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mrgsolve (version 1.1.1)
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
1,214
Version
1.1.1
License
GPL (>= 2)
Issues
75
Pull Requests
1
Stars
131
Forks
36
Repository
https://github.com/metrumresearchgroup/mrgsolve
Maintainer
Kyle T Baron
Last Published
August 16th, 2023
Functions in mrgsolve (1.1.1)
Search all functions
cama
Run the model cama function
carry_out
Select items to carry into simulated output
collapse_omega
Collapse OMEGA or SIGMA matrix lists
check_data_names
Check input data set names against model parameters
cmt_list-class
S4 cmt_list class
design
Set observation designs for the simulation
details
Extract model details
code
Extract the code from a model
ev_days
Schedule dosing events on days of the week
cmtn
Get the compartment number from a compartment name
ev_assign
Replicate a list of events into a data set
collapse_matrix
Collapse the matrices of a matlist object
env_ls
List objects in the model environment
ev_rep
Replicate an event object
ev_repeat
Repeat a block of dosing events
ev_methods
Various methods for event objects
ev_rx
Create intervention objects from Rx input
expand_observations
Insert observations into a data set
expand.idata
Create template data sets for simulation
ev-class
S4 events class
ev_ops
Operations for ev objects
is.mrgmod
Check if an object is a model object
inventory
Check whether all required parameters needed in a model are present in an object
$,ev-method
Select columns from an ev object
ev
Event objects for simulating PK and other interventions
mutate.ev
dplyr verbs for event objects
matlist
Methods for working with matrix-list objects
c,matlist-method
Operations with matlist objects
mcRNG
Set RNG to use L'Ecuyer-CMRG
ev_seq
Schedule a series of event objects
as_bmat
Coerce R objects to block or diagonal matrices
idata_set
Select and modify a idata set for simulation
init
Methods for working with the model compartment list
cvec
Create create character vectors
env_update
Update objects in model environment
env_eval
Re-evaluate the code in the ENV block
data_set
Select and modify a data set for simulation
file_show
Show model specification and C++ files
house
Return a pre-compiled, PK/PD model
modlib
Internal model library
matrix_helpers
Create matrices from vector input
lower2matrix
Create a square numeric matrix from the lower-triangular elements
matlist-class
S4 class matlist
modlib_details
modlib: PK/PD Model parameters, compartments, and output variables
mrgsims
Methods for working with
mrgsims
objects
modelparse
Parse model specification text
modMATRIX
Create a matrix
mrgsims-class
S4 class for mrgsolve simulation output
mcode
Write, compile, and load model code
mrgsims_dplyr
Methods for handling output with dplyr verbs
mrgsims_modify
Methods for modifying mrgsims objects
modlib_pk
modlib: Pharmacokinetic models
modlib_pkpd
modlib: Pharmacokinetic / pharmacodynamic models
numericlist-class
S4 class numeric list
is.mrgsims
Check if an object is mrgsim output
evd
Create an event object with data-like names
exdatasets
Example input data sets
env_get
Return model environment
nmext
Import model estimates from a NONMEM ext file
names,mrgmod-method
Get all names from a model object
mrgsim
Simulate from a model object
$,mrgmod-method
Select parameter values from a model object
mread
Read a model specification file
loadso
Load the model shared object
knobs
Run sensitivity analysis on model settings
lctran
Change the case of nmtran-like data items
modlib_tmdd
modlib: Target mediated disposition model
numericlist
Methods for numericlist
mrgsim_q
Simulate from a model object with quicker turnaround
mrgsim_variants
mrgsim variant functions
modlib_viral
modlib: HCV viral dynamics models
mrgsolve
mrgsolve
outvars
Show names of current output variables
nmxml
Import model estimates from a NONMEM xml file
mod
Return the model object
plot_sims
Plot data as an mrgsims object
obsaug
Augment observations in the simulated output
numerics_only
Prepare data.frame for input to mrgsim
qsim
Basic, simple simulation from model object
mrgmod-class
S4 class for mrgsolve model object
numeric2diag
Create a diagonal numeric matrix from diagonal elements
merge.list
Merge two lists
param
Create and work with parameter objects
see
Print model code to the console
obsonly
Collect only observations in the simulated output
omega
Manipulate OMEGA matrices
plot,batch_mrgsims,missing-method
Plot method for mrgsims objects
tgrid
Create a simtime object
plot_mrgsims
Generate a quick plot of simulated data
param_tags
Return parameter tags
parameter_list-class
S4 parameter_list class
realize_addl
Make addl doses explicit in an event object or data set
read_nmext
Extract estimates from NONMEM ext file
c,tgrid-method
Operations with tgrid objects
show,parameter_list-method
Show the parameter list
valid_idata_set
Validate and prepare idata data sets for simulation
show,mrgmod-method
Print model details
show,cmt_list-method
Show the compartment list
update
Update the model object
revar
Get model random effect variances and covariances
reserved
Reserved words
mvgauss
Simulate from a multivariate normal distribution with mean zero
render
Render a model to a document
reexports
Objects exported from other packages
scrape_and_call
Scrape options and pass to function
simargs
Access or clear arguments for calls to mrgsim
sigma
Manipulate SIGMA matrices
zero_re
Zero out random effects in a model object
scrape_opts
Scrape options from a code block
stime
Get the times at which the model will be evaluated
soloc
Return the location of the model shared object
summary.mrgmod
Print summary of a mrgmod object
%>%
Forward pipe
within
Update parameters, initials, and settings within a model object
tscale
Re-scale time in the simulated output
touch_funs
Get inits from compiled function
solversettings
Optional inputs for lsoda
valid_data_set
Validate and prepare a data sets for simulation
wf_sweep
Simulate a sequence of parameters
as_deslist
Create a list of designs from a data frame
as.list,mrgsims-method
Coerce an mrgsims object to list
PKMODEL
Parse PKMODEL BLOCK data
aboutsolver
About the lsoda differential equation solver used by mrgsolve
Req
Request simulated output
blocks
Return the code blocks from a model specification file
as.ev
Coerce an object to class ev
BLOCK_PARSE
Functions to parse code blocks
as_data_set
Create a simulation data set from ev objects
as.list,mrgmod-method
Coerce a model object to list