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All functions

[PARAM()](BLOCK%5FPARSE.html) [FIXED()](BLOCK%5FPARSE.html) [THETA()](BLOCK%5FPARSE.html) [INIT()](BLOCK%5FPARSE.html) [CMT()](BLOCK%5FPARSE.html) [CAPTURE()](BLOCK%5FPARSE.html) [HANDLEMATRIX()](BLOCK%5FPARSE.html)

Functions to parse code blocks

[PKMODEL()](PKMODEL.html)

Parse PKMODEL BLOCK data

[Req()](Req.html) [req()](Req.html)

Request simulated output

[aboutsolver](aboutsolver.html)

About the lsoda differential equation solver used by mrgsolve

[as.ev()](as.ev.html)

Coerce an object to class ev

[as.list(_<mrgmod>_)](as.list-mrgmod-method.html)

Coerce a model object to list

[as.list(_<mrgsims>_)](as.list-mrgsims-method.html)

Coerce an mrgsims object to list

[as_data_set()](as%5Fdata%5Fset.html)

Create a simulation data set from ev objects or data frames

[as_deslist()](as%5Fdeslist.html)

Create a list of designs from a data frame

[blocks()](blocks.html)

Return the code blocks from a model specification file

[carry_out()](carry%5Fout.html) [carry.out()](carry%5Fout.html)

Select items to carry into simulated output

[check_data_names()](check%5Fdata%5Fnames.html)

Check input data set names against model parameters

[cmtn()](cmtn.html)

Get the compartment number from a compartment name

[code()](code.html)

Extract the code from a model

[collapse_omega()](collapse%5Fmatrices.html) [collapse_sigma()](collapse%5Fmatrices.html)

Collapse OMEGA or SIGMA matrix lists

[collapse_matrix()](collapse%5Fmatrix.html)

Collapse the matrices of a matlist object

[data_set()](data%5Fset.html)

Select and modify a data set for simulation

[design()](design.html)

Set observation designs for the simulation

[details()](details.html)

Extract model details

[env_eval()](env%5Feval.html)

Re-evaluate the code in the ENV block

[env_get()](env%5Fget.html) [env_get_env()](env%5Fget.html)

Return model environment

[env_ls()](env%5Fls.html)

List objects in the model environment

[env_update()](env%5Fupdate.html)

Update objects in model environment

[ev()](ev.html)

Event objects for simulating PK and other interventions

[ev_assign()](ev%5Fassign.html) [assign_ev()](ev%5Fassign.html)

Replicate a list of events into a data set

[ev_days()](ev%5Fdays.html)

Schedule dosing events on days of the week

[mutate(_<ev>_)](ev%5Fdplyr.html) [select(_<ev>_)](ev%5Fdplyr.html) [filter(_<ev>_)](ev%5Fdplyr.html)

dplyr verbs for event objects

[`$`(_<ev>_)](ev%5Fextract.html) [`[[`(_<ev>_)](ev%5Fextract.html)

Select columns from an ev object

[ev_rep()](ev%5Frep.html)

Replicate an event object

[ev_repeat()](ev%5Frepeat.html)

Repeat a block of dosing events

[ev_rx()](ev%5Frx.html) [parse_rx()](ev%5Frx.html)

Create intervention objects from Rx input

[ev_seq()](ev%5Fseq.html) [seq(_<ev>_)](ev%5Fseq.html)

Schedule a series of event objects

[evd()](evd.html) [as.evd()](evd.html)

Create an event object with data-like names

[exidata](exdatasets.html) [extran1](exdatasets.html) [extran2](exdatasets.html) [extran3](exdatasets.html) [exTheoph](exdatasets.html) [exBoot](exdatasets.html)

Example input data sets

[expand.idata()](expand.idata.html) [expand.ev()](expand.idata.html) [expand.evd()](expand.idata.html) [ev_expand()](expand.idata.html) [evd_expand()](expand.idata.html)

Create template data sets for simulation

[expand_observations()](expand%5Fobservations.html)

