pomp-methods {pomp}R Documentation

Methods of the "pomp" class

Description

Methods of the pomp class.

Usage

## S4 method for signature 'pomp':
coef(object, pars, ...)
## S4 method for signature 'pomp':
coef(object, pars, ...) <- value
## S4 method for signature 'pomp':
data.array(object, vars, ...)
## S4 method for signature 'pomp':
states(object, vars, ...)
## S4 method for signature 'pomp':
time(x, t0 = FALSE, ...)
## S4 method for signature 'pomp':
show(object)
## S4 method for signature 'pomp':
as(object, class)
## S4 method for signature 'pomp, data.frame':
coerce(from, to = "data.frame", strict = TRUE)
## S4 method for signature 'pomp':
print(x, ...)
## S4 method for signature 'pomp':
plot(x, y, variables, panel = lines,
      nc = NULL, yax.flip = FALSE,
      mar = c(0, 5.1, 0, if (yax.flip) 5.1 else 2.1),
      oma = c(6, 0, 5, 0), axes = TRUE, ...)

Arguments

object, x The pomp object.
pars optional character; names of parameters to be retrieved or set.
vars optional character; names of observed variables to be retrieved.
value numeric; values to be assigned to the parameters.
t0 logical; if TRUE, the zero time is prepended to the time vector.
class character; name of the class to which object should be coerced.
from, to the classes betwen which coercion should be performed.
strict ignored.
y ignored.
variables optional character; names of variables to plot.
panel a 'function(x, col, bg, pch, type, ...)' which gives the action to be carried out in each panel of the display.
nc the number of columns to use. Defaults to 1 for up to 4 series, otherwise to 2.
yax.flip logical; if TRUE, the y-axis (ticks and numbering) should flip from side 2 (left) to 4 (right) from series to series.
mar, oma the 'par' settings for 'mar' and 'oma' to use. Modify with care!
axes logical; indicates if x- and y- axes should be drawn.
... Further arguments (either ignored or passed to underlying functions).

Details

coef
coef(object) returns the contents of the params slot of object. coef(object,pars) returns only those parameters named in pars.
coef<-
Assigns values to the params slot of the pomp object. If coef(object) exists, then coef(object) <- value has the effect of replacing the parameters of object with value; the names of value will be ignored and the names of coef(object) will be unchanged. If coef(object) does not exist, then coef(object) <- value assigns value to the parameters of object; the names of coef(object) will be those of value and an error will be generated if value does not have names. If coef(object) exists, then coef(object,pars) <- value replaces those parameters of object named in pars with the elements of value; the names of value are ignored. If coef(object) does not exist, then coef(object,pars) <- value assigns value to the parameters of object; in this case, the names of object will be pars and the names of value will be ignored.
data.array
data.array(object) returns the array of observations. data.array(object,vars) gives just the observations of variables vars. vars may specify the variables by position or by name.
states
states(object) returns the array of states. states(object,vars) gives just the state variables named in vars. vars may specify the variables by position or by name.
time
time(object) returns the vector of observation times. time(object,t0=TRUE) returns the vector of observation times with the zero-time t0 prepended.
show
Displays the pomp object.
plot
Plots the data and state trajectories (if the latter exist). Additional arguments are passed to the low-level plotting routine.
print
Prints the pomp object in a nice way.
as, coerce
The coerce method should typically not be used directly. It is defined by setAs as a method to be used by as. A pomp object can be coerced to a data frame via as(object,"data.frame"). The data frame contains the times, the data, and the state trajectories, if they exist.
rprocess
simulates the process model. See rprocess-pomp.
dprocess
evaluates the process model density. See dprocess-pomp.
rmeasure
simulates the measurement model. See rmeasure-pomp.
dmeasure
evaluates the measurement-model density. See dmeasure-pomp.
skeleton
evaluates the deterministic skeleton (be it a vector field or a map). See skeleton-pomp.
init.state
returns a vector of initialial conditions. See init.state-pomp.
simulate
simulate can be used to simulate state and observation trajectories. See documentation under simulate-pomp.

Author(s)

Aaron A. King (kingaa at umich dot edu)

See Also

pomp, pomp-class, rprocess, dprocess, rmeasure, dmeasure, init.state, simulate-pomp


[Package pomp version 0.22-6 Index]