Statistical inference for partially observed Markov processes

Documentation for package ‘pomp’ version 0.53-5

DESCRIPTION file.
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A B C D E F G L M N O P R S T V W misc

pomp-package

Partially-observed Markov processes

-- A --

abc	The ABC algorithm
abc-abc	The ABC algorithm
abc-class	The ABC algorithm
abc-method	The ABC algorithm
abc-methods	Methods of the "abc" class
abc-pomp	The ABC algorithm
abc-probed.pomp	The ABC algorithm
abcList-class	Methods of the "abc" class
as-method	Methods of the "pfilterd.pomp" class
as-method	Methods of the "pomp" class
as-method	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
as.data.frame.pfilterd.pomp	Methods of the "pfilterd.pomp" class
as.data.frame.pomp	Methods of the "pomp" class

-- B --

basic.probes	Some probes for partially-observed Markov processes
bbs	SIR models.
blowflies	Model for Nicholson's blowflies.
blowflies1	Model for Nicholson's blowflies.
blowflies2	Model for Nicholson's blowflies.
bsmc	Liu and West Bayesian Particle Filter
bsmc-method	Liu and West Bayesian Particle Filter
bsmc-pomp	Liu and West Bayesian Particle Filter
bspline.basis	B-spline bases

-- C --

c-abc	Methods of the "abc" class
c-abcList	Methods of the "abc" class
c-method	Methods of the "abc" class
c-method	Methods of the "mif" class
c-method	Methods of the "pmcmc" class
c-mif	Methods of the "mif" class
c-mifList	Methods of the "mif" class
c-pmcmc	Methods of the "pmcmc" class
c-pmcmcList	Methods of the "pmcmc" class
coef-method	Methods of the "pomp" class
coef-pomp	Methods of the "pomp" class
coef<-	Methods of the "pomp" class
coef<--method	Methods of the "pomp" class
coef<--pomp	Methods of the "pomp" class
coerce-method	Methods of the "pfilterd.pomp" class
coerce-method	Methods of the "pomp" class
coerce-method	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
compare.mif	Methods of the "mif" class
cond.logLik	Methods of the "pfilterd.pomp" class
cond.logLik-method	Methods of the "pfilterd.pomp" class
cond.logLik-pfilterd.pomp	Methods of the "pfilterd.pomp" class
continue	Iterated filtering
continue-abc	The ABC algorithm
continue-method	The ABC algorithm
continue-method	Iterated filtering
continue-method	The PMCMC algorithm
continue-mif	Iterated filtering
continue-pmcmc	The PMCMC algorithm
conv.rec	Methods of the "mif" class
conv.rec-abc	Methods of the "abc" class
conv.rec-abcList	Methods of the "abc" class
conv.rec-method	Methods of the "abc" class
conv.rec-method	Methods of the "mif" class
conv.rec-method	Methods of the "pmcmc" class
conv.rec-mif	Methods of the "mif" class
conv.rec-mifList	Methods of the "mif" class
conv.rec-pmcmc	Methods of the "pmcmc" class
conv.rec-pmcmcList	Methods of the "pmcmc" class
Csnippet	C code snippets
Csnippet-class	C code snippets

-- D --

dacca	Model of cholera transmission for historic Bengal.
data.array	Methods of the "pomp" class
data.array-method	Methods of the "pomp" class
data.array-pomp	Methods of the "pomp" class
data.frame-pomp	Partially-observed Markov process object.
deulermultinom	Euler-multinomial death process
discrete.time.sim	Plug-ins for dynamical models based on stochastic Euler algorithms

-- E --

eff.sample.size	Methods of the "pfilterd.pomp" class
eff.sample.size-method	Methods of the "pfilterd.pomp" class
eff.sample.size-pfilterd.pomp	Methods of the "pfilterd.pomp" class
euler.sim	Plug-ins for dynamical models based on stochastic Euler algorithms
euler.sir	SIR models.
eulermultinom	Euler-multinomial death process

-- F --

filter.mean	Methods of the "pfilterd.pomp" class
filter.mean-method	Methods of the "pfilterd.pomp" class
filter.mean-pfilterd.pomp	Methods of the "pfilterd.pomp" class

-- G --

gillespie.sim	Plug-ins for dynamical models based on stochastic Euler algorithms
gillespie.sir	SIR models.
gompertz	Gompertz model with log-normal observations.

