Statistical inference for partially observed Markov processes


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Documentation for package ‘pomp’ version 0.53-5

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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