Simulate from ODE-Based Models

Documentation for package ‘mrgsolve’ version 1.5.1

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A B C D E F G H I L M N O P Q R S T U V W Y Z misc

mrgsolve: Simulate from ODE-Based Models

-- A --

aboutsolver	About the lsoda differential equation solver used by mrgsolve
allparam	Create and work with parameter objects
as.ev	Coerce an object to class ev
as.ev-method	Coerce an object to class ev
as.evd	Create an event object with data-like names
as.list-method	Coerce a model object to list
as.list-method	Coerce an mrgsims object to list
as.tbl.mrgsims	Methods for handling output with dplyr verbs
assign_ev	Replicate a list of events into a data set
as_bmat	Coerce R objects to block or diagonal matrices
as_bmat-method	Coerce R objects to block or diagonal matrices
as_cmat	Coerce R objects to block or diagonal matrices
as_data_frame.mrgsims	Methods for handling output with dplyr verbs
as_data_set	Create a simulation data set from ev objects or data frames
as_data_set-method	Create a simulation data set from ev objects or data frames
as_deslist	Create a list of designs from a data frame
as_dmat	Coerce R objects to block or diagonal matrices
as_dmat-method	Coerce R objects to block or diagonal matrices
as_tibble.mrgsims	Methods for handling output with dplyr verbs

-- B --

blocks	Return the code blocks from a model specification file
blocks-method	Return the code blocks from a model specification file
BLOCK_PARSE	Functions to parse code blocks
bmat	Create matrices from vector input

-- C --

c-method	Operations with matlist objects
c-method	Operations with tgrid objects
CAPTURE	Functions to parse code blocks
carry.out	Select items to carry into simulated output
carry_out	Select items to carry into simulated output
check_data_names	Check input data set names against model parameters
cmat	Create matrices from vector input
CMT	Functions to parse code blocks
cmtn	Get the compartment number from a compartment name
cmtn-method	Get the compartment number from a compartment name
code	Extract the code from a model
collapse_matrix	Collapse the matrices of a matlist object
collapse_omega	Collapse OMEGA or SIGMA matrix lists
collapse_sigma	Collapse OMEGA or SIGMA matrix lists

-- D --

data_set	Select and modify a data set for simulation
data_set-method	Select and modify a data set for simulation
design	Set observation designs for the simulation
details	Extract model details
distinct.mrgsims	Methods for handling output with dplyr verbs
dmat	Create matrices from vector input
do.mrgsims	Methods for handling output with dplyr verbs
dorender	Render a model to a document
do_mrgsim	Simulate from a model object

-- E --

env_eval	Re-evaluate the code in the ENV block
env_get	Return model environment
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-method	Event objects for simulating PK and other interventions
evd	Create an event object with data-like names
evd-method	Create an event object with data-like names
evd_expand	Create template data sets for simulation
ev_assign	Replicate a list of events into a data set
ev_days	Schedule dosing events on days of the week
ev_expand	Create template data sets for simulation
ev_rep	Replicate an event object
ev_repeat	Repeat a block of dosing events
ev_rx	Create intervention objects from Rx input
ev_rx-method	Create intervention objects from Rx input
ev_seq	Schedule a series of event objects
exBoot	Example input data sets
exdatasets	Example input data sets
exidata	Example input data sets
expand.ev	Create template data sets for simulation
expand.evd	Create template data sets for simulation
expand.idata	Create template data sets for simulation
expand_observations	Insert observations into a data set
exTheoph	Example input data sets
extran1	Example input data sets
extran2	Example input data sets
extran3	Example input data sets

-- F --

filter.ev	dplyr verbs for event objects
filter.mrgsims	Methods for handling output with dplyr verbs
filter_sims	Methods for modifying mrgsims objects
FIXED	Functions to parse code blocks

-- G --

group_by.mrgsims

Methods for handling output with dplyr verbs

-- H --

HANDLEMATRIX

Functions to parse code blocks

-- I --

idata_set	Select and modify a idata set for simulation
idata_set-method	Select and modify a idata set for simulation
INIT	Functions to parse code blocks
init	Methods for working with the model compartment list
init-method	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

-- L --

lctran	Change the case of nmtran-like data items
lctran.data.frame	Change the case of nmtran-like data items
lctran.ev	Change the case of nmtran-like data items
loadso	Load the model shared object
loadso.mrgmod	Load the model shared object

