Man pages for acorg/ablandscapes
Making Antibody landscapes Using R
| ablandscape.control | Get defaults for antibody landscape fitting |
| ablandscape.delta.fit | Fitting an antibody delta landscape |
| ablandscape.fit | Fitting with antibody landscapes |
| ablandscape.par | Get defaults for antibody landscape plotting |
| build_lndscp | Build an antibody landscape |
| calc_mean_titer_negll | Calculate the total negative log-likelihood of a mean titer |
| calc_titer_diffs | Get titer differences |
| calc_titer_lims | Get titer limits |
| fit_ci2coords | Get landscape confidence interval |
| fit_height2point | Fit landscape to single coordinate point |
| fit_lndscp2coords | Fit landscape to a set of coordinates |
| fit_lndscp2point | Fit landscape to single coordinate point |
| h3coords2015 | Antigenic coordinates of H3N2 influenza strains. |
| lndscp3d_map | Generate a 3D map plot for an antibody landscape |
| lndscp3d_surface | Add a surface to a 3d landscape plot |
| lndscp3d_titers | Add titer impulses to a 3d landscape plot |
| lndscp_checkChull | Check if coordinates are within convex hull of ag coordinates |
| lndscp_contour_ggplot | Plot an ablandscape contour plot |
| lndscp.cv.test | Perform cross-validation testing |
| lndscp_r3jsplot | View method for the antibody landscape object |
| logfoldchange.mean | Function for calculating the mean foldchange from a group of... |
| logtiter.mean | Calculate the geometric mean titer |
| mean_fromlims | Calculate maximum likelihood mean from measurement limits |
| model_lndscp_height | Function to model the landscape height |
| negll_titer_lm | Calculate the negative log likelihood of a linear model |
| plot.cv.summary | Plotting CV summary results |
| predict.ablandscape.fit | Predict method for antibody landscapes |
| summary.lndscp.cv | Print a summary of cv testing results |
| tricubic.weights | Calculate the antigen weights |
