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DOBAD (version 1.0.6)

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

Description

Provides Frequentist (EM) and Bayesian (MCMC) Methods for Inference of Birth-Death-Immigration Markov Chains.

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Version

Install

install.packages('DOBAD')

Monthly Downloads

45

Version

1.0.6

License

GPL (>= 2)

Maintainer

Charles Doss

Last Published

December 7th, 2017

Functions in DOBAD (1.0.6)

ARsim

Accept-Reject Simulation
BDloglikelihood.PO

Calculate log likelihood of Partially Observed BD process
BD.EMInference.prodExpecs

Functions That Calculate Product Expectations Needed for Inference via EM Algorithm
BDPOloglikeGradSqr.CTMC_PO_many

Gradient-Squared of PartialData likelihood
BD.MCMC.SC

MCMC on Linear Birth Death Process
CTMC-class

Class "CTMC"
BDsummaryStats

Get summary statistics for EM Algorithm on Linear Birth-Death Process
CTMC.simulate

Simulate from ("regular") CTMC
BDMC-class

Class "BDMC"
BDMC_many-class

Class "BDMC_many"
CTMC.simulate.piecewise

Simulate from piecewise constant/homogeneous CTMC
EM.BD.SC

Expectation-Maximization on Linear Birth Death (_S_pecial _C_ase with constrained immigration)
CTMC2list

Convert Between two representations of a Continuous Time Markov Chain.
EMutilities

Functions related to implementing the EM algorithm on partially observed Birth-Death Chain
CTMCPO2indepIntervals

Converts CTMC_PO (either CTMC_PO_1 or CTMC_PO_many) to independent intervals.
EM.BD.SC.cov.1sv

Expectation-Maximization on Linear Birth Death (and constrained Immigration) with Covariates
add.uncond.mean.one

ENplus, ENminus, Eholdtime, unconditional on ending state.
Nij

Count transitions in a fully observed CTMC.
bdARsimCondEnd

Conditional Simulation of BD via Accept-Reject
CTMC_PO_many-class

Class "CTMC_PO_many"
combineCTMC

Combine several CTMCs into one CTMC
doublebracket-methods

Methods for Function [[ in Package DOBAD
derivType

Helper for getting means from generating functions
getBDMCsPOlist-methods

Methods for Function getBDMCsPOlist in Package DOBAD
getMCstate

Get the state of a CTMC at various times
getNewParams.SC

Solve for new parameters in restricted model in EM algorithm.
getBDinform.PO

Get Information Matrix for MLE estimates on Partially Observed Linear Birth Death (_S_pecial _C_ase with constrained immigration)
getSubMC

Extract a Sub Markov Chain
getT-methods

~~ Methods for Function getT in Package `DOBAD' ~~
getBDinform

Helpers for Getting Information Matrix for MLE estimates on Partially Observed Linear Birth Death (_S_pecial _C_ase with constrained immigration)
num.deriv

Numerical Differentiation
Nplus

Calculate summary statistics for BDMCs and CTMC_POs
plot-methods

Plot CTMCs
add.generator

Generating functions for birth-death processes with immigration
power.coef.one

Gets coefficients of a power series..
process.prob.one

Calculate transition probability for linear birth death process.
add.joint.mean.many

Mean counts and particle time averages for birth-death processes with immigration
sampleJumpTime2

Functions for Simulating Conditionally the first Jump of a chain.
getPartialData

Get "partially Observed " Chain from a fully observed one.
sim.condBD

Simulate birth-death process, Conditionally upon observing its state at finite, discrete time points
getStates

Get list of jump states.
getIthJumpTime

Get the jump times from a CTMC.
simplify

Transform Lists to Vectors
graph.CTMC

Plot CTMCs (possibly Partially Observed)
sub-methods

Subscripting CTMCs
birth.death.simulant

Simulation of birth-death processes with immigration
getTs-methods

~~ Methods for Function getTs in Package `DOBAD' ~~
bracket-methods

Methods for Function [ in Package DOBAD
getInitParams

Get multiple starting parameters for EM
CTMC_PO_1-class

Class "CTMC_PO_1"
getBDjTimes

Get Jump times of a BD process.
getDataSummary.CTMC_PO_many

Calculate Some Summarizing Information for the Given Data
getTimes

Get list of jump times.
list2CTMC

Convert a list representation of a CTMC to the class version