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mrgsolve (version 0.9.0)

Simulate from ODE-Based Models

Description

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

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Version

Install

install.packages('mrgsolve')

Monthly Downloads

1,043

Version

0.9.0

License

GPL (>= 2)

Issues

82

Pull Requests

4

Stars

141

Forks

35

Maintainer

Kyle T Baron

Last Published

January 23rd, 2019

Functions in mrgsolve (0.9.0)

BLOCK_PARSE

Functions to parse code blocks
blocks

Return the code blocks from a model specification file
cmt_list-class

S4 cmt_list class
file_show

Show model specification and C++ files
house

Return a pre-compiled, PK/PD model
idata_set

Select and modify a idata set for simulation
aboutsolver

About the ODEPACK differential equation solver used by mrgsolve
Req

Request simulated output
init

Methods for working with the model compartment list
code

Extract the code from a model
cmtn

Get the compartment number from a compartment name
as.ev

Coerce an object to class ev
cvec

Create create character vectors
mcRNG

Set RNG to use L'Ecuyer-CMRG
as.list,mrgmod-method

Coerce a model object to list
mcode

Write, compile, and load model code
nmxml

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

Read a model specification file
mrgmod-class

S4 class for mrgsolve model object
data_qsim

DEPRECATED: Create a matrix of events and observations for simulation
numeric2diag

Create a diagonal numeric matrix from diagonal elements
stime

Get the times at which the model will be evaluated
data_set

Select and modify a data set for simulation
as.list,mrgsims-method

Coerce an mrgsims object to list
ev_assign

Replicate a list of events into a data set
as_data_set

Create a simulation data set from ev objects
ev_days

Schedule dosing events on days of the week
mutate.ev

dplyr verbs for event objects
ev_methods

Various methods for event objects
env_eval

Re-evaluate the code in the ENV block
tgrid

Create a simtime object
wf_sweep

Simulate a sequence of parameters
ev_rep

Replicate an event object
ev_ops

Operations for ev objects
lctran

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

Forward pipe
ev_seq

Schedule a series of event objects
loadso

Load the model shared object
exdatasets

Example input data sets
ev-class

S4 events class
ev

Event objects for simulating PK and other interventions
env_get

Return model environment
merge.list

Merge two lists
ev_repeat

Repeat a block of dosing events
is.mrgsims

Check if an object is mrgsim output
mod

Return the model object
ev_rx

Create intervention objects from Rx input
knobs

Run sensitivity analysis on model settings
as_bmat

Coerce R objects to block or diagonal matrices
mrgsim_q

Simulate from a model object with quicker turnaround
design

Set observation designs for the simulation
details

Extract model details
expand.idata

Create template data sets for simulation
env_ls

List objects in the model environment
modMATRIX

Create a matrix
env_update

Update objects in model environment
lower2matrix

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

Parse model specification text
mrgsim

Simulate from a model object
$,mrgmod-method

Select parameter values from a model object
mrgsim_variants

mrgsim variant functions
expand_observations

Insert observations into a data set
inventory

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

S4 class matlist
is.mrgmod

Check if an object is a model object
mvgauss

Simulate from a multivariate normal distribution with mean zero
numerics_only

Prepare data.frame for input to mrgsim
obsaug

Augment observations in the simulated output
obsonly

Collect only observations in the simulated output
names,mrgmod-method

Get all names from a model object
omega

Manipulate OMEGA matrices
matrix_helpers

Create matrices from vector input
modlib

Internal model library
matlist

Methods for working with matrix-list objects
read_nmext

Extract estimates from NONMEM ext file
realize_addl

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

modlib: Pharmacokinetic models
soloc

Return the location of the model shared object
c,matlist-method

Operations with matlist objects
modlib_pkpd

modlib: Pharmacokinetic / pharmacodynamic models
reserved

Reserved words
mrgsims_dplyr

Methods for handling output with dplyr verbs
solversettings

Optional inputs for DLSODA
mrgsolve

mrgsolve
revar

Get model random effect variances and covariances
modlib_details

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

modlib: Target mediated disposition model
modlib_viral

modlib: HCV viral dynamics models
see

Print model code to the console
plot,batch_mrgsims,missing-method

Plot method for mrgsims objects
numericlist-class

S4 class numeric list
mrgsims-class

S4 class for mrgsolve simulation output
mrgsims

Methods for working with mrgsims objects
numericlist

Methods for numericlist
show,cmt_list-method

Show the compartment list
plot_mrgsims

Generate a quick plot of simulated data
scrape_and_call

Scrape options and pass to function
parameter_list-class

S4 parameter_list class
valid_data_set

Validate and prepare a data sets for simulation
recmatrix

DEPRECATED: Create a matrix of events for simulation
render

Render a model to a document
show,mrgmod-method

Print model details
scrape_opts

Scrape options from a code block
sigma

Manipulate SIGMA matrices
simargs

Access or clear arguments for calls to mrgsim
tscale

Re-scale time in the simulated output
show,parameter_list-method

Show the parameter list
c,tgrid-method

Operations with tgrid objects
valid_idata_set

Validate and prepare idata data sets for simulation
plot_sims

Plot data as an mrgsims object
qsim

DEPRECATED: A quick simulation function
touch_funs

Get inits from compiled function
update

Update the model object
as_deslist

Create a list of designs from a data frame
PKMODEL

Parse PKMODEL BLOCK data
param

Create and work with parameter objects
cama

Run the model cama function
carry_out

Select items to carry into simulated output