Learn R Programming
⚠️There's a newer version (1.7.2) of this package.Take me there.

mrgsolve (version 0.10.1)

Simulate from ODE-Based Models

Description

Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

Copy Link

Version

Install

install.packages('mrgsolve')

Monthly Downloads

2,295

Version

0.10.1

License

GPL (>= 2)

Issues

88

Pull Requests

4

Stars

159

Forks

36

Maintainer

Kyle T Baron

Last Published

February 21st, 2020

Functions in mrgsolve (0.10.1)

BLOCK_PARSE

Functions to parse code blocks
code

Extract the code from a model
PKMODEL

Parse PKMODEL BLOCK data
Req

Request simulated output
aboutsolver

About the lsoda differential equation solver used by mrgsolve
as.ev

Coerce an object to class ev
as.list,mrgmod-method

Coerce a model object to list
data_set

Select and modify a data set for simulation
design

Set observation designs for the simulation
details

Extract model details
as.list,mrgsims-method

Coerce an mrgsims object to list
cvec

Create create character vectors
env_ls

List objects in the model environment
$,ev-method

Select columns from an ev object
cmtn

Get the compartment number from a compartment name
as_data_set

Create a simulation data set from ev objects
mutate.ev

dplyr verbs for event objects
cmt_list-class

S4 cmt_list class
as_deslist

Create a list of designs from a data frame
ev-class

S4 events class
blocks

Return the code blocks from a model specification file
env_update

Update objects in model environment
ev_repeat

Repeat a block of dosing events
ev_rep

Replicate an event object
ev_methods

Various methods for event objects
drop_re

Deprecated: drop random effect matrices from model object
ev

Event objects for simulating PK and other interventions
ev_assign

Replicate a list of events into a data set
carry_out

Select items to carry into simulated output
cama

Run the model cama function
ev_ops

Operations for ev objects
env_eval

Re-evaluate the code in the ENV block
expand_observations

Insert observations into a data set
init

Methods for working with the model compartment list
inventory

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

Show model specification and C++ files
is.mrgsims

Check if an object is mrgsim output
is.mrgmod

Check if an object is a model object
idata_set

Select and modify a idata set for simulation
house

Return a pre-compiled, PK/PD model
ev_days

Schedule dosing events on days of the week
ev_seq

Schedule a series of event objects
ev_rx

Create intervention objects from Rx input
matlist

Methods for working with matrix-list objects
env_get

Return model environment
matlist-class

S4 class matlist
modlib_tmdd

modlib: Target mediated disposition model
modlib_pkpd

modlib: Pharmacokinetic / pharmacodynamic models
mrgsolve

mrgsolve
expand.idata

Create template data sets for simulation
modMATRIX

Create a matrix
mod

Return the model object
mvgauss

Simulate from a multivariate normal distribution with mean zero
exdatasets

Example input data sets
loadso

Load the model shared object
lower2matrix

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

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

Write, compile, and load model code
knobs

Run sensitivity analysis on model settings
merge.list

Merge two lists
matrix_helpers

Create matrices from vector input
numeric2diag

Create a diagonal numeric matrix from diagonal elements
c,matlist-method

Operations with matlist objects
realize_addl

Make addl doses explicit in an event object or data set
numericlist-class

S4 class numeric list
modlib

Internal model library
scrape_and_call

Scrape options and pass to function
scrape_opts

Scrape options from a code block
read_nmext

Extract estimates from NONMEM ext file
as_bmat

Coerce R objects to block or diagonal matrices
mcRNG

Set RNG to use L'Ecuyer-CMRG
modelparse

Parse model specification text
$,mrgmod-method

Select parameter values from a model object
names,mrgmod-method

Get all names from a model object
mrgmod-class

S4 class for mrgsolve model object
nmxml

Get THETA, OMEGA and SIGMA from a completed NONMEM run
stime

Get the times at which the model will be evaluated
reserved

Reserved words
param

Create and work with parameter objects
modlib_viral

modlib: HCV viral dynamics models
mrgsims_dplyr

Methods for handling output with dplyr verbs
mread

Read a model specification file
revar

Get model random effect variances and covariances
parameter_list-class

S4 parameter_list class
mrgsims

Methods for working with mrgsims objects
within

Update parameters, initials, and settings within a model object
summary.mrgmod

Print summary of a mrgmod object
modlib_pk

modlib: Pharmacokinetic models
%>%

Forward pipe
modlib_details

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

Simulate from a model object
obsaug

Augment observations in the simulated output
mrgsim_variants

mrgsim variant functions
obsonly

Collect only observations in the simulated output
soloc

Return the location of the model shared object
solversettings

Optional inputs for lsoda
mrgsims-class

S4 class for mrgsolve simulation output
numericlist

Methods for numericlist
mrgsim_q

Simulate from a model object with quicker turnaround
render

Render a model to a document
reexports

Objects exported from other packages
valid_data_set

Validate and prepare a data sets for simulation
omega

Manipulate OMEGA matrices
update

Update the model object
outvars

Show names of current output variables
plot,batch_mrgsims,missing-method

Plot method for mrgsims objects
plot_mrgsims

Generate a quick plot of simulated data
numerics_only

Prepare data.frame for input to mrgsim
qsim

Basic, simple simulation from model object
plot_sims

Plot data as an mrgsims object
see

Print model code to the console
sigma

Manipulate SIGMA matrices
simargs

Access or clear arguments for calls to mrgsim
show,cmt_list-method

Show the compartment list
tscale

Re-scale time in the simulated output
tgrid

Create a simtime object
show,mrgmod-method

Print model details
c,tgrid-method

Operations with tgrid objects
touch_funs

Get inits from compiled function
show,parameter_list-method

Show the parameter list
valid_idata_set

Validate and prepare idata data sets for simulation
wf_sweep

Simulate a sequence of parameters