mif-methods {pomp}R Documentation

Methods of the "mif" class

Description

Methods of the "mif" class.

Usage

## S4 method for signature 'mif':
coef(object, pars, ...)
## S4 method for signature 'mif':
logLik(object, ...)
conv.rec(object, ...)
## S4 method for signature 'mif':
conv.rec(object, pars, ...)
pred.mean(object, ...)
## S4 method for signature 'mif':
pred.mean(object, pars, ...)
pred.var(object, ...)
## S4 method for signature 'mif':
pred.var(object, pars, ...)
filter.mean(object, ...)
## S4 method for signature 'mif':
filter.mean(object, pars, ...)

Arguments

object The "mif" object.
pars Names of parameters.
... Further arguments (either ignored or passed to underlying functions).

Methods

coef
Returns the value of the coef slot. These represent the best-fit parameters, generated by MIF.
coef<-
Assigns values to coefficients. coef(object,pars=NULL,...) <- value has the effect of replacing the coefficients with the specified names with the given values. By default, if value has a names attribute, these names are used, otherwise the names attribute of coef(object) is used.
conv.rec
conv.rec(object, pars = NULL) returns the columns of the convergence-record matrix corresponding to the names in pars. By default, all rows are returned.
logLik
Returns the value in the loglik slot.
mif
Re-runs the MIF iterations. See the documentation under Re-running MIF Iterations below.
plot
Plots a series of diagnostic plots.
pred.mean
pred.mean(object, pars = NULL) returns the rows of the prediction-mean matrix corresponding to the names in pars. By default, all rows are returned.
pred.var
pred.mean(object, pars = NULL) returns the rows of the prediction-variance matrix corresponding to the names in pars. By default, all rows are returned.
filter.mean
filter.mean(object, pars = NULL) returns the rows of the filtering-mean matrix corresponding to the names in pars. By default, all rows are returned.
predvarplot
predvarplot(object, pars = NULL, mean = FALSE, ...) produces a plot of the scaled prediction variances for each parameter. This can be used to diagnose a good value of the mif parameters CC and T0. If used in this way, one should run mif with Nmif=1 first. Additional arguments in ... will be passed to the actual plotting function.
pred.var
pred.var(object, pars = NULL) returns the rows of the prediction-variance matrix corresponding to the names in pars. By default, all rows are returned.
print
Prints a summary of the "mif" object.
show
Displays the "mif" object.
pfilter
See pfilter-mif.
simulate
See simulate-mif.

Author(s)

Aaron A. King (kingaa at umich dot edu)

References

E. L. Ionides, C. Bret{'o}, & A. A. King, Inference for nonlinear dynamical systems, Proc. Natl. Acad. Sci. U.S.A., 103:18438–18443, 2006.

See Also

mif, pomp, pomp-class, pfilter


[Package pomp version 0.17-3 Index]