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mrgsolve (version 1.5.1)
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
1,610
Version
1.5.1
License
GPL (>= 2)
Issues
77
Pull Requests
3
Stars
129
Forks
36
Repository
https://github.com/metrumresearchgroup/mrgsolve
Maintainer
Kyle T Baron
Last Published
July 26th, 2024
Functions in mrgsolve (1.5.1)
Search all functions
code
Extract the code from a model
cvec
Create create character vectors
data_set
Select and modify a data set for simulation
env_eval
Re-evaluate the code in the ENV block
cmt_list-class
S4 cmt_list class
ev_assign
Replicate a list of events into a data set
ev_days
Schedule dosing events on days of the week
env_ls
List objects in the model environment
env_update
Update objects in model environment
collapse_matrix
Collapse the matrices of a matlist object
ev_ops
Operations for ev objects
ev_rx
Create intervention objects from Rx input
ev
Event objects for simulating PK and other interventions
ev_seq
Schedule a series of event objects
carry_out
Select items to carry into simulated output
ev_methods
Various methods for event objects
$,ev-method
Select columns from an ev object
env_get
Return model environment
inventory
Check whether all required parameters needed in a model are present in an object
design
Set observation designs for the simulation
ev-class
S4 events class
evd
Create an event object with data-like names
idata_set
Select and modify a idata set for simulation
is.mrgmod
Check if an object is a model object
mutate.ev
dplyr verbs for event objects
is.mrgsims
Check if an object is mrgsim output
matlist-class
S4 class matlist
lower2matrix
Create a square numeric matrix from the lower-triangular elements
exdatasets
Example input data sets
modlib
Internal model library
details
Extract model details
knobs
Run sensitivity analysis on model settings
ev_rep
Replicate an event object
c,matlist-method
Operations with matlist objects
matlist
Methods for working with matrix-list objects
file_show
Show model specification and C++ files
ev_repeat
Repeat a block of dosing events
expand_observations
Insert observations into a data set
expand.idata
Create template data sets for simulation
house
Return a pre-compiled, PK/PD model
mrgsims_dplyr
Methods for handling output with dplyr verbs
as_bmat
Coerce R objects to block or diagonal matrices
mrgsims
Methods for working with
mrgsims
objects
modlib_pk
modlib: Pharmacokinetic models
init
Methods for working with the model compartment list
loadso
Load the model shared object
lctran
Change the case of nmtran-like data items
modlib_pkpd
modlib: Pharmacokinetic / pharmacodynamic models
matrix_helpers
Create matrices from vector input
modlib_details
modlib: PK/PD Model parameters, compartments, and output variables
mrgsims_modify
Methods for modifying mrgsims objects
modlib_viral
modlib: HCV viral dynamics models
modlib_tmdd
modlib: Target mediated disposition model
mwrite_yaml
Write model code to yaml format
numeric2diag
Create a diagonal numeric matrix from diagonal elements
$,mrgmod-method
Select parameter values from a model object
mrgmod-class
S4 class for mrgsolve model object
mcode
Write, compile, and load model code
mcRNG
Set RNG to use L'Ecuyer-CMRG
numericlist-class
S4 class numeric list
names,mrgmod-method
Get all names from a model object
numerics_only
Prepare data.frame for input to mrgsim
render
Render a model to a document
reserved
Reserved words
numericlist
Methods for numericlist
mrgsims-class
S4 class for mrgsolve simulation output
modelparse
Parse model specification text
mrgsim_variants
mrgsim variant functions
modMATRIX
Create a matrix
solversettings
Optional inputs for lsoda
outvars
Show names of current output variables
nmxml
Import model estimates from a NONMEM xml file
nmext
Import model estimates from a NONMEM ext file
omega
Manipulate OMEGA matrices
stime
Get the times at which the model will be evaluated
see
Print model code to the console
update
Update the model object
valid_idata_set
Validate and prepare idata data sets for simulation
tscale
Re-scale time in the simulated output
valid_data_set
Validate and prepare data sets for simulation
scrape_opts
Scrape options from a code block
plot_mrgsims
Generate a quick plot of simulated data
plot_sims
Plot data as an mrgsims object
simargs
Access or clear arguments for calls to mrgsim
soloc
Return the location of the model shared object
mrgsim
Simulate from a model object
mrgsim_q
Simulate from a model object with quicker turnaround
mvgauss
Simulate from a multivariate normal distribution with mean zero
mwrite_cpp
Write a model to native mrgsolve format
obsaug
Augment observations in the simulated output
obsonly
Collect only observations in the simulated output
mread_yaml
Read a model from yaml format
mread
Read a model specification file
revar
Get model random effect variances and covariances
plot,batch_mrgsims,missing-method
Plot method for mrgsims objects
c,tgrid-method
Operations with tgrid objects
mod
Return the model object
scrape_and_call
Scrape options and pass to function
parameter_list-class
S4 parameter_list class
merge.list
Merge two lists
realize_addl
Make addl doses explicit in an event object or data set
touch_funs
Get inits from compiled function
reexports
Objects exported from other packages
sigma
Manipulate SIGMA matrices
within
Update parameters, initials, and settings within a model object
show,parameter_list-method
Show the parameter list
wf_sweep
Simulate a sequence of parameters
mrgsolve-package
mrgsolve: Simulate from ODE-Based Models
param_tags
Return parameter tags
qsim
Basic, simple simulation from model object
read_nmext
Extract estimates from NONMEM ext file
show,cmt_list-method
Show the compartment list
param
Create and work with parameter objects
zero_re
Zero out random effects in a model object
show,mrgmod-method
Print model details
summary.mrgmod
Print summary of a mrgmod object
tgrid
Create a simtime object
%>%
Forward pipe
PKMODEL
Parse PKMODEL BLOCK data
BLOCK_PARSE
Functions to parse code blocks
as.list,mrgsims-method
Coerce an mrgsims object to list
cama
Run the model cama function
as_data_set
Create a simulation data set from ev objects or data frames
Req
Request simulated output
cmtn
Get the compartment number from a compartment name
aboutsolver
About the lsoda differential equation solver used by mrgsolve
collapse_omega
Collapse OMEGA or SIGMA matrix lists
as.ev
Coerce an object to class ev
as.list,mrgmod-method
Coerce a model object to list
blocks
Return the code blocks from a model specification file
as_deslist
Create a list of designs from a data frame
check_data_names
Check input data set names against model parameters