-- L --

logLik-method	Methods of the "mif" class
logLik-method	Fit Model to Data Using Nonlinear Forecasting (NLF)
logLik-method	Methods of the "pfilterd.pomp" class
logLik-method	Methods of the "pmcmc" class
logLik-method	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
logLik-method	Trajectory matching
logLik-mif	Methods of the "mif" class
logLik-nlfd.pomp	Fit Model to Data Using Nonlinear Forecasting (NLF)
logLik-pfilterd.pomp	Methods of the "pfilterd.pomp" class
logLik-pmcmc	Methods of the "pmcmc" class
logLik-probed.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
logLik-traj.matched.pomp	Trajectory matching
logmeanexp	The log-mean-exp trick
LondonYorke	Historical childhood disease incidence data

-- M --

matrix-pomp	Partially-observed Markov process object.
mif	Iterated filtering
mif-class	Iterated filtering
mif-method	Iterated filtering
mif-methods	Methods of the "mif" class
mif-mif	Iterated filtering
mif-pfilterd.pomp	Iterated filtering
mif-pomp	Iterated filtering
mifList-class	Methods of the "mif" class

-- N --

nlf	Fit Model to Data Using Nonlinear Forecasting (NLF)
nlf-method	Fit Model to Data Using Nonlinear Forecasting (NLF)
nlf-nlfd.pomp	Fit Model to Data Using Nonlinear Forecasting (NLF)
nlf-pomp	Fit Model to Data Using Nonlinear Forecasting (NLF)
nlfd.pomp-class	Fit Model to Data Using Nonlinear Forecasting (NLF)
numeric-pomp	Partially-observed Markov process object.

-- O --

obs	Methods of the "pomp" class
obs-method	Methods of the "pomp" class
obs-pomp	Methods of the "pomp" class
onestep.dens	Plug-ins for dynamical models based on stochastic Euler algorithms
onestep.sim	Plug-ins for dynamical models based on stochastic Euler algorithms
ou2	Two-dimensional discrete-time Ornstein-Uhlenbeck process

-- P --

parmat	Create a matrix of parameters
partrans	Methods of the "pomp" class
partrans-method	Methods of the "pomp" class
partrans-pomp	Methods of the "pomp" class
periodic.bspline.basis	B-spline bases
pfilter	Particle filter
pfilter-method	Particle filter
pfilter-pfilterd.pomp	Particle filter
pfilter-pomp	Particle filter
pfilterd.pomp-class	Particle filter
plot-abc	Methods of the "abc" class
plot-abcList	Methods of the "abc" class
plot-bsmcd.pomp	Liu and West Bayesian Particle Filter
plot-method	Methods of the "abc" class
plot-method	Liu and West Bayesian Particle Filter
plot-method	Methods of the "mif" class
plot-method	Methods of the "pmcmc" class
plot-method	Methods of the "pomp" class
plot-method	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
plot-mif	Methods of the "mif" class
plot-mifList	Methods of the "mif" class
plot-pmcmc	Methods of the "pmcmc" class
plot-pmcmcList	Methods of the "pmcmc" class
plot-pomp	Methods of the "pomp" class
plot-probe.matched.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
plot-probed.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
plot-spect.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
plugins	Plug-ins for dynamical models based on stochastic Euler algorithms
pmcmc	The PMCMC algorithm
pmcmc-class	The PMCMC algorithm
pmcmc-method	The PMCMC algorithm
pmcmc-methods	Methods of the "pmcmc" class
pmcmc-pfilterd.pomp	The PMCMC algorithm
pmcmc-pmcmc	The PMCMC algorithm
pmcmc-pomp	The PMCMC algorithm
pmcmcList-class	Methods of the "pmcmc" class
pomp	Partially-observed Markov process object.
pomp-class	Partially-observed Markov process object.
pomp-method	Partially-observed Markov process object.
pomp-methods	Methods of the "pomp" class
pomp-pomp	Partially-observed Markov process object.
pompBuilder	Write, compile, link, and build a pomp object using native codes
pompExample	Pre-built examples of pomp objects.
pred.mean	Methods of the "pfilterd.pomp" class
pred.mean-method	Methods of the "pfilterd.pomp" class
pred.mean-pfilterd.pomp	Methods of the "pfilterd.pomp" class
pred.var	Methods of the "pfilterd.pomp" class
pred.var-method	Methods of the "pfilterd.pomp" class
pred.var-pfilterd.pomp	Methods of the "pfilterd.pomp" class
print-method	Methods of the "pomp" class
print-pomp	Methods of the "pomp" class
probe	Probe a partially-observed Markov process.
probe-method	Probe a partially-observed Markov process.
probe-pomp	Probe a partially-observed Markov process.
probe-probed.pomp	Probe a partially-observed Markov process.
probe.acf	Some probes for partially-observed Markov processes
probe.ccf	Some probes for partially-observed Markov processes
probe.marginal	Some probes for partially-observed Markov processes
probe.match	Probe a partially-observed Markov process.
probe.match-method	Probe a partially-observed Markov process.
probe.match-pomp	Probe a partially-observed Markov process.
probe.match-probe.matched.pomp	Probe a partially-observed Markov process.
probe.match-probed.pomp	Probe a partially-observed Markov process.
probe.match.objfun	Probe a partially-observed Markov process.
probe.match.objfun-method	Probe a partially-observed Markov process.
probe.match.objfun-pomp	Probe a partially-observed Markov process.
probe.match.objfun-probed.pomp	Probe a partially-observed Markov process.
probe.matched.pomp-class	Probe a partially-observed Markov process.
probe.matched.pomp-methods	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
probe.mean	Some probes for partially-observed Markov processes
probe.median	Some probes for partially-observed Markov processes
probe.nlar	Some probes for partially-observed Markov processes
probe.period	Some probes for partially-observed Markov processes
probe.quantile	Some probes for partially-observed Markov processes
probe.sd	Some probes for partially-observed Markov processes
probe.var	Some probes for partially-observed Markov processes
probed.pomp-class	Probe a partially-observed Markov process.
probed.pomp-methods	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
profileDesign	Design matrices for likelihood profile calculations.

