| mrgsolve: Simulate from ODE-Based Models | mrgsolve-package mrgsolve |
| Select columns from an ev object | $,ev-method [[,ev-method |
| Select parameter values from a model object | $,mrgmod-method [,mrgmod-method [[,mrgmod-method |
| About the lsoda differential equation solver used by mrgsolve | aboutsolver |
| Coerce R objects to block or diagonal matrices | as_bmat as_bmat,ANY-method as_bmat,data.frame-method as_bmat,list-method as_bmat,numeric-method as_cmat as_dmat as_dmat,ANY-method as_dmat,data.frame-method as_dmat,list-method as_dmat,numeric-method |
| Create a simulation data set from ev objects or data frames | as_data_set as_data_set,data.frame-method as_data_set,ev-method |
| Create a list of designs from a data frame | as_deslist |
| Coerce an object to class ev | as.ev as.ev,data.frame-method as.ev,ev-method |
| Coerce a model object to list | as.list,mrgmod-method |
| Coerce an mrgsims object to list | as.list,mrgsims-method |
| Functions to parse code blocks | BLOCK_PARSE CAPTURE CMT FIXED HANDLEMATRIX INIT PARAM THETA |
| Return the code blocks from a model specification file | blocks blocks,character-method blocks,mrgmod-method |
| Operations with matlist objects | c,matlist-method |
| Operations with tgrid objects | *,tgrid,numeric-method *,tgrids,numeric-method +,tgrid,numeric-method +,tgrids,numeric-method c,tgrid-method c,tgrids-method tgrids_*_numeric tgrids_+_numeric tgrid_*_numeric tgrid_+_numeric |
| Select items to carry into simulated output | carry.out carry_out |
| Check input data set names against model parameters | check_data_names |
| Get the compartment number from a compartment name | cmtn cmtn,mrgmod-method |
| Extract the code from a model | code |
| Collapse the matrices of a matlist object | collapse_matrix |
| Collapse OMEGA or SIGMA matrix lists | collapse_omega collapse_sigma |
| Customize tolerances for specific compartments | custom_atol custom_rtol custom_tol |
| Select a data set for simulation | data_set data_set,mrgmod,ANY-method data_set,mrgmod,data.frame-method data_set,mrgmod,ev-method |
| Set observation designs for the simulation | design |
| Extract model details | details |
| DSL preprocessing functions | convert_fort_if convert_pow convert_semicolons dsl_preprocess warn_int_div |
| Re-evaluate the code in the ENV block | env_eval |
| Return model environment or objects from the model environment | env_get env_get.mrgmod env_get.mrgsims env_get_env env_get_env.mrgmod env_get_env.mrgsims env_get_obj |
| List objects in the model environment | env_ls |
| Update objects in model environment | env_update |
| Event objects for simulating PK and other interventions | ev ev,ev-method ev,missing-method ev,mrgmod-method |
| Replicate a list of events into a data set | assign_ev ev_assign |
| Schedule dosing events on days of the week | ev_days |
| Replicate an event object | ev_rep |
| Repeat a block of dosing events | ev_repeat |
| Create intervention objects from Rx input | ev_rx ev_rx,character,missing-method ev_rx,mrgmod,character-method parse_rx |
| Schedule a series of event objects | ev_seq seq.ev |
| Create an event object with data-like names | as.evd evd evd,ev-method evd,missing-method evd,mrgmod-method |
| Example input data sets | exBoot exdatasets exidata exTheoph extran1 extran2 extran3 |
| Insert observations into a data set | expand_observations |
| Create template data sets for simulation | evd_expand ev_expand expand.ev expand.evd expand.idata |
| Extract rtol and atol information from a model object | get_tol get_tol_list |
| Select a idata set for simulation | idata_set idata_set,mrgmod,ANY-method idata_set,mrgmod,data.frame-method |
| Methods for working with the model compartment list | init init,ANY-method init,list-method init,missing-method init,mrgmod-method init,mrgsims-method |
| Check whether all required parameters needed in a model are present in an object | inventory |
| Check if an object is a model object | is.mrgmod |
| Check if an object is mrgsims output | is.mrgsims |
| DEFUNCT: Run sensitivity analysis on model settings | knobs |