Insert observations into a data set

[idata_set()](idata%5Fset.html)

Select and modify a idata set for simulation

[init()](init.html)

Methods for working with the model compartment list

[inventory()](inventory.html)

Check whether all required parameters needed in a model are present in an object

[is.mrgmod()](is.mrgmod.html)

Check if an object is a model object

[is.mrgsims()](is.mrgsims.html)

Check if an object is mrgsims output

[lctran()](lctran.html) [uctran()](lctran.html)

Change the case of nmtran-like data items

[loadso()](loadso.html)

Load the model shared object

[c(_<matlist>_)](matlist%5Fops.html)

Operations with matlist objects

[as_bmat()](matrix%5Fconverters.html) [as_dmat()](matrix%5Fconverters.html) [as_cmat()](matrix%5Fconverters.html)

Coerce R objects to block or diagonal matrices

[bmat()](matrix%5Fhelpers.html) [cmat()](matrix%5Fhelpers.html) [dmat()](matrix%5Fhelpers.html)

Create matrices from vector input

[mcRNG()](mcRNG.html)

Set RNG to use L'Ecuyer-CMRG

[mcode()](mcode.html) [mcode_cache()](mcode.html)

Write, compile, and load model code

[modlib()](modlib.html)

Internal model library

[modlib_details](modlib%5Fdetails.html)

modlib: PK/PD Model parameters, compartments, and output variables

[modlib_pk](modlib%5Fpk.html)

modlib: Pharmacokinetic models

[modlib_pkpd](modlib%5Fpkpd.html)

modlib: Pharmacokinetic / pharmacodynamic models

[modlib_tmdd](modlib%5Ftmdd.html)

modlib: Target mediated disposition model

[modlib_viral](modlib%5Fviral.html)

modlib: HCV viral dynamics models

[mread()](mread.html) [mread_cache()](mread.html) [mread_file()](mread.html)

Read a model specification file

[mread_yaml()](mread%5Fyaml.html) [yaml_to_cpp()](mread%5Fyaml.html)

Read a model from yaml format

[`$`(_<mrgmod>_)](mrgmod%5Fextract.html) [`[[`(_<mrgmod>_)](mrgmod%5Fextract.html) [`[`(_<mrgmod>_)](mrgmod%5Fextract.html)

Select parameter values from a model object

[mrgsim()](mrgsim.html) [mrgsim_df()](mrgsim.html) [do_mrgsim()](mrgsim.html)

Simulate from a model object

[mrgsim_q()](mrgsim%5Fq.html)

Simulate from a model object with quicker turnaround

[mrgsim_e()](mrgsim%5Fvariants.html) [mrgsim_d()](mrgsim%5Fvariants.html) [mrgsim_ei()](mrgsim%5Fvariants.html) [mrgsim_di()](mrgsim%5Fvariants.html) [mrgsim_i()](mrgsim%5Fvariants.html) [mrgsim_0()](mrgsim%5Fvariants.html)

mrgsim variant functions

[pull(_<mrgsims>_)](mrgsims%5Fdplyr.html) [filter(_<mrgsims>_)](mrgsims%5Fdplyr.html) [group_by(_<mrgsims>_)](mrgsims%5Fdplyr.html) [distinct(_<mrgsims>_)](mrgsims%5Fdplyr.html) [mutate(_<mrgsims>_)](mrgsims%5Fdplyr.html) [summarise(_<each>_)](mrgsims%5Fdplyr.html) [summarise(_<mrgsims>_)](mrgsims%5Fdplyr.html) [do(_<mrgsims>_)](mrgsims%5Fdplyr.html) [select(_<mrgsims>_)](mrgsims%5Fdplyr.html) [slice(_<mrgsims>_)](mrgsims%5Fdplyr.html) [as_data_frame.mrgsims()](mrgsims%5Fdplyr.html) [as_tibble(_<mrgsims>_)](mrgsims%5Fdplyr.html) [as.tbl.mrgsims()](mrgsims%5Fdplyr.html)

