Analysis of Discretely Observed Linear Birth-and-Death(-and-Immigration) Markov Chains


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Documentation for package ‘DOBAD’ version 1.0.6

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A B C D E F G H L M N P R S T W misc

-- A --

add.cond.mean.many Mean counts and particle time averages for birth-death processes with immigration
add.cond.mean.one Mean counts and particle time averages for birth-death processes with immigration
add.cond.meanSq.one Mean counts and particle time averages for birth-death processes with immigration
add.generator Generating functions for birth-death processes with immigration
add.joint.mean.many Mean counts and particle time averages for birth-death processes with immigration
add.joint.mean.one Mean counts and particle time averages for birth-death processes with immigration
add.joint.meanSq.one Mean counts and particle time averages for birth-death processes with immigration
add.uncond.mean.one ENplus, ENminus, Eholdtime, unconditional on ending state.
addhold.cond.mean.one Mean counts and particle time averages for birth-death processes with immigration
addhold.generator Generating functions for birth-death processes with immigration
addhold.joint.mean.one Mean counts and particle time averages for birth-death processes with immigration
addrem.cond.mean.one Mean counts and particle time averages for birth-death processes with immigration
addrem.generator Generating functions for birth-death processes with immigration
addrem.joint.mean.one Mean counts and particle time averages for birth-death processes with immigration
addremhold.generator Generating functions for birth-death processes with immigration
all.cond.mean.PO Mean counts and particle time averages for birth-death processes with immigration
all.cond.mean2.PO Mean counts and particle time averages for birth-death processes with immigration
ARsim Accept-Reject Simulation

-- B --

BD.MCMC.SC MCMC on Linear Birth Death Process
bdARsimCondEnd Conditional Simulation of BD via Accept-Reject
bdARsimCondEnd.1 Conditional Simulation of BD via Accept-Reject
BDloglikelihood.PO Calculate log likelihood of Partially Observed BD process
BDloglikelihood.PO.CTMC_PO_1 Calculate log likelihood of Partially Observed BD process
BDloglikelihood.PO.CTMC_PO_many Calculate log likelihood of Partially Observed BD process
BDloglikelihood.PO.list Calculate log likelihood of Partially Observed BD process
BDMC-class Class "BDMC"
BDMC_many-class Class '"BDMC_many"'
BDPOloglikeGradSqr.CTMC_PO_many Gradient-Squared of PartialData likelihood
BDsummaryStats Get summary statistics for EM Algorithm on Linear Birth-Death Process
BDsummaryStats-method Get summary statistics for EM Algorithm on Linear Birth-Death Process
BDsummaryStats.PO Get summary statistics for EM Algorithm on Linear Birth-Death Process
BDsummaryStats.PO-method Get summary statistics for EM Algorithm on Linear Birth-Death Process
birth.death.simulant Simulation of birth-death processes with immigration

-- C --

combineCTMC Combine several CTMCs into one CTMC
CTMC-class Class "CTMC"
CTMC.simulate Simulate from ("regular") CTMC
CTMC.simulate.piecewise Simulate from piecewise constant/homogeneous CTMC
CTMC2list Convert Between two representations of a Continuous Time Markov Chain.
CTMCPO2indepIntervals Converts CTMC_PO (either CTMC_PO_1 or CTMC_PO_many) to independent intervals.
CTMCPO2indepIntervals.CTMC_PO_1 Converts CTMC_PO (either CTMC_PO_1 or CTMC_PO_many) to independent intervals.
CTMCPO2indepIntervals.CTMC_PO_many Converts CTMC_PO (either CTMC_PO_1 or CTMC_PO_many) to independent intervals.
CTMC_PO_1-class Class "CTMC_PO_1"
CTMC_PO_many-class Class "CTMC_PO_many"

-- D --

derivType Helper for getting means from generating functions

-- E --

E.step.SC Functions related to implementing the EM algorithm on partially observed Birth-Death Chain
EM.BD.SC Expectation-Maximization on Linear Birth Death (_S_pecial _C_ase with constrained immigration)
EM.BD.SC.1 Expectation-Maximization on Linear Birth Death (_S_pecial _C_ase with constrained immigration)
EM.BD.SC.cov.1sv Expectation-Maximization on Linear Birth Death (and constrained Immigration) with Covariates

-- F --

f.i Functions for Simulating Conditionally the first Jump of a chain.

