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mrgsolve (version 0.8.10)

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.packages('mrgsolve')

Monthly Downloads

1,043

Version

0.8.10

License

GPL (>= 2)

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Repository

https://github.com/metrumresearchgroup/mrgsolve

Maintainer

Kyle T Baron

Last Published

November 1st, 2017

Functions in mrgsolve (0.8.10)

Functions to parse code blocks.

Request simulated output.

About the ODEPACK differential equation solver used by mrgsolve.

Get the compartment number from a compartment name.

Extract the code from a model.

S4 events class

Replicate a list of events into a data set.

Schedule a series of event objects

Event objects for simulating PK and other interventions.

Set RNG to use L'Ecuyer-CMRG.

Write, compile, and load model code.

Parse PKMODEL BLOCK data.

Functions for chaining commands together.

Schedule dosing events on days of the week.

Operations for ev objects.

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.

Internal model library.

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

Simulate from a model object.

S4 class for mrgsolve simulation output.

numericlist-class

S4 class numeric list.

modlib: Pharmacokinetic models.

S4 cmt_list class

modlib: Pharmacokinetic / pharmacodynamic models.

mrgsolve_example

Extract example model from system library

Methods for numericlist.

rename columns from vector for new names

Render a model to a document.

scrape_and_call

Scrape options and pass to function.

Scrape options from a code block.

Get the times at which the model will be evaluated.

stime,mrgmod-method

Create a simtime object.

Manipulate OMEGA matrices.

$,mrgmod-method

Create and work with parameter objects.

A quick simulation function.

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

Access or clear arguments for calls to mrgsim.

Create matrices from vector input.

Run the model cama function.

Return the location of the model shared object.

Validate and prepare data sets for simulation.

Return the code blocks from a model specification file.

Select items to carry into simulated output.

Replicate an event object

Repeat a block of dosing events

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

Check if an object is a model object.

Methods for working with matrix-list objects.

c,matlist-method

Operations with matlist objects.

Merge two lists.

Return the model object.

Read a model specification file.

S4 class for mrgsolve model object.

Create a simulatinon data set from ev objects.

Create a list of designs from a data frame.

Set observation designs for the simulation.

Extract model details.

Re-evaluate the code in the ENV block.

mrgsolve_template

Create model specification file from template

Simulate from a multivariate normal distribution with mean zero.

plot,batch_mrgsims,missing-method

Plot method for mrgsims objects.

as.list,mrgmod-method

Coerce a model object to list.

Coerce R objects to block or diagonal matrices.

Create create character vectors.

Select and modify a data set for simulation.

Return model environment.

Example input data sets.

Create template data sets for simulation.

Check if an object is mrgsim output.

Run sensitivity analysis on model settings.

modlib: Target mediated disposition model.

modlib: HCV viral dynamics models.

S4 class matlist.

Generate a quick plot of simulated data.

Reserved words.

Get model random effect variances and covariances.

Rescale time in the simulated output.

Get all names from a model object.

Create a modlist object.

Augment observations in the simulated output.

Collect only observations in the simulated output.

parameter_list-class

S4 parameter_list class

Simulate from 1- or 2-compartment PK model.

List objects in the model environment.

Update objects in model environment.

Show model specification and C++ files.

Print model code to the console.

show,modlist-method

Show a modlist object.

Operations with tgrid objects.

Get inits from compiled function.

Return a pre-compiled, PK/PD model.

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

Load the model shared object.

Create a matrix.

Parse model specification text.

Methods for working with mrgsims objects.

Methods for handling output with dplyr verbs.

Get THETA, OMEGA and SIGMA from a completed NONMEM run

Create a diagonal numeric matrix from diagonal elements.

Create a matrix of events for simulation.

Update model or project in an model object.

show,mrgmod-method

Print model details.

Manipulate SIGMA matrices.