Man pages for dlill/MRAr
Functions to do MRA with
| algo | Run the algorithm |
| algo_noisy | Run the algorithm |
| cluster_matrices_and_print_perturbations | clustering and print function |
| combine_dr_list | Combine a list of dose_response data.frames with different... |
| dose_response_fun | Compute dose-response curves |
| expand.grid.alt | Alternative version of expand.grid |
| get_r0_r1_ropt_rkept | Get the relevant matrices for a perturbation and... |
| local_response_matrix_eq10 | Calculate the local response matrix r from the global... |
| mname.function | This function is needed such that the new mstrust works with... |
| obj_alpha | Objective function to minimize certain elements of the local... |
| obj_alpha_no_derivs | Objective function which doesn't compute derivatives |
| p_ic_fun | Automatically generate parameter trafos to quickly test... |
| p_ic_list_fun | Generate a list of parameter trafos. |
| plot_dose_response | Plot dose_response curves |
| p_pert_fun | Convenient simulation of perturbation experiments |
| r_alpha_fun | Parametric local response matrix |
| reduce_ic_list | Reduce list of initial conditions to include only pars with... |
| R_fun | Compute R from fractional changes of steady states |
| R_fun_2 | Compute R from fractional changes of steady states, but do... |
| r_kept_fun | Which elements to keep in the optimization procedure? |
| r_kept_fun2 | Function to compare two local response matrices in order to... |
| r_opt_dose_response | Compute dose responses for one parameter |
| r_opt_dose_response_separate_scanning | Compute dose responses for one parameter, scan pars_opt... |
| ropt_gadget | Shiny Gadget for quick exploration of Complexes and alpha |
| run_different_perturbations | Run a set of different perturbations over varying alphas and... |
| run_different_perturbations_noisy | Run the simulations and add noise to the data |
| run_different_perturbations_noisy_with_replicates | Run the simulations and add noise to the data |
| run_simulations | Run the optimization procedure at many conditions (old, not... |
| run_simulations_with_noise | Run simulations with noise |
| runsteadyC | Interface to runsteady() |
| scan_grid | Scan a n-d grid of free parameters |
| svdinv | Inverse of matrix using singular value decomposition |
| which_pars_opt | Which pars_opt are associated with an element kept in the... |
| Xs_steady | Steady state prediction function for ODE models. |
