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

## Documentation for package ‘mrgsolve’ version 0.8.10

- DESCRIPTION file.

## Help Pages

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_assign | Replicate a list of events into a data set.
ev_days | Schedule dosing events on days of the week.
ev_ops | Operations for ev objects.
ev_rep | Replicate an event object
ev_repeat | Repeat a block of dosing events
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.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.
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.

## -- 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.
mread_file | 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.
seq.ev | Schedule a series of event objects
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.