Description Usage Arguments Running ABC Re-running ABC iterations Continuing ABC iterations Methods Author(s) References See Also
The approximate Bayesian computation (ABC) algorithm for estimating the parameters of a partially-observed Markov process.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## S4 method for signature 'data.frame'
abc(data, Nabc = 1, proposal, scale, epsilon,
probes, params, rinit, rprocess, rmeasure, dprior, ...,
verbose = getOption("verbose", FALSE))
## S4 method for signature 'pomp'
abc(data, Nabc = 1, proposal, scale, epsilon, probes,
..., verbose = getOption("verbose", FALSE))
## S4 method for signature 'probed_pomp'
abc(data, probes, ...,
verbose = getOption("verbose", FALSE))
## S4 method for signature 'abcd_pomp'
abc(data, Nabc, proposal, scale, epsilon, probes,
..., verbose = getOption("verbose", FALSE))
|
data |
either a data frame holding the time series data, or an object of class ‘pomp’, i.e., the output of another pomp calculation. |
Nabc |
the number of ABC iterations to perform. |
proposal |
optional function that draws from the proposal distribution. Currently, the proposal distribution must be symmetric for proper inference: it is the user's responsibility to ensure that it is. Several functions that construct appropriate proposal function are provided: see MCMC proposals for more information. |
scale |
named numeric vector of scales. |
epsilon |
ABC tolerance. |
probes |
a single probe or a list of one or more probes. A probe is simply a scalar- or vector-valued function of one argument that can be applied to the data array of a ‘pomp’. A vector-valued probe must always return a vector of the same size. A number of useful probes are provided with the package: see basic probes. |
params |
optional; named numeric vector of parameters.
This will be coerced internally to storage mode |
rinit |
simulator of the initial-state distribution.
This can be furnished either as a C snippet, an R function, or the name of a pre-compiled native routine available in a dynamically loaded library.
Setting |
rprocess |
simulator of the latent state process, specified using one of the rprocess plugins.
Setting |
rmeasure |
simulator of the measurement model, specified either as a C snippet, an R function, or the name of a pre-compiled native routine available in a dynamically loaded library.
Setting |
dprior |
optional; prior distribution density evaluator, specified either as a C snippet, an R function, or the name of a pre-compiled native routine available in a dynamically loaded library.
For more information, see here.
Setting |
... |
additional arguments supply new or modify existing model characteristics or components.
See When named arguments not recognized by |
verbose |
logical; if |
abc
returns an object of class ‘abcd_pomp’.
One or more ‘abcd_pomp’ objects can be joined to form an ‘abcList’ object.
To re-run a sequence of ABC iterations, one can use the abc
method on a ‘abcd_pomp’ object.
By default, the same parameters used for the original ABC run are re-used (except for verbose
, the default of which is shown above).
If one does specify additional arguments, these will override the defaults.
One can continue a series of ABC iterations from where one left off using the continue
method.
A call to abc
to perform Nabc=m
iterations followed by a call to continue
to perform Nabc=n
iterations will produce precisely the same effect as a single call to abc
to perform Nabc=m+n
iterations.
By default, all the algorithmic parameters are the same as used in the original call to abc
.
Additional arguments will override the defaults.
The following can be applied to the output of an abc
operation:
produces a series of diagnostic plots
produces a mcmc
object, to which the various coda convergence diagnostics can be applied
Edward L. Ionides, Aaron A. King
J.-M. Marin, P. Pudlo, C. P. Robert, and R. J. Ryder, Approximate Bayesian computational methods. Statistics and Compuing 22:1167–1180, 2012.
T. Toni and M. P. H. Stumpf, Simulation-based model selection for dynamical systems in systems and population biology, Bioinformatics 26:104–110, 2010.
T. Toni, D. Welch, N. Strelkowa, A. Ipsen, and M. P. H. Stumpf, Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems Journal of the Royal Society, Interface 6:187–202, 2009.
MCMC proposals
Other summary statistics methods: basic_probes
,
probe.match
, probe
,
spect
Other pomp parameter estimation methods: bsmc2
,
kalman
, mif2
,
nlf
, pmcmc
,
pomp2-package
, probe.match
,
spect.match
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