| Change the case of nmtran-like data items | lctran lctran.data.frame lctran.ev uctran uctran.data.frame uctran.ev |
| Load the model shared object | loadso loadso.mrgmod |
| Create matrices from vector input | bmat cmat dmat matrix_helpers |
| Write, compile, and load model code | mcode mcode_cache |
| Set RNG to use L'Ecuyer-CMRG | mcRNG |
| Internal model library | modlib |
| modlib: PK/PD Model parameters, compartments, and output variables | modlib_details |
| modlib: Pharmacokinetic models | modlib_pk |
| modlib: Pharmacokinetic / pharmacodynamic models | modlib_pkpd |
| modlib: Target mediated disposition model | modlib_tmdd |
| modlib: HCV viral dynamics models | modlib_viral |
| Read a model specification file | mread mread_cache mread_file |
| Read a model from yaml format | mread_yaml yaml_to_cpp |
| Simulate from a model object | do_mrgsim mrgsim mrgsim_df |
| Simulate from a model object with quicker turnaround | mrgsim_q |
| mrgsim variant functions | mrgsim_0 mrgsim_d mrgsim_di mrgsim_e mrgsim_ei mrgsim_i mrgsim_variants |
| Methods for handling output with dplyr verbs | as.tbl.mrgsims as_data_frame.mrgsims as_tibble.mrgsims distinct.mrgsims do.mrgsims filter.mrgsims group_by.mrgsims mrgsims_dplyr mutate.mrgsims pull.mrgsims select.mrgsims slice.mrgsims summarise.each summarise.mrgsims |
| Methods for modifying mrgsims objects | filter_sims mrgsims_modify mutate_sims select_sims |
| dplyr verbs for event objects | filter.ev mutate.ev select.ev |
| Write a model to native mrgsolve format | mwrite_cpp |
| Write model code to yaml format | mwrite_yaml |
| Get all names from a model object | names,mrgmod-method |
| Import model estimates from a NONMEM ext file | nmext |
| Import model estimates from a NONMEM xml file | NMXML nmxml |
| Prepare data.frame for input to mrgsim() | numerics_only |
| Augment observations in the simulated output | obsaug |
| Collect only observation records in the simulated output | obsonly |
| Manipulate OMEGA matrices | omat omat,list-method omat,matrix-method omat,missing-method omat,mrgmod-method omat,mrgsims-method omat,NULL-method omat,omegalist-method OMEGA omega |
| Show names of current output variables | outvars |
| Create and work with parameter objects | allparam param param,ANY-method param,list-method param,missing-method param,mrgmod-method param,mrgsims-method |
| Return parameter tags | param_tags |
| Parse PKMODEL BLOCK data | PKMODEL |
| Generate a quick plot of simulated data | plot plot,mrgsims,character-method plot,mrgsims,formula-method plot,mrgsims,missing-method plot_mrgsims |
| Plot data as an mrgsims object | plot_sims |
| Basic, simple simulation from model object | qsim |
| Extract estimates from NONMEM ext file | read_nmext |
| Make addl doses explicit in an event object or data set | realize_addl realize_addl.data.frame realize_addl.ev |
| Request simulated output | Req req req.mrgmod |
| Reserved words | reserved |
| Reset all model tolerances | reset_atol reset_rtol reset_tol |
| Get model random effect variances and covariances | revar revar,mrgmod-method |
| Print model code to the console | see see,mrgmod-method |
| Manipulate SIGMA matrices | SIGMA sigma smat smat,list-method smat,matrix-method smat,missing-method smat,mrgmod-method smat,mrgsims-method smat,NULL-method smat,sigmalist-method |
| Access or clear arguments for calls to mrgsim() | simargs |
| Return the location of the model shared object | soloc |
| Optional inputs for lsoda | solversettings |
| Print summary of a mrgmod object | summary.mrgmod |
| Re-scale time in the simulated output | tscale |
| Update the model object | update update,mrgmod-method update,omegalist-method update,parameter_list-method update,sigmalist-method |
| Set up a model object to use either scalar or custom tolerances | use_custom_tol use_scalar_tol |
| Validate and prepare data sets for simulation | valid_data_set valid_data_set.matrix |
| Validate and prepare idata data sets for simulation | valid_idata_set |
| Update parameters, initials, and settings within a model object | within within,mrgmod-method within.mrgmod |
| Zero out random effects in a model object | zero_re zero_re,mrgmod-method |
