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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
`$`(<ev>) `[[`(<ev>)
Select columns from an ev object
ev_rep()
Replicate an event object
ev_repeat()
Repeat a block of dosing events
ev_rx() parse_rx()
Create intervention objects from Rx input
ev_seq() seq(<ev>)
Schedule a series of event objects
evd() as.evd()
Create an event object with data-like names
exidata extran1 extran2 extran3 exTheoph exBoot
Example input data sets
expand.idata() expand.ev() expand.evd() ev_expand() evd_expand()
Create template data sets for simulation
expand_observations()
Insert observations into a data set
idata_set()
Select and modify a idata set for simulation
init()
Methods for working with the model compartment list
inventory()
Check whether all required parameters needed in a model are present in an object
is.mrgmod()
Check if an object is a model object
is.mrgsims()
Check if an object is mrgsim output
lctran() uctran()
Change the case of nmtran-like data items
loadso()
Load the model shared object
c(<matlist>)
Operations with matlist objects
as_bmat() as_dmat() as_cmat()
Coerce R objects to block or diagonal matrices
bmat() cmat() dmat()
Create matrices from vector input
mcRNG()
Set RNG to use L'Ecuyer-CMRG
mcode() mcode_cache()
Write, compile, and load model code
modlib()
Internal model library
modlib_details
modlib: PK/PD Model parameters, compartments, and output variables
modlib_pk
modlib: Pharmacokinetic models
modlib_pkpd
modlib: Pharmacokinetic / pharmacodynamic models
modlib_tmdd
modlib: Target mediated disposition model
modlib_viral
modlib: HCV viral dynamics models
mread() mread_cache() mread_file()
Read a model specification file
`$`(<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