The method run launches LibBi with a particular set of command
line arguments. Normally, this function would not be run by the user,
but instead one of the client functions sample,
filter, or optimise, or rewrite,
which pass any options on to run. Note that any options specified
here are stored in the libbi object and do not have to be
specified again if another command is run on the object.
# S3 method for libbi
run(
x,
client,
proposal = c("model", "prior"),
model,
fix,
config,
log_file_name = character(0),
init,
input,
obs,
time_dim = character(0),
coord_dims = list(),
thin,
output_every,
chain = TRUE,
seed = TRUE,
debug = FALSE,
...
)an updated libbi object, except if client is
'rewrite', in which case invisible NULL will be returned but the rewritten
model code printed
a libbi object; if this is not given, an empty
libbi object will be created
client to pass to LibBi
proposal distribution to use; either "model" (default: proposal distribution in the model) or "prior" (propose from the prior distribution)
either a character vector giving the path to a model file
(typically ending in ".bi"), or a bi_model object; by default, will
use any model given in x
any variable to fix, as a named vector
path to a configuration file, containing multiple arguments
path to a file to text file to report the output of
LibBi; if set to an empty vector (character(0)) or an empty
string (""), which is the default, a temporary log file will be generated
initialisation of the model, either supplied as a list of values
and/or data frames, or a (netcdf) file name, or a libbi
object which has been run (in which case the output of that run is used).
If the object given as x has been run before, it will be used here
with init-np set to the last iteration of the previous run, unless
init is given explicitly.
input of the model, either supplied as a list of values and/or
data frames, or a (netcdf) file name, or a libbi object which
has been run (in which case the output of that run is used as input)
observations of the model, either supplied as a list of values
and/or data frames, or a (netcdf) file name, or a libbi
object which has been run (in which case the output of that run is used as
observations)
The time dimension in any R objects that have been passed
(init, input) and obs); if NULL (default), will be
guessed from the given observation
The coord dimension(s) in any obs R objects that
have been passed; if NULL (default), will be guessed from the given
observation file given
any thinning of MCMC chains (1 means all will be kept, 2 skips
every other sample etc.); note that LibBi itself will write all data
to the disk. Only when the results are read in with bi_read
will thinning be applied.
real; if given, noutputs will be set so that there
is output every output_every time steps; if set to 0, only generate
an output at the final time
logical; if set to TRUE and x has been run before, the
previous output file will be used as init file, and init-np
will be set to the last iteration of the previous run (unless
target=="prediction"). This is useful for running inference chains.
Either a number (the seed to supply to LibBi), or a
logical variable: TRUE if a seed is to be generated for RBi, FALSE
if LibBi is to generate its own seed
logical; if TRUE, print more verbose messages and write all variables to the output file, irrespective of their setting of 'has_output'
list of additional arguments to pass to the call to LibBi.
Any arguments starting with `enable`/`disable` can be specified as boolean
(e.g., `assert=TRUE` or `cuda=TRUE`). Any `dry-` options can be specified
with a `"dry"` argument, e.g., `dry="parse"`. Any options that would be
specified with `with`/`without` can be specified as character vector to an
option named `with`/`without`, respectively, e.g.
with="transform-obs-to-state".
libbi