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mrgsolve (version 0.8.12)

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

Description

Facilitates simulation from hierarchical, ordinary differential equation (ODE) based models typically employed in drug development. A model specification file is created consisting of R and C++ code that is parsed, compiled, and dynamically loaded into the R session. Input data are passed in and simulated data are returned as R objects. A dosing event engine allows interventions (bolus and infusion) to be managed separately from the model code. Differential equations are solved with the 'DLSODA' routine in 'ODEPACK' ().

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Install

install.packages('mrgsolve')

Monthly Downloads

1,137

Version

0.8.12

License

GPL (>= 2)

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Repository

https://github.com/metrumresearchgroup/mrgsolve

Maintainer

Kyle T Baron

Last Published

April 27th, 2018

Functions in mrgsolve (0.8.12)

Functions to parse code blocks

Repeat a block of dosing events

Schedule a series of event objects

Run sensitivity analysis on model settings.

Convert select upper case column names to lower case to conform to mrgsolve data expectations

Load the model shared object

Create a square numeric matrix from the lower-triangular elements

modlib: HCV viral dynamics models

S4 class matlist.

Simulate from a multivariate normal distribution with mean zero

Create a diagonal numeric matrix from diagonal elements

numericlist-class

S4 class numeric list

rename columns from vector for new names

Render a model to a document

Print model code to the console

show,modlist-method

Show a modlist object.

as.list,mrgmod-method

Coerce a model object to list.

Coerce R objects to block or diagonal matrices

Functions for chaining commands together

List objects in the model environment

S4 cmt_list class

Update objects in model environment

Methods for working with the model compartment list

DEPRECATED: get an events object from a model object

Example input data sets.

Check whether all required parameters needed in a model are present in an object

c,matlist-method

Operations with matlist objects.

Set RNG to use L'Ecuyer-CMRG

Create a modlist object.

Read a model specification file

mrgsim_variants

mrgsim variant functions

S4 class for mrgsolve simulation output.

Create and work with parameter objects

parameter_list-class

S4 parameter_list class

Reserved words.

Get model random effect variances and covariances

Access or clear arguments for calls to mrgsim

Return the location of the model shared object

Create a simulatinon data set from ev objects

Create a simtime object

Operations with tgrid objects

Create a list of designs from a data frame

Get the compartment number from a compartment name

Extract the code from a model

S4 events class

Event objects for simulating PK and other interventions

dplyr verbs for event objects

Various methods for event objects

Check if an object is a model object

Check if an object is mrgsim output.

Write, compile, and load model code

Merge two lists

as.list,mrgsims-method

Corece an mrgsims object to list

Run the model cama function

Coerce an object to class ev

modlib: Pharmacokinetic / pharmacodynamic models

Select items to carry into simulated output

modlib: Target mediated disposition model

Methods for working with mrgsims objects.

Select and modify a data set for simulation

Methods for handling output with dplyr verbs

Generate a quick plot of simulated data

Set observation designs for the simulation

plot,batch_mrgsims,missing-method

Plot method for mrgsims objects.

Create a matrix of events for simulation

Return a pre-compiled, PK/PD model

Replicate a list of events into a data set

Schedule dosing events on days of the week

Select and modify a idata set for simulation

S4 class matlist

Parse model specification text.

Request simulated output

Methods for working with matrix-list objects

Update model or project in an model object

Optional inputs for DLSODA

About the ODEPACK differential equation solver used by mrgsolve

Internal model library.

Return the code blocks from a model specification file

Get the times at which the model will be evaluated

names,mrgmod-method

Get all names from a model object

Create matrices from vector input

Get THETA, OMEGA and SIGMA from a completed NONMEM run

Re-evaluate the code in the ENV block

Return model environment

Operations for ev objects

Collect only observations in the simulated output

Plot data as an mrgsims object

Manipulate OMEGA matrices

Replicate an event object

Create template data sets for simulation

A quick simulation function

Show model specification and C++ files.

show,mrgmod-method

Print model details

Return the model object

Create a matrix

Manipulate SIGMA matrices

Get inits from compiled function

Rescale time in the simulated output

modlib: PK/PD Model parameters, compartments, and output variables

modlib: Pharmacokinetic models

S4 class for mrgsolve model object

Simulate from a model object

Methods for numericlist

Augment observations in the simulated output

Extract estimates from NONMEM ext file

Make addl doses explicit in an event object or data set

Scrape options from a code block.

scrape_and_call

Scrape options and pass to function.

Validate and prepare data sets for simulation

Update the model object

Parse PKMODEL BLOCK data.

Create create character vectors

Create a matrix of events and observations for simulation

Extract model details.

Do an mrgsim run