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

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

AuthorCharles Doss, Vladimir Minin, Marc Suchard
Date of publication2016-03-24 23:29:52
MaintainerCharles Doss <cdoss@umn.edu>
LicenseGPL (>= 2)
Version1.0.5

View on CRAN

Man pages

add.generator: Generating functions for birth-death processes with...

add.joint.mean.many: Mean counts and particle time averages for birth-death...

add.uncond.mean.one: ENplus, ENminus, Eholdtime, unconditional on ending state.

ARsim: Accept-Reject Simulation

bdARsimCondEnd: Conditional Simulation of BD via Accept-Reject

BD.EMInference.prodExpecs: Functions That Calculate Product Expectations Needed for...

BDloglikelihood.PO: Calculate log likelihood of Partially Observed BD process

BDMC-class: Class "BDMC"

BDMC_many-class: Class '"BDMC_many"'

BD.MCMC.SC: MCMC on Linear Birth Death Process

BDPOloglikeGradSqr.CTMC_PO_many: Gradient-Squared of PartialData likelihood

BDsummaryStats: Get summary statistics for EM Algorithm on Linear Birth-Death...

birth.death.simulant: Simulation of birth-death processes with immigration

bracket-methods: Methods for Function '[' in Package 'DOBAD'

combineCTMC: Combine several CTMCs into one CTMC

CTMC2list: Convert Between two representations of a Continuous Time...

CTMC-class: Class "CTMC"

CTMC_PO_1-class: Class "CTMC_PO_1"

CTMCPO2indepIntervals: Converts CTMC_PO (either CTMC_PO_1 or CTMC_PO_many) to...

CTMC_PO_many-class: Class "CTMC_PO_many"

CTMC.simulate: Simulate from ("regular") CTMC

CTMC.simulate.piecewise: Simulate from piecewise constant/homogeneous CTMC

derivType: Helper for getting means from generating functions

doublebracket-methods: Methods for Function '[[' in Package 'DOBAD'

EM.BD.SC: Expectation-Maximization on Linear Birth Death (_S_pecial...

EMutilities: Functions related to implementing the EM algorithm on...

getBDinform: Helpers for Getting Information Matrix for MLE estimates on...

getBDinform.PO: Get Information Matrix for MLE estimates on Partially...

getBDjTimes: Get Jump times of a BD process.

getBDMCsPOlist-methods: Methods for Function 'getBDMCsPOlist' in Package 'DOBAD'

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.

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.

getSubMC: Extract a Sub Markov Chain

getTimes: Get list of jump times.

getT-methods: ~~ Methods for Function getT in Package 'DOBAD' ~~

getTs-methods: ~~ Methods for Function getTs in Package 'DOBAD' ~~

graph.CTMC: Plot CTMCs (possibly Partially Observed)

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

Nij: Count transitions in a fully observed CTMC.

Nplus: Calculate summary statistics for BDMCs and CTMC_POs

num.deriv: Numerical Differentiation

plot-methods: Plot CTMCs

power.coef.one: Gets coefficients of a power series..

process.prob.one: Calculate transition probability for linear birth death...

sampleJumpTime: Functions for Simulating Conditionally the first Jump of a...

sim.condBD: Simulate birth-death process, Conditionally upon observing...

simplify: Transform Lists to Vectors

sub-methods: Subscripting CTMCs

Files in this package

DOBAD
DOBAD/inst
DOBAD/inst/doc
DOBAD/inst/doc/BD_MCMC.Rnw
DOBAD/inst/doc/BD_EM_wImmig.R
DOBAD/inst/doc/BD_MCMC.R
DOBAD/inst/doc/BD_MCMC.pdf
DOBAD/inst/doc/sim_condBD.Rnw
DOBAD/inst/doc/BD_EM.R
DOBAD/inst/doc/sim_condBD.R
DOBAD/inst/doc/sim_condBD.pdf
DOBAD/inst/doc/BD_EM_wImmig.Rnw
DOBAD/inst/doc/BD_EM.pdf
DOBAD/inst/doc/BD_EM.Rnw
DOBAD/inst/doc/BD_EM_wImmig.pdf
DOBAD/NAMESPACE
DOBAD/R
DOBAD/R/CTMCutils_helpers.R DOBAD/R/accRejSim_helpers.R DOBAD/R/numDeriv_helpers.R DOBAD/R/CTMC.simulate.R DOBAD/R/BD_chooseSim_helpers.R DOBAD/R/OPS_helpers.R DOBAD/R/numDeriv.R DOBAD/R/BD_EM_inference.R DOBAD/R/CTMCPO2indepIntervals_helpers.R DOBAD/R/BD_chooseSim.R DOBAD/R/accRejSim.R DOBAD/R/sim.condBD.R DOBAD/R/BD_EM_inference_helpers.R DOBAD/R/BD_calc_helpers.R DOBAD/R/BD_exactSim_helpers.R DOBAD/R/BD_calc.R DOBAD/R/BD_EM.R DOBAD/R/BD_sim.R DOBAD/R/combineCTMC.R DOBAD/R/BD_MCMC_helpers.R DOBAD/R/CTMCutils.R DOBAD/R/CTMCPO2indepIntervals.R DOBAD/R/BD.MCMC.SC.R DOBAD/R/OPS.R DOBAD/R/BD_EM_helpers.R DOBAD/R/getDataSummary_helpers.R DOBAD/R/BDclasses.R DOBAD/R/ARsim.R DOBAD/R/CTMC.simulate.piecewise.R
DOBAD/vignettes
DOBAD/vignettes/DOBADbiblio.bib
DOBAD/vignettes/BD_MCMC.Rnw
DOBAD/vignettes/versions.sty
DOBAD/vignettes/sim_condBD.Rnw
DOBAD/vignettes/BD_EM_wImmig.Rnw
DOBAD/vignettes/BD_EM.Rnw
DOBAD/vignettes/biom.bst
DOBAD/MD5
DOBAD/build
DOBAD/build/vignette.rds
DOBAD/DESCRIPTION
DOBAD/man
DOBAD/man/getMCstate.Rd DOBAD/man/combineCTMC.Rd DOBAD/man/CTMCPO2indepIntervals.Rd DOBAD/man/Nij.Rd DOBAD/man/CTMC-class.Rd DOBAD/man/doublebracket-methods.Rd DOBAD/man/plot-methods.Rd DOBAