Simulate from ODE-Based Population PK/PD and Systems Pharmacology Models

Documentation for package ‘mrgsolve’ version 0.8.6

DESCRIPTION file.

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

mrgsolve-package

mrgsolve

-- A --

aboutsolver	About the ODEPACK differential equation solver used by mrgsolve.
allparam	Create and work with parameter objects.
as.data.frame-method	Event objects for simulating PK and other interventions.
as.data.frame-method	Run sensitivity analysis on model settings.
as.data.frame-method	Methods for working with 'mrgsims' objects.
as.data.frame-method	Methods for numericlist.
as.ev	Event objects for simulating PK and other interventions.
as.ev-method	Event objects for simulating PK and other interventions.
as.init	Methods for working with the model compartment list.
as.init-method	Methods for working with the model compartment list.
as.list-method	Coerce a model object to list.
as.list-method	Methods for working with matrix-list objects.
as.list-method	Methods for numericlist.
as.matrix-method	Event objects for simulating PK and other interventions.
as.matrix-method	Methods for working with matrix-list objects.
as.matrix-method	Methods for working with 'mrgsims' objects.
as.numeric-method	Methods for numericlist.
as.param	Create and work with parameter objects.
as.param-method	Create and work with parameter objects.
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_data_frame.mrgsims	Methods for handling output with dplyr verbs.
as_data_set	Create a simulatinon data set from ev objects.
as_data_set-method	Create a simulatinon data set from ev objects.
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.

-- 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 for ev objects.
c-method	Operations with matlist objects.
c-method	Operations with tgrid objects.
cama	Run the model cama function.
CAPTURE	Functions to parse code blocks.
carry.out	Select items to carry into simulated output.
carry_out	Select items to carry into simulated output.
ch	Create create character vectors.
chain	Functions for chaining commands together.
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.
cmt_list-class	S4 cmt_list class
code	Extract the code from a model.
cvec	Create create character vectors.
cvec-method	Create create character vectors.

-- 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.
dim-method	Methods for working with matrix-list objects.
dim-method	Methods for working with 'mrgsims' objects.
distinct_.mrgsims	Methods for handling output with dplyr verbs.
dmat	Create matrices from vector input.
dorender	Render a model to a document.
do_.mrgsims	Methods for handling output with dplyr verbs.
drop.re	Methods for working with matrix-list objects.
drop.re-method	Methods for working with matrix-list objects.
drop_re	Methods for working with matrix-list objects.

-- E --

env_eval	Re-evaluate the code in the ENV block.
env_get	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-class	S4 events class
ev-method	Event objects for simulating PK and other interventions.
events	Event objects for simulating PK and other interventions.
events-method	Event objects for simulating PK and other interventions.
ev_days	Schedule dosing events on days of the week.
ev_ops	Operations for ev 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.idata	Create template data sets for simulation.
exTheoph	Example input data sets.
extran1	Example input data sets.
extran2	Example input data sets.
extran3	Example input data sets.

-- F --

file_show	Show model specification and C++ files.
filter_.mrgsims	Methods for handling output with dplyr verbs.
FIXED	Functions to parse code blocks.

-- G --

group_by_.mrgsims

Methods for handling output with dplyr verbs.

-- H --

head-method	Methods for working with 'mrgsims' objects.
house	Return a pre-compiled, PK/PD model.

-- 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.
is.mrgmod	Check if an object is a model object.
is.mrgsims	Check if an object is mrgsim output.

-- K --

knobs	Run sensitivity analysis on model settings.
knobs-method	Run sensitivity analysis on model settings.

-- L --

labels-method	Methods for working with matrix-list objects.
lctran	Convert select upper case column names to lower case to conform to mrgsolve data expectations.
length-method	Methods for working with matrix-list objects.
length-method	Methods for numericlist.
loadso	Load the model shared object.
loadso-method	Load the model shared object.
lower2matrix	Create a square numeric matrix from the lower-triangular elements.

-- M --

matlist	Methods for working with matrix-list objects.
matlist-class	S4 class matlist.
mcode	Write, compile, and load model code.
mcode_cache	Write, compile, and load model code.
mcRNG	Set RNG to use L'Ecuyer-CMRG.
merge.list	Merge two lists.
mod	Return the model object.
mod-method	Return the model object.
modelparse	Parse model specification text.
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.
modlist	Create a modlist object.
modlist-class	S4 class matlist.
modMATRIX	Create a matrix.
mread	Read a model specification file.
mread_cache	Read a model specification file.
mrgmod-class	S4 class for mrgsolve model object.
mrgsim	Simulate from a model object.
mrgsims	Methods for working with 'mrgsims' objects.
mrgsims-class	S4 class for mrgsolve simulation output.
mrgsims_dplyr	Methods for handling output with dplyr verbs.
mrgsolve	mrgsolve
mrgsolve_example	Extract example model from system library
mrgsolve_template	Create model specification file from template
mutate_.mrgsims	Methods for handling output with dplyr verbs.
mvgauss	Simulate from a multivariate normal distribution with mean zero.

-- N --

names-method	Methods for working with matrix-list objects.
names-method	Methods for working with 'mrgsims' objects.
names-method	Methods for numericlist.
names-method	Get all names from a model object.
NMXML	Get THETA, OMEGA and SIGMA from a completed NONMEM run
nmxml	Get THETA, OMEGA and SIGMA from a completed NONMEM run
nrow-method	Methods for working with matrix-list objects.
numeric2diag	Create a diagonal numeric matrix from diagonal elements.
numericlist	Methods for numericlist.
numericlist-class	S4 class numeric list.

-- 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.
omegalist-class	S4 class matlist.

-- P --

PARAM	Functions to parse code blocks.
param	Create and work with parameter objects.
param-method	Create and work with parameter objects.
parameter_list-class	S4 parameter_list class
PKMODEL	Parse PKMODEL BLOCK data.
pkmodel	Simulate from 1- or 2-compartment PK model.
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.

-- Q --

qsim	A quick simulation function.

-- R --

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.
recmatrix	Create a matrix of events for simulation.
relocate	Update model or project in an model object.
relocate-method	Update model or project in an model object.
rename_cols	rename columns from vector for new names
render	Render a model to a document.
render-method	Render a model to a document.
Req	Request simulated output.
req	Request simulated output.
Req-method	Request simulated output.
req-method	Request simulated output.
reserved	Reserved words.
revar	Get model random effect variances and covariances.
revar-method	Get model random effect variances and covariances.

-- S --

s	Create create character vectors.
scrape_and_call	Scrape options and pass to function.
scrape_opts	Scrape options from a code block.
see	Print model code to the console.
see-method	Print model code to the console.
select_.mrgsims	Methods for handling output with dplyr verbs.
show-method	Event objects for simulating PK and other interventions.
show-method	Methods for working with the model compartment list.
show-method	Run sensitivity analysis on model settings.
show-method	Methods for working with matrix-list objects.
show-method	Methods for working with 'mrgsims' objects.
show-method	Create and work with parameter objects.
show-method	Show a modlist object.
show-method	Print model details.
show-method	Create a simtime object.
SIGMA	Manipulate SIGMA matrices.
sigma	Manipulate SIGMA matrices.
sigmalist-class	S4 class matlist.
simargs	Access or clear arguments for calls to mrgsim.
simargs.mrgmod	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.
stime	Get the times at which the model will be evaluated.
stime-method	Create a simtime object.
subset-method	Methods for working with 'mrgsims' objects.
summarise.each	Methods for handling output with dplyr verbs.
summarise_.mrgsims	Methods for handling output with dplyr verbs.
summary-method	Methods for working with 'mrgsims' objects.

-- T --

tail-method	Methods for working with 'mrgsims' objects.
tgrid	Create a simtime object.
tgrid-class	Get the times at which the model will be evaluated.
tgrids-class	Get the times at which the model will be evaluated.
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.
touch_funs	Get inits from compiled function.
tscale	Rescale time in the simulated output.

-- U --

update	Get all names from a model object.
update-method	Get all names from a model object.

-- V --

valid_data	Validate and prepare data sets for simulation.
valid_data_set	Validate and prepare data sets for simulation.
valid_data_set.data.frame	Validate and prepare data sets for simulation.
valid_data_set.default	Validate and prepare data sets for simulation.
valid_data_set.matrix	Validate and prepare data sets for simulation.
valid_idata_set	Validate and prepare data sets for simulation.

-- Z --

zero.re	Methods for working with matrix-list objects.
zero.re-method	Methods for working with matrix-list objects.
zero_re	Methods for working with matrix-list objects.

-- misc --

$-method	S4 class matlist.
$-method	Methods for working with 'mrgsims' objects.
$-method	Methods for numericlist.
$-method	Create and work with parameter objects.
%>%	Forward pipe.
%T>%	Forward pipe.
%then%	Operations for ev objects.
%then%-method	Operations for ev objects.
*-method	Operations with tgrid objects.
+-method	Operations for ev objects.
+-method	Operations with tgrid objects.
[-method	Methods for numericlist.