-- G --

genDoneSided Numerical Differentiation
getBDinform.full.SC.manual Helpers for Getting Information Matrix for MLE estimates on Partially Observed Linear Birth Death (_S_pecial _C_ase with constrained immigration)
getBDinform.lost.SC.manual Helpers for Getting Information Matrix for MLE estimates on Partially Observed Linear Birth Death (_S_pecial _C_ase with constrained immigration)
getBDinform.PO Get Information Matrix for MLE estimates on Partially Observed Linear Birth Death (_S_pecial _C_ase with constrained immigration)
getBDinform.PO.SC Get Information Matrix for MLE estimates on Partially Observed Linear Birth Death (_S_pecial _C_ase with constrained immigration)
getBDinform.PO.SC.manual Helpers for Getting Information Matrix for MLE estimates on Partially Observed Linear Birth Death (_S_pecial _C_ase with constrained immigration)
getBDjTimes Get Jump times of a BD process.
getBDMCsPOlist Methods for Function 'getBDMCsPOlist' in Package 'DOBAD'
getBDMCsPOlist-method Methods for Function 'getBDMCsPOlist' in Package 'DOBAD'
getBDMCsPOlist-methods Methods for Function 'getBDMCsPOlist' in Package 'DOBAD'
getBDsummaryExpecs Functions That Calculate Product Expectations Needed for Inference via EM Algorithm
getBDsummaryProdExpecs Functions That Calculate Product Expectations Needed for Inference via EM Algorithm
getDataSummary Calculate Some Summarizing Information for the Given Data
getDataSummary.CTMC_PO_many Calculate Some Summarizing Information for the Given Data
getInitParams Get multiple starting parameters for EM
getIthJumpTime Get the jump times from a CTMC.
getIthJumpTimes Get the jump times from a CTMC.
getIthState Get the jump times from a CTMC.
getMCstate Get the state of a CTMC at various times
getNewParams.SC Solve for new parameters in restricted model in EM algorithm.
getPartialData Get "partially Observed " Chain from a fully observed one.
getStates Get list of jump states.
getStates-method Get list of jump states.
getSubMC Extract a Sub Markov Chain
getT ~~ Methods for Function getT in Package 'DOBAD' ~~
getT-method ~~ Methods for Function getT in Package 'DOBAD' ~~
getT-methods ~~ Methods for Function getT in Package 'DOBAD' ~~
getTimes Get list of jump times.
getTimes-method Get list of jump times.
getTs ~~ Methods for Function getTs in Package 'DOBAD' ~~
getTs-method ~~ Methods for Function getTs in Package 'DOBAD' ~~
getTs-methods ~~ Methods for Function getTs in Package 'DOBAD' ~~
graph.CTMC Plot CTMCs (possibly Partially Observed)
graph.CTMC.PO Plot CTMCs (possibly Partially Observed)

-- H --

hessianOneSided Numerical Differentiation
hold.cond.mean.one Mean counts and particle time averages for birth-death processes with immigration
hold.cond.meanSq.one Mean counts and particle time averages for birth-death processes with immigration
hold.generator Generating functions for birth-death processes with immigration
hold.joint.meanSq.one Mean counts and particle time averages for birth-death processes with immigration
hold.uncond.mean.one ENplus, ENminus, Eholdtime, unconditional on ending state.
holdTime Calculate summary statistics for BDMCs and CTMC_POs

-- L --

list2CTMC Convert a list representation of a CTMC to the class version

-- M --

M.step.SC Functions related to implementing the EM algorithm on partially observed Birth-Death Chain

-- N --

Nij Count transitions in a fully observed CTMC.
NijBD Get summary statistics for EM Algorithm on Linear Birth-Death Process
NijBD.CTMC_many Get summary statistics for EM Algorithm on Linear Birth-Death Process
Nminus Calculate summary statistics for BDMCs and CTMC_POs
Nminus.CTMC_PO_many Calculate summary statistics for BDMCs and CTMC_POs
Nplus Calculate summary statistics for BDMCs and CTMC_POs
Nplus.CTMC_PO_many Calculate summary statistics for BDMCs and CTMC_POs
num.deriv Numerical Differentiation

-- P --

p.i Functions for Simulating Conditionally the first Jump of a chain.
plot-method Plot CTMCs
plot-methods Plot CTMCs
power.coef.many Gets coefficients of a power series..
power.coef.one Gets coefficients of a power series..
process.generator Generating functions for birth-death processes with immigration
process.prob.many Calculate transition probability for linear birth death process.
process.prob.one Calculate transition probability for linear birth death process.

-- R --

rem.cond.mean.many Mean counts and particle time averages for birth-death processes with immigration
rem.cond.mean.one Mean counts and particle time averages for birth-death processes with immigration
rem.cond.meanSq.one Mean counts and particle time averages for birth-death processes with immigration
rem.generator Generating functions for birth-death processes with immigration
rem.joint.mean.many Mean counts and particle time averages for birth-death processes with immigration
rem.joint.mean.one Mean counts and particle time averages for birth-death processes with immigration
rem.joint.meanSq.one Mean counts and particle time averages for birth-death processes with immigration
rem.uncond.mean.one ENplus, ENminus, Eholdtime, unconditional on ending state.
remhold.cond.mean.one Mean counts and particle time averages for birth-death processes with immigration
remhold.generator Generating functions for birth-death processes with immigration
remhold.joint.mean.one Mean counts and particle time averages for birth-death processes with immigration

-- S --

sampleJumpTime2 Functions for Simulating Conditionally the first Jump of a chain.
sim.condBD Simulate birth-death process, Conditionally upon observing its state at finite, discrete time points
sim.condBD.1 Simulate birth-death process, Conditionally upon observing its state at finite, discrete time points
sim.condBD.main Simulate birth-death process, Conditionally upon observing its state at finite, discrete time points
sim.condBD.main.CTMC_PO_1 Simulate birth-death process, Conditionally upon observing its state at finite, discrete time points
sim.condBD.main.default Simulate birth-death process, Conditionally upon observing its state at finite, discrete time points
sim.condBD.main.list Simulate birth-death process, Conditionally upon observing its state at finite, discrete time points
simplify Transform Lists to Vectors

-- T --

timeave.cond.mean.many Mean counts and particle time averages for birth-death processes with immigration
timeave.cond.mean.one Mean counts and particle time averages for birth-death processes with immigration
timeave.joint.mean.many Mean counts and particle time averages for birth-death processes with immigration
timeave.joint.mean.one Mean counts and particle time averages for birth-death processes with immigration
timeave.laplace Generating functions for birth-death processes with immigration

-- W --

waitTimes Get summary statistics for EM Algorithm on Linear Birth-Death Process

-- misc --

[-method Methods for Function '[' in Package 'DOBAD'
[-method Subscripting CTMCs
[[-method Methods for Function '[[' in Package 'DOBAD'
[[-method Subscripting CTMCs