-- R --

reulermultinom	Euler-multinomial death process
rgammawn	Euler-multinomial death process
ricker	Ricker model with Poisson observations.
rw2	Two-dimensional random-walk process

-- S --

sannbox	Simulated annealing with box constraints.
show-method	Methods of the "pomp" class
show-pomp	Methods of the "pomp" class
simulate-method	Running simulations of a partially-observed Markov process
simulate-pomp	Running simulations of a partially-observed Markov process
sliceDesign	Design matrices for likelihood slices.
sobol	Sobol' low-discrepancy sequence
sobolDesign	Sobol' low-discrepancy sequence
spect	Power spectrum computation for partially-observed Markov processes.
spect-method	Power spectrum computation for partially-observed Markov processes.
spect-pomp	Power spectrum computation for partially-observed Markov processes.
spect-spect.pomp	Power spectrum computation for partially-observed Markov processes.
spect.match	Power spectrum computation for partially-observed Markov processes.
spect.match-method	Power spectrum computation for partially-observed Markov processes.
spect.match-pomp	Power spectrum computation for partially-observed Markov processes.
spect.match-spect.pomp	Power spectrum computation for partially-observed Markov processes.
spect.matched.pomp-class	Power spectrum computation for partially-observed Markov processes.
spect.matched.pomp-methods	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
spect.pomp-class	Power spectrum computation for partially-observed Markov processes.
spect.pomp-methods	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
states	Methods of the "pomp" class
states-method	Methods of the "pomp" class
states-pomp	Methods of the "pomp" class
summary-method	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
summary-method	Trajectory matching
summary-probe.matched.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
summary-probed.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
summary-spect.matched.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
summary-spect.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
summary-traj.matched.pomp	Trajectory matching

-- T --

time-method	Methods of the "pomp" class
time-pomp	Methods of the "pomp" class
time<-	Methods of the "pomp" class
time<--method	Methods of the "pomp" class
time<--pomp	Methods of the "pomp" class
timezero	Methods of the "pomp" class
timezero-method	Methods of the "pomp" class
timezero-pomp	Methods of the "pomp" class
timezero<-	Methods of the "pomp" class
timezero<--method	Methods of the "pomp" class
timezero<--pomp	Methods of the "pomp" class
traj.match	Trajectory matching
traj.match-method	Trajectory matching
traj.match-pomp	Trajectory matching
traj.match-traj.matched.pomp	Trajectory matching
traj.match.objfun	Trajectory matching
traj.match.objfun-method	Trajectory matching
traj.match.objfun-pomp	Trajectory matching
traj.matched.pomp-class	Trajectory matching
trajectory	Compute trajectories of the deterministic skeleton.
trajectory-method	Compute trajectories of the deterministic skeleton.
trajectory-pomp	Compute trajectories of the deterministic skeleton.

-- V --

verhulst

Simple Verhulst-Pearl (logistic) model.

-- W --

window-method	Methods of the "pomp" class
window-pomp	Methods of the "pomp" class

-- misc --

$-bsmcd.pomp	Liu and West Bayesian Particle Filter
$-method	Liu and West Bayesian Particle Filter
$-method	Fit Model to Data Using Nonlinear Forecasting (NLF)
$-method	Methods of the "pfilterd.pomp" class
$-method	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
$-method	Trajectory matching
$-nlfd.pomp	Fit Model to Data Using Nonlinear Forecasting (NLF)
$-pfilterd.pomp	Methods of the "pfilterd.pomp" class
$-probe.matched.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
$-probed.pomp	Methods of the "probed.pomp", "probe.matched.pomp", "spect.pomp", and "spect.matched.pomp" classes
$-traj.matched.pomp	Trajectory matching
[-abcList	Methods of the "abc" class
[-method	Methods of the "abc" class
[-method	Methods of the "mif" class
[-method	Methods of the "pmcmc" class
[-mifList	Methods of the "mif" class
[-pmcmcList	Methods of the "pmcmc" class