Man pages for openanalytics/BIGL
Biochemically Intuitive Generalized Loewe Model
| 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... |
| 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... |
| directAntivirals_ALL | Full data with combination experiments of direct-acting... |
| fitMarginals | Fit two 4-parameter log-logistic functions for a synergy... |
| fitSurface | Fit response surface model and compute meanR and maxR... |
| fitted.MarginalFit | Compute fitted values from monotherapy estimation |
| fitted.ResponseSurface | Predicted values of the response surface according to the... |
| generalizedLoewe | Compute combined predicted response from drug doses according... |
| generateData | Generate data from parameters of marginal monotherapy model |
| get.abs_tval | Return absolute t-value, used in optimization call in... |
| 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 |
| get.summ.data | Summarize data by factor |
| 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... |
| isobologram | Isobologram of the response surface predicted by the null... |
| L4 | 4-parameter logistic dose-response function |
| marginalNLS | Fit two 4-parameter log-logistic functions with non-linear... |
| marginalOptim | Fit two 4-parameter log-logistic functions with common... |
| 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... |
| optim.boxcox | Find optimal Box-Cox transformation parameters |
| outsidePoints | List non-additive points |
| plot.BIGLconfInt | Plot confidence intervals in a contour plot |
| plotConfInt | Plot confidence intervals from BIGL object 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... |
| plotMeanVarFit | Make a mean-variance plot |
| plotResponseSurface | Plot response surface |
| plot.ResponseSurface | Method for plotting response surface objects |
| predict.MarginalFit | Predict values on the dose-response curve |
| predictOffAxis | Compute off-axis predictions |
| predictResponseSurface | Predict the entire response surface, so including on-axis... |
| 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'... |
| 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... |
| simulateNull | Simulate data from a given null model and monotherapy... |
| 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 |