Methods for handling output with dplyr verbs

[mutate_sims()](mrgsims%5Fmodify.html) [select_sims()](mrgsims%5Fmodify.html) [filter_sims()](mrgsims%5Fmodify.html)

Methods for modifying mrgsims objects

[mrgsolve](mrgsolve%5Fpackage.html) [mrgsolve-package](mrgsolve%5Fpackage.html)

mrgsolve: Simulate from ODE-Based Models

[mwrite_cpp()](mwrite%5Fcpp.html)

Write a model to native mrgsolve format

[mwrite_yaml()](mwrite%5Fyaml.html)

Write model code to yaml format

[names(_<mrgmod>_)](names-mrgmod-method.html)

Get all names from a model object

[nmext()](nmext.html)

Import model estimates from a NONMEM ext file

[nmxml()](nmxml.html)

Import model estimates from a NONMEM xml file

[numerics_only()](numerics%5Fonly.html)

Prepare data.frame for input to mrgsim()

[obsaug()](obsaug.html)

Augment observations in the simulated output

[obsonly()](obsonly.html)

Collect only observation records in the simulated output

[omat()](omega.html)

Manipulate OMEGA matrices

[outvars()](outvars.html)

Show names of current output variables

[param()](param.html) [allparam()](param.html)

Create and work with parameter objects

[param_tags()](param%5Ftags.html)

Return parameter tags

[plot(_<batchmrgsims>_,_<missing>_)](plot%5Fbatch%5Fmrgsims.html) [plot(_<batchmrgsims>_,_<formula>_)](plot%5Fbatch%5Fmrgsims.html)

Plot method for mrgsims objects

[plot(_<mrgsims>_,_<missing>_)](plot%5Fmrgsims.html) [plot(_<mrgsims>_,_<formula>_)](plot%5Fmrgsims.html) [plot(_<mrgsims>_,_<character>_)](plot%5Fmrgsims.html)

Generate a quick plot of simulated data

[plot_sims()](plot%5Fsims.html)

Plot data as an mrgsims object

[qsim()](qsim.html)

Basic, simple simulation from model object

[read_nmext()](read%5Fnmext.html)

Extract estimates from NONMEM ext file

[realize_addl()](realize%5Faddl.html)

Make addl doses explicit in an event object or data set

[render()](render.html) [dorender()](render.html)

Render a model to a document

[reserved()](reserved.html)

Reserved words

[revar()](revar.html)

Get model random effect variances and covariances

[see()](see.html)

Print model code to the console

[smat()](sigma.html)

Manipulate SIGMA matrices

[simargs()](simargs.html)

Access or clear arguments for calls to mrgsim()

[soloc()](soloc.html)

Return the location of the model shared object

[solversettings](solversettings.html)

Optional inputs for lsoda

[summary(_<mrgmod>_)](summary.mrgmod.html)

Print summary of a mrgmod object

[c(_<tgrid>_)](tgrid%5Fops.html) [c(_<tgrids>_)](tgrid%5Fops.html) [`+`(_<tgrid>_,_<numeric>_)](tgrid%5Fops.html) [`*`(_<tgrid>_,_<numeric>_)](tgrid%5Fops.html) [`+`(_<tgrids>_,_<numeric>_)](tgrid%5Fops.html) [`*`(_<tgrids>_,_<numeric>_)](tgrid%5Fops.html)

Operations with tgrid objects

[tscale()](tscale.html)

Re-scale time in the simulated output

[update(_<mrgmod>_)](update.html) [update(_<omegalist>_)](update.html) [update(_<sigmalist>_)](update.html) [update(_<parameterlist>_)](update.html)

Update the model object

[valid_data_set()](valid%5Fdata%5Fset.html) [valid_data_set.matrix()](valid%5Fdata%5Fset.html)

Validate and prepare data sets for simulation

[valid_idata_set()](valid%5Fidata%5Fset.html)

Validate and prepare idata data sets for simulation

[within(_<mrgmod>_)](within.html)

Update parameters, initials, and settings within a model object

[zero_re()](zero%5Fre.html)

Zero out random effects in a model object