All functions

PARAM() FIXED() THETA() INIT() CMT() CAPTURE() HANDLEMATRIX()

Functions to parse code blocks

PKMODEL()

Parse PKMODEL BLOCK data

Req() req()

Request simulated output

aboutsolver

About the lsoda differential equation solver used by mrgsolve

as.ev()

Coerce an object to class ev

as.list(<mrgmod>)

Coerce a model object to list

as.list(<mrgsims>)

Coerce an mrgsims object to list

as_data_set()

Create a simulation data set from ev objects

as_deslist()

Create a list of designs from a data frame

blocks()

Return the code blocks from a model specification file

carry_out() carry.out()

Select items to carry into simulated output

cmtn()

Get the compartment number from a compartment name

code()

Extract the code from a model

collapse_omega() collapse_sigma()

Collapse OMEGA or SIGMA matrix lists

collapse_matrix()

Collapse the matrices of a matlist object

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() env_get_env()

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() assign_ev()

Replicate a list of events into a data set

ev_days()

Schedule dosing events on days of the week

mutate(<ev>) select(<ev>) filter(<ev>)

dplyr verbs for event objects

`$`(<ev>) `[[`(<ev>)

Select columns from an ev object

ev_rep()

Replicate an event object

ev_repeat()

Repeat a block of dosing events

ev_rx() parse_rx()

Create intervention objects from Rx input

ev_seq() seq(<ev>)

Schedule a series of event objects

evd() as.evd()

Create an event object with data-like names

exidata extran1 extran2 extran3 exTheoph exBoot

Example input data sets

expand.idata() expand.ev() ev_expand()

Create template data sets for simulation

expand_observations()

Insert observations into a data set

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 present in an object

is.mrgmod()

Check if an object is a model object

is.mrgsims()

Check if an object is mrgsim output

lctran() uctran()

Change the case of nmtran-like data items

loadso()

Load the model shared object

c(<matlist>)

Operations with matlist objects

as_bmat() as_dmat() as_cmat()

Coerce R objects to block or diagonal matrices

bmat() cmat() dmat()

Create matrices from vector input

mcRNG()

Set RNG to use L'Ecuyer-CMRG

mcode() mcode_cache()

Write, compile, and load model code

modlib()

Internal model library

modlib_details

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

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

mread() mread_cache() mread_file()

Read a model specification file

`$`(<mrgmod>) `[[`(<mrgmod>) `[`(<mrgmod>)

Select parameter values from a model object

mrgsim() mrgsim_df() do_mrgsim()

Simulate from a model object

mrgsim_q()

Simulate from a model object with quicker turnaround

mrgsim_e() mrgsim_d() mrgsim_ei() mrgsim_di() mrgsim_i() mrgsim_0()

mrgsim variant functions

pull(<mrgsims>) filter(<mrgsims>) group_by(<mrgsims>) distinct(<mrgsims>) mutate(<mrgsims>) summarise(<each>) summarise(<mrgsims>) do(<mrgsims>) select(<mrgsims>) slice(<mrgsims>) as_data_frame.mrgsims() as_tibble(<mrgsims>) as.tbl.mrgsims()

Methods for handling output with dplyr verbs

mutate_sims() select_sims() filter_sims()

Methods for modifying mrgsims objects

mrgsolve

mrgsolve

names(<mrgmod>)

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

numerics_only()

Prepare data.frame for input to mrgsim

obsaug()

Augment observations in the simulated output

obsonly()

Collect only observations in the simulated output

omega

Manipulate OMEGA matrices

outvars()

Show names of current output variables

param() allparam()

Create and work with parameter objects

plot(<batch_mrgsims>,<missing>) plot(<batch_mrgsims>,<formula>)

Plot method for mrgsims objects

plot(<mrgsims>,<missing>) plot(<mrgsims>,<formula>) plot(<mrgsims>,<character>)

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

render() dorender()

Render a model to a document

reserved()

Reserved words

revar()

Get model random effect variances and covariances

see()

Print model code to the console

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

summary(<mrgmod>)

Print summary of a mrgmod object

c(<tgrid>) c(<tgrids>) `+`(<tgrid>,<numeric>) `*`(<tgrid>,<numeric>) `+`(<tgrids>,<numeric>) `*`(<tgrids>,<numeric>)

Operations with tgrid objects

tscale()

Re-scale time in the simulated output

update(<mrgmod>) update(<omegalist>) update(<sigmalist>) update(<parameter_list>)

Update the model object

valid_data_set() valid_data_set.matrix()

Validate and prepare a data sets for simulation

valid_idata_set()

Validate and prepare idata data sets for simulation

within(<mrgmod>)

Update parameters, initials, and settings within a model object

zero_re()

Zero out random effects in a model object