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. |

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