plot
Plot of effect-size object
Plot monotherapy curve estimates
Plot of maxR object
Plot bootstrapped cumulative distribution function of meanR null distr...
Method for plotting response surface objects
Plot confidence intervals from BIGL object in a contour plot
Make a mean-variance plot
Compute off-axis predictions
Predict the entire response surface, so including on-axis points, and ...
Predict variance
Print summary of BIGLconfInt object
Print method for summary of MarginalFit object
Print summary of maxR object
Print summary of meanR object
Print method for the summary function of ResponseSurface object
Residuals from marginal model estimation
Run the BIGL application for demonstrating response surfaces
Sample residuals according to a new model
Simulate data from a given null model and monotherapy coefficients
Summary of confidence intervals object
Summary of MarginalFit object
Summary of maxR object
Summary of meanR object
Summary of ResponseSurface object
Plot 2D cross section of response surface
Estimate of coefficient variance-covariance matrix
Sample residuals according to a new model
Response surface methods for drug synergy analysis. Available methods include generalized and classical Loewe formulations as well as Highest Single Agent methodology. Response surfaces can be plotted in an interactive 3-D plot and formal statistical tests for presence of synergistic effects are available. Implemented methods and tests are described in the article "BIGL: Biochemically Intuitive Generalized Loewe null model for prediction of the expected combined effect compatible with partial agonism and antagonism" by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas, Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017) <doi:10.1038/s41598-017-18068-5>.