mread {mrgsolve} | R Documentation |
Read a model specification file
Description
mread
reads and parses the mrgsolve
model specification file,
builds the model, and returns a model object for simulation.
mread_cache
does the same, but caches the compilation result for
later use.
Usage
mread(
model,
project = getOption("mrgsolve.project", getwd()),
code = NULL,
file = NULL,
udll = TRUE,
ignore.stdout = TRUE,
raw = FALSE,
compile = TRUE,
audit = TRUE,
quiet = getOption("mrgsolve_mread_quiet", FALSE),
check.bounds = FALSE,
warn = TRUE,
soloc = getOption("mrgsolve.soloc", tempdir()),
capture = NULL,
preclean = FALSE,
recover = FALSE,
...
)
mread_cache(
model = NULL,
project = getOption("mrgsolve.project", getwd()),
file = paste0(model, ".cpp"),
code = NULL,
soloc = getOption("mrgsolve.soloc", tempdir()),
quiet = FALSE,
preclean = FALSE,
capture = NULL,
...
)
mread_file(file, ...)
Arguments
model |
model name |
project |
location of the model specification file an any
headers to be included; see also the discussion about model; this argument
can be set via |
code |
a character string with model specification code to be used instead of a model file |
file |
the full file name (with extension, but without path) where the model is specified |
udll |
use unique name for shared object |
ignore.stdout |
passed to system call for compiling model |
raw |
if TRUE, return a list of raw output |
compile |
logical; if |
audit |
check the model specification file for errors |
quiet |
don't print messages when compiling |
check.bounds |
check boundaries of parameter list |
warn |
logical; if |
soloc |
the directory location where the model shared object is built
and stored; see details; this argument can be set via |
capture |
a character vector or comma-separated string of additional
model variables to capture; these variables will be added to the capture
list for the current call to |
preclean |
logical; if |
recover |
if |
... |
passed to |
Details
The model
argument is required. For typical use,
the file
argument is omitted and the value
for file
is generated from the value for model
.
To determine the source file name, mrgsolve
will look for
a file extension in model
. A file extension is
assumed when it finds a period followed by one to three alpha-numeric
characters at the end of the string (e.g. mymodel.txt
but not
my.model
). If no file extension is found, the extension .cpp
is assumed (e.g. file
is <model-name>.cpp
). If a file
extension is found, file
is <model-name>
.
Best practice is to avoid using .
in model
unless
you are using model
to point to the model specification
file name. Otherwise, use mread_file
.
Use the soloc
argument to specify a directory location for building
the model. This is the location where the model shared object will be
stored on disk. The default is a temporary directory, so compilation
artifacts are lost when R restarts when the default is used. Changing
soloc
to a persistent directory location will preserve those
artifacts across R restarts. Also, if simulation from a single model is
being done in separate processes on separate compute nodes, it might be
necessary to store these compilation artifacts in a local directory
to make them accessible to the different nodes. If the soloc
directory does not exist, 'mread' will attempt to create it.
Similarly, using mread_cache
will cache results in the temporary
directory and the cache cannot be accessed after the R process is
restarted.
Model Library
mrgsolve
comes bundled with several precoded PK, PK/PD, and
other systems models that are accessible via the mread
interface.
Models available in the library include:
PK models:
pk1cmt
,pk2cmt
,pk3cmt
,pk1
,pk2
,popex
,tmdd
PKPD models:
irm1
,irm2
,irm3
,irm4
,emax
,effect
Other models:
viral1
,viral2
When the library model is accessed, mrgsolve
will compile and load
the model as you would for any other model. It is only necessary to
reference the correct model name and point the project
argument
to the mrgsolve
model library location via modlib
.
For more details, see modlib_pk
, modlib_pkpd
,
modlib_tmdd
, modlib_viral
, and
modlib_details
for more information about the state
variables and parameters in each model.
See Also
Examples
## Not run:
code <- '
$PARAM CL = 1, VC = 5
$CMT CENT
$ODE dxdt_CENT = -(CL/VC)*CENT;
'
mod <- mcode("ex_mread", code)
mod
mod %>% init(CENT=1000) %>% mrgsim %>% plot
mod <- mread("irm3", modlib())
mod
# if the model is in the file mymodel.cpp
mod <- mread("mymodel")
# if the model is in the file mymodel.txt
mod <- mread(file = "mymodel.txt")
or
mod <- mread_file("mymodel.txt")
## End(Not run)