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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
1.0.6
1.0.5
1.0.4
1.0.3
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Install
install.packages('DOBAD')
Monthly Downloads
196
Version
1.0.6
License
GPL (>= 2)
Maintainer
Charles Doss
Last Published
December 7th, 2017
Functions in DOBAD (1.0.6)
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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