Man pages for mrgsolve
Simulate from ODE-Based Models
| aboutsolver | About the lsoda differential equation solver used by mrgsolve |
| as_data_set | Create a simulation data set from ev objects or data frames |
| as_deslist | Create a list of designs from a data frame |
| as.ev | Coerce an object to class ev |
| as.list-mrgmod-method | Coerce a model object to list |
| as.list-mrgsims-method | Coerce an mrgsims object to list |
| BLOCK_PARSE | Functions to parse code blocks |
| blocks | Return the code blocks from a model specification file |
| cama | Run the model cama function |
| carry_out | Select items to carry into simulated output |
| check_data_names | Check input data set names against model parameters |
| cmt_list-class | S4 cmt_list class |
| cmtn | Get the compartment number from a compartment name |
| code | Extract the code from a model |
| collapse_matrices | Collapse OMEGA or SIGMA matrix lists |
| collapse_matrix | Collapse the matrices of a matlist object |
| custom_tol | Customize tolerances for specific compartments |
| cvec | Create create character vectors |
| data_set | Select and modify a data set for simulation |
| design | Set observation designs for the simulation |
| details | Extract model details |
| env_eval | Re-evaluate the code in the ENV block |
| env_get | Return model environment |
| env_ls | List objects in the model environment |
| env_update | Update objects in model environment |
| ev | Event objects for simulating PK and other interventions |
| ev_assign | Replicate a list of events into a data set |
| ev-class | S4 events class |
| evd | Create an event object with data-like names |
| ev_days | Schedule dosing events on days of the week |
| ev_dplyr | dplyr verbs for event objects |
| ev_extract | Select columns from an ev object |
| ev_methods | Various methods for event objects |
| ev_ops | Operations for ev objects |
| ev_rep | Replicate an event object |
| ev_repeat | Repeat a block of dosing events |
| ev_rx | Create intervention objects from Rx input |
| ev_seq | Schedule a series of event objects |
| exdatasets | Example input data sets |
| expand.idata | Create template data sets for simulation |
| expand_observations | Insert observations into a data set |
| file_show | Show model specification and C++ files |
| get_tol | Extract rtol and atol information from a model object |
| house | Return a pre-compiled, PK/PD model |
| idata_set | Select and modify a idata set for simulation |
| init | Methods for working with the model compartment list |
| inventory | Check whether all required parameters needed in a model are... |
| is.mrgmod | Check if an object is a model object |
| is.mrgsims | Check if an object is mrgsims output |
| knobs | Run sensitivity analysis on model settings |
| lctran | Change the case of nmtran-like data items |
| loadso | Load the model shared object |
| lower2matrix | Create a square numeric matrix from the lower-triangular... |
| matlist | Methods for working with matrix-list objects |
| matlist-class | S4 class matlist |
| matlist_ops | Operations with matlist objects |
| matrix_converters | Coerce R objects to block or diagonal matrices |
| matrix_helpers | Create matrices from vector input |
| mcode | Write, compile, and load model code |
| mcRNG | Set RNG to use L'Ecuyer-CMRG |
| merge | Merge two lists |
| mod | Return the model object |
| modelparse | Parse model specification text |
| modlib | Internal model library |
| modlib_details | modlib: PK/PD Model parameters, compartments, and output... |
| modlib_pk | modlib: Pharmacokinetic models |
| modlib_pkpd | modlib: Pharmacokinetic / pharmacodynamic models |
| modlib_tmdd | modlib: Target mediated disposition model |
| modlib_viral | modlib: HCV viral dynamics models |
| modMATRIX | Create a matrix |
| mread | Read a model specification file |
| mread_yaml | Read a model from yaml format |
| mrgmod-class | S4 class for mrgsolve model object |
| mrgmod_extract | Select parameter values from a model object |
| mrgsim | Simulate from a model object |
| mrgsim_q | Simulate from a model object with quicker turnaround |
| mrgsims | Methods for working with 'mrgsims' objects |
| mrgsims-class | S4 class for mrgsolve simulation output |
| mrgsims_dplyr | Methods for handling output with dplyr verbs |
| mrgsims_modify | Methods for modifying mrgsims objects |
| mrgsim_variants | mrgsim variant functions |
| mrgsolve_package | mrgsolve: Simulate from ODE-Based Models |
| mvgauss | Simulate from a multivariate normal distribution with mean... |
| mwrite_cpp | Write a model to native mrgsolve format |
| mwrite_yaml | Write model code to yaml format |
| names-mrgmod-method | Get all names from a model object |
| nmext | Import model estimates from a NONMEM ext file |
| nmxml | Import model estimates from a NONMEM xml file |
| numeric2diag | Create a diagonal numeric matrix from diagonal elements |
| numericlist | Methods for numericlist |
| numericlist-class | S4 class numeric list |
| numerics_only | Prepare data.frame for input to mrgsim() |
| obsaug | Augment observations in the simulated output |
| obsonly | Collect only observation records in the simulated output |
| omega | Manipulate OMEGA matrices |
| outvars | Show names of current output variables |
| param | Create and work with parameter objects |
| parameter_list-class | S4 parameter_list class |
| param_tags | Return parameter tags |
| PKMODEL | Parse PKMODEL BLOCK data |
| plot_batch_mrgsims | Plot method for mrgsims objects |
| plot_mrgsims | Generate a quick plot of simulated data |
| plot_sims | Plot data as an mrgsims object |
| qsim | Basic, simple simulation from model object |
| read_nmext | Extract estimates from NONMEM ext file |
| realize_addl | Make addl doses explicit in an event object or data set |
| reexports | Objects exported from other packages |
| render | Render a model to a document |
| Req | Request simulated output |
| reserved | Reserved words |
| reset_tol | Reset all model tolerances |
| revar | Get model random effect variances and covariances |
| scrape_and_call | Scrape options and pass to function |
| scrape_opts | Scrape options from a code block |
| see | Print model code to the console |
| show-cmt_list-method | Show the compartment list |
| show-mrgmod-method | Print model details |
| show-parameter_list-method | Show the parameter list |
| sigma | Manipulate SIGMA matrices |
| simargs | Access or clear arguments for calls to mrgsim() |
| soloc | Return the location of the model shared object |
| solversettings | Optional inputs for lsoda |
| stime | Get the times at which the model will be evaluated |
| summary.mrgmod | Print summary of a mrgmod object |
| tgrid | Create a simtime object |
| tgrid_ops | Operations with tgrid objects |
| touch_funs | Get inits from compiled function |
| tscale | Re-scale time in the simulated output |
| update | Update the model object |
| use_custom_tol | Set up a model object to use either scalar or custom... |
| valid_data_set | Validate and prepare data sets for simulation |
| valid_idata_set | Validate and prepare idata data sets for simulation |
| wf_sweep | Simulate a sequence of parameters |
| within | Update parameters, initials, and settings within a model... |
| zchain | Forward pipe |
| zero_re | Zero out random effects in a model object |
