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mrgsolve (version 0.11.0)

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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Install

install.packages('mrgsolve')

Monthly Downloads

2,295

Version

0.11.0

License

GPL (>= 2)

Issues

88

Pull Requests

4

Stars

159

Forks

36

Maintainer

Kyle T Baron

Last Published

March 28th, 2021

Functions in mrgsolve (0.11.0)

as.list,mrgmod-method

Coerce a model object to list
Req

Request simulated output
as_data_set

Create a simulation data set from ev objects
as_deslist

Create a list of designs from a data frame
aboutsolver

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

Coerce an object to class ev
blocks

Return the code blocks from a model specification file
as.list,mrgsims-method

Coerce an mrgsims object to list
BLOCK_PARSE

Functions to parse code blocks
PKMODEL

Parse PKMODEL BLOCK data
cama

Run the model cama function
details

Extract model details
mutate.ev

dplyr verbs for event objects
carry_out

Select items to carry into simulated output
$,ev-method

Select columns from an ev object
cmtn

Get the compartment number from a compartment name
env_get

Return model environment
cvec

Create create character vectors
ev_assign

Replicate a list of events into a data set
env_eval

Re-evaluate the code in the ENV block
code

Extract the code from a model
env_ls

List objects in the model environment
ev_days

Schedule dosing events on days of the week
cmt_list-class

S4 cmt_list class
drop_re

Deprecated: drop random effect matrices from model object
exdatasets

Example input data sets
ev_rep

Replicate an event object
ev_rx

Create intervention objects from Rx input
env_update

Update objects in model environment
expand.idata

Create template data sets for simulation
idata_set

Select and modify a idata set for simulation
house

Return a pre-compiled, PK/PD model
ev_seq

Schedule a series of event objects
modMATRIX

Create a matrix
ev_repeat

Repeat a block of dosing events
loadso

Load the model shared object
lower2matrix

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

Return the model object
expand_observations

Insert observations into a data set
knobs

Run sensitivity analysis on model settings
matlist

Methods for working with matrix-list objects
matlist-class

S4 class matlist
lctran

Convert select upper case column names to lower case to conform to mrgsolve data expectations
c,matlist-method

Operations with matlist objects
file_show

Show model specification and C++ files
is.mrgmod

Check if an object is a model object
modlib_pkpd

modlib: Pharmacokinetic / pharmacodynamic models
mrgsim_q

Simulate from a model object with quicker turnaround
modlib_pk

modlib: Pharmacokinetic models
mrgsim

Simulate from a model object
modlib_details

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

mrgsim variant functions
as_bmat

Coerce R objects to block or diagonal matrices
mrgsims-class

S4 class for mrgsolve simulation output
modlib_tmdd

modlib: Target mediated disposition model
numericlist

Methods for numericlist
mrgsims

Methods for working with mrgsims objects
obsaug

Augment observations in the simulated output
mrgmod-class

S4 class for mrgsolve model object
numerics_only

Prepare data.frame for input to mrgsim
reexports

Objects exported from other packages
render

Render a model to a document
modlib

Internal model library
is.mrgsims

Check if an object is mrgsim output
modelparse

Parse model specification text
mcRNG

Set RNG to use L'Ecuyer-CMRG
matrix_helpers

Create matrices from vector input
design

Set observation designs for the simulation
data_set

Select and modify a data set for simulation
ev-class

S4 events class
$,mrgmod-method

Select parameter values from a model object
scrape_and_call

Scrape options and pass to function
mrgsims_dplyr

Methods for handling output with dplyr verbs
names,mrgmod-method

Get all names from a model object
mvgauss

Simulate from a multivariate normal distribution with mean zero
scrape_opts

Scrape options from a code block
valid_idata_set

Validate and prepare idata data sets for simulation
tscale

Re-scale time in the simulated output
wf_sweep

Simulate a sequence of parameters
touch_funs

Get inits from compiled function
read_nmext

Extract estimates from NONMEM ext file
realize_addl

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

Import model estimates from a NONMEM ext file
numeric2diag

Create a diagonal numeric matrix from diagonal elements
numericlist-class

S4 class numeric list
ev

Event objects for simulating PK and other interventions
reserved

Reserved words
qsim

Basic, simple simulation from model object
plot_sims

Plot data as an mrgsims object
stime

Get the times at which the model will be evaluated
obsonly

Collect only observations in the simulated output
ev_ops

Operations for ev objects
init

Methods for working with the model compartment list
ev_methods

Various methods for event objects
inventory

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

Write, compile, and load model code
plot,batch_mrgsims,missing-method

Plot method for mrgsims objects
modlib_viral

modlib: HCV viral dynamics models
merge.list

Merge two lists
update

Update the model object
revar

Get model random effect variances and covariances
plot_mrgsims

Generate a quick plot of simulated data
sigma

Manipulate SIGMA matrices
mrgsims_modify

Methods for modifying mrgsims objects
mread

Read a model specification file
valid_data_set

Validate and prepare a data sets for simulation
param

Create and work with parameter objects
see

Print model code to the console
nmxml

Import model estimates from a NONMEM xml file
omega

Manipulate OMEGA matrices
show,mrgmod-method

Print model details
show,cmt_list-method

Show the compartment list
parameter_list-class

S4 parameter_list class
mrgsolve

mrgsolve
outvars

Show names of current output variables
show,parameter_list-method

Show the parameter list
simargs

Access or clear arguments for calls to mrgsim
soloc

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

Operations with tgrid objects
tgrid

Create a simtime object
solversettings

Optional inputs for lsoda
within

Update parameters, initials, and settings within a model object
%>%

Forward pipe
summary.mrgmod

Print summary of a mrgmod object