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