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mrgsolve (version 1.3.0)
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
1,214
Version
1.3.0
License
GPL (>= 2)
Issues
75
Pull Requests
1
Stars
131
Forks
36
Repository
https://github.com/metrumresearchgroup/mrgsolve
Maintainer
Kyle T Baron
Last Published
December 4th, 2023
Functions in mrgsolve (1.3.0)
Search all functions
ev-class
S4 events class
env_eval
Re-evaluate the code in the ENV block
design
Set observation designs for the simulation
env_get
Return model environment
evd
Create an event object with data-like names
ev
Event objects for simulating PK and other interventions
exdatasets
Example input data sets
ev_days
Schedule dosing events on days of the week
ev_assign
Replicate a list of events into a data set
ev_ops
Operations for ev objects
cmt_list-class
S4 cmt_list class
ev_methods
Various methods for event objects
ev_rx
Create intervention objects from Rx input
ev_seq
Schedule a series of event objects
details
Extract model details
$,ev-method
Select columns from an ev object
mutate.ev
dplyr verbs for event objects
knobs
Run sensitivity analysis on model settings
is.mrgsims
Check if an object is mrgsim output
inventory
Check whether all required parameters needed in a model are present in an object
is.mrgmod
Check if an object is a model object
matlist-class
S4 class matlist
env_update
Update objects in model environment
mcRNG
Set RNG to use L'Ecuyer-CMRG
env_ls
List objects in the model environment
lower2matrix
Create a square numeric matrix from the lower-triangular elements
matrix_helpers
Create matrices from vector input
as_bmat
Coerce R objects to block or diagonal matrices
expand_observations
Insert observations into a data set
expand.idata
Create template data sets for simulation
modMATRIX
Create a matrix
ev_rep
Replicate an event object
ev_repeat
Repeat a block of dosing events
modlib
Internal model library
modlib_details
modlib: PK/PD Model parameters, compartments, and output variables
mcode
Write, compile, and load model code
file_show
Show model specification and C++ files
init
Methods for working with the model compartment list
modlib_tmdd
modlib: Target mediated disposition model
idata_set
Select and modify a idata set for simulation
mod
Return the model object
modlib_viral
modlib: HCV viral dynamics models
lctran
Change the case of nmtran-like data items
loadso
Load the model shared object
merge.list
Merge two lists
house
Return a pre-compiled, PK/PD model
modlib_pkpd
modlib: Pharmacokinetic / pharmacodynamic models
c,matlist-method
Operations with matlist objects
modlib_pk
modlib: Pharmacokinetic models
modelparse
Parse model specification text
matlist
Methods for working with matrix-list objects
mread
Read a model specification file
mrgmod-class
S4 class for mrgsolve model object
numerics_only
Prepare data.frame for input to mrgsim
mrgsolve-package
mrgsolve: Simulate from ODE-Based Models
mrgsim
Simulate from a model object
mvgauss
Simulate from a multivariate normal distribution with mean zero
$,mrgmod-method
Select parameter values from a model object
mrgsims_dplyr
Methods for handling output with dplyr verbs
numeric2diag
Create a diagonal numeric matrix from diagonal elements
nmxml
Import model estimates from a NONMEM xml file
mrgsims_modify
Methods for modifying mrgsims objects
outvars
Show names of current output variables
mrgsims-class
S4 class for mrgsolve simulation output
nmext
Import model estimates from a NONMEM ext file
names,mrgmod-method
Get all names from a model object
param
Create and work with parameter objects
mrgsims
Methods for working with
mrgsims
objects
mrgsim_variants
mrgsim variant functions
plot_sims
Plot data as an mrgsims object
mrgsim_q
Simulate from a model object with quicker turnaround
numericlist-class
S4 class numeric list
numericlist
Methods for numericlist
param_tags
Return parameter tags
scrape_opts
Scrape options from a code block
parameter_list-class
S4 parameter_list class
scrape_and_call
Scrape options and pass to function
omega
Manipulate OMEGA matrices
obsonly
Collect only observations in the simulated output
sigma
Manipulate SIGMA matrices
qsim
Basic, simple simulation from model object
simargs
Access or clear arguments for calls to mrgsim
render
Render a model to a document
reexports
Objects exported from other packages
reserved
Reserved words
revar
Get model random effect variances and covariances
update
Update the model object
valid_data_set
Validate and prepare a data sets for simulation
show,mrgmod-method
Print model details
show,parameter_list-method
Show the parameter list
obsaug
Augment observations in the simulated output
valid_idata_set
Validate and prepare idata data sets for simulation
wf_sweep
Simulate a sequence of parameters
see
Print model code to the console
tgrid
Create a simtime object
c,tgrid-method
Operations with tgrid objects
within
Update parameters, initials, and settings within a model object
plot_mrgsims
Generate a quick plot of simulated data
plot,batch_mrgsims,missing-method
Plot method for mrgsims objects
%>%
Forward pipe
realize_addl
Make addl doses explicit in an event object or data set
read_nmext
Extract estimates from NONMEM ext file
summary.mrgmod
Print summary of a mrgmod object
tscale
Re-scale time in the simulated output
touch_funs
Get inits from compiled function
show,cmt_list-method
Show the compartment list
stime
Get the times at which the model will be evaluated
zero_re
Zero out random effects in a model object
solversettings
Optional inputs for lsoda
soloc
Return the location of the model shared object
PKMODEL
Parse PKMODEL BLOCK data
BLOCK_PARSE
Functions to parse code blocks
Req
Request simulated output
aboutsolver
About the lsoda differential equation solver used by mrgsolve
cvec
Create create character vectors
data_set
Select and modify a data set for simulation
code
Extract the code from a model
as.list,mrgmod-method
Coerce a model object to list
as.ev
Coerce an object to class ev
cmtn
Get the compartment number from a compartment name
check_data_names
Check input data set names against model parameters
as.list,mrgsims-method
Coerce an mrgsims object to list
as_deslist
Create a list of designs from a data frame
cama
Run the model cama function
blocks
Return the code blocks from a model specification file
carry_out
Select items to carry into simulated output
as_data_set
Create a simulation data set from ev objects
collapse_omega
Collapse OMEGA or SIGMA matrix lists
collapse_matrix
Collapse the matrices of a matlist object