-- M --

matrix_helpers	Create matrices from vector input
mcode	Write, compile, and load model code
mcode_cache	Write, compile, and load model code
mcRNG	Set RNG to use L'Ecuyer-CMRG
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	Read a model specification file
mread_cache	Read a model specification file
mread_file	Read a model specification file
mread_yaml	Read a model from yaml format
mrgsim	Simulate from a model object
mrgsims_dplyr	Methods for handling output with dplyr verbs
mrgsims_modify	Methods for modifying mrgsims objects
mrgsim_0	mrgsim variant functions
mrgsim_d	mrgsim variant functions
mrgsim_df	Simulate from a model object
mrgsim_di	mrgsim variant functions
mrgsim_e	mrgsim variant functions
mrgsim_ei	mrgsim variant functions
mrgsim_i	mrgsim variant functions
mrgsim_q	Simulate from a model object with quicker turnaround
mrgsim_variants	mrgsim variant functions
mrgsolve	mrgsolve: Simulate from ODE-Based Models
mutate.ev	dplyr verbs for event objects
mutate.mrgsims	Methods for handling output with dplyr verbs
mutate_sims	Methods for modifying mrgsims objects
mwrite_cpp	Write a model to native mrgsolve format
mwrite_yaml	Write model code to yaml format

-- N --

names-method	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
nmxml	Import model estimates from a NONMEM xml file
numerics_only	Prepare data.frame for input to mrgsim

-- O --

obsaug	Augment observations in the simulated output
obsonly	Collect only observations in the simulated output
omat	Manipulate OMEGA matrices
omat-method	Manipulate OMEGA matrices
OMEGA	Manipulate OMEGA matrices
omega	Manipulate OMEGA matrices
outvars	Show names of current output variables

-- P --

PARAM	Functions to parse code blocks
param	Create and work with parameter objects
param-method	Create and work with parameter objects
param_tags	Return parameter tags
parse_rx	Create intervention objects from Rx input
PKMODEL	Parse PKMODEL BLOCK data
plot-method	Plot method for mrgsims objects
plot-method	Generate a quick plot of simulated data
plot_mrgsims	Generate a quick plot of simulated data
plot_sims	Plot data as an mrgsims object
pull.mrgsims	Methods for handling output with dplyr verbs

-- Q --

qsim	Basic, simple simulation from model object

-- R --

read_nmext	Extract estimates from NONMEM ext file
realize_addl	Make addl doses explicit in an event object or data set
realize_addl.data.frame	Make addl doses explicit in an event object or data set
realize_addl.ev	Make addl doses explicit in an event object or data set
render	Render a model to a document
render-method	Render a model to a document
Req	Request simulated output
req	Request simulated output
req.mrgmod	Request simulated output
reserved	Reserved words
revar	Get model random effect variances and covariances
revar-method	Get model random effect variances and covariances

-- S --

see	Print model code to the console
see-method	Print model code to the console
select.ev	dplyr verbs for event objects
select.mrgsims	Methods for handling output with dplyr verbs
select_sims	Methods for modifying mrgsims objects
seq.ev	Schedule a series of event objects
SIGMA	Manipulate SIGMA matrices
sigma	Manipulate SIGMA matrices
simargs	Access or clear arguments for calls to mrgsim
slice.mrgsims	Methods for handling output with dplyr verbs
smat	Manipulate SIGMA matrices
smat-method	Manipulate SIGMA matrices
soloc	Return the location of the model shared object
solversettings	Optional inputs for lsoda
summarise.each	Methods for handling output with dplyr verbs
summarise.mrgsims	Methods for handling output with dplyr verbs
summary.mrgmod	Print summary of a mrgmod object

-- T --

tgrids_*_numeric	Operations with tgrid objects
tgrids_+_numeric	Operations with tgrid objects
tgrid_*_numeric	Operations with tgrid objects
tgrid_+_numeric	Operations with tgrid objects
THETA	Functions to parse code blocks
tscale	Re-scale time in the simulated output

-- U --

uctran	Change the case of nmtran-like data items
uctran.data.frame	Change the case of nmtran-like data items
uctran.ev	Change the case of nmtran-like data items
update	Update the model object
update-method	Update the model object

-- V --

valid_data_set	Validate and prepare data sets for simulation
valid_data_set.matrix	Validate and prepare data sets for simulation
valid_idata_set	Validate and prepare idata data sets for simulation

-- W --

within	Update parameters, initials, and settings within a model object
within-method	Update parameters, initials, and settings within a model object
within.mrgmod	Update parameters, initials, and settings within a model object

-- Y --

yaml_to_cpp

Read a model from yaml format

-- Z --

zero_re	Zero out random effects in a model object
zero_re-method	Zero out random effects in a model object

-- misc --

$-method	Select columns from an ev object
$-method	Select parameter values from a model object
*-method	Operations with tgrid objects
+-method	Operations with tgrid objects
[-method	Select parameter values from a model object
[[-method	Select columns from an ev object
[[-method	Select parameter values from a model object