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mrgsolve (version 0.8.9)

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

1,043

Version

0.8.9

License

GPL (>= 2)

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Repository

https://github.com/metrumresearchgroup/mrgsolve

Maintainer

Kyle T Baron

Last Published

August 28th, 2017

Functions in mrgsolve (0.8.9)

Return the code blocks from a model specification file.

Create matrices from vector input.

Create a simulatinon data set from ev objects.

Create a list of designs from a data frame.

Create create character vectors.

Select and modify a data set for simulation.

S4 events class

Replicate a list of events into a data set.

Example input data sets.

Create template data sets for simulation.

Request simulated output.

About the ODEPACK differential equation solver used by mrgsolve.

Functions for chaining commands together.

Methods for working with matrix-list objects.

c,matlist-method

Operations with matlist objects.

Internal model library.

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

Set observation designs for the simulation.

Extract model details.

Schedule dosing events on days of the week.

as.list,mrgmod-method

Coerce a model object to list.

Get the compartment number from a compartment name.

Extract the code from a model.

Functions to parse code blocks.

Parse PKMODEL BLOCK data.

Run the model cama function.

Select items to carry into simulated output.

Coerce R objects to block or diagonal matrices.

Operations for ev objects.

Show model specification and C++ files.

Return a pre-compiled, PK/PD model.

Check if an object is mrgsim output.

Read a model specification file.

S4 class for mrgsolve model object.

mrgsolve_template

Create model specification file from template

S4 cmt_list class

Re-evaluate the code in the ENV block.

Return model environment.

Schedule a series of event objects

List objects in the model environment.

Update objects in model environment.

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

Check if an object is a model object.

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

Event objects for simulating PK and other interventions.

Set RNG to use L'Ecuyer-CMRG.

Write, compile, and load model code.

Create a matrix.

Run sensitivity analysis on model settings.

modlib: Target mediated disposition model.

modlib: HCV viral dynamics models.

Replicate an event object

Repeat a block of dosing events

Select and modify a idata set for simulation.

Methods for working with the model compartment list.

Create a square numeric matrix from the lower-triangular elements.

S4 class matlist.

modlib: Pharmacokinetic models.

modlib: Pharmacokinetic / pharmacodynamic models.

Simulate from a model object.

S4 class for mrgsolve simulation output.

Get THETA, OMEGA and SIGMA from a completed NONMEM run

Create a diagonal numeric matrix from diagonal elements.

parameter_list-class

S4 parameter_list class

Simulate from 1- or 2-compartment PK model.

Print model code to the console.

show,modlist-method

Show a modlist object.

Get the times at which the model will be evaluated.

stime,mrgmod-method

Create a simtime object.

Parse model specification text.

S4 class matlist.

Create a modlist object.

numericlist-class

S4 class numeric list.

Methods for numericlist.

Create a matrix of events for simulation.

Update model or project in an model object.

show,mrgmod-method

Print model details.

Manipulate SIGMA matrices.

Validate and prepare data sets for simulation.

Load the model shared object.

Merge two lists.

Return the model object.

mrgsolve_example

Extract example model from system library

Simulate from a multivariate normal distribution with mean zero.

rename columns from vector for new names

Render a model to a document.

Access or clear arguments for calls to mrgsim.

Augment observations in the simulated output.

Collect only observations in the simulated output.

A quick simulation function.

Make addl doses explicit in an event object or data set.

Return the location of the model shared object.

Methods for working with mrgsims objects.

Methods for handling output with dplyr verbs.

Manipulate OMEGA matrices.

$,mrgmod-method

Create and work with parameter objects.

plot,batch_mrgsims,missing-method

Plot method for mrgsims objects.

Generate a quick plot of simulated data.

scrape_and_call

Scrape options and pass to function.

Scrape options from a code block.

Rescale time in the simulated output.

Get all names from a model object.

Reserved words.

Get model random effect variances and covariances.

Operations with tgrid objects.

Get inits from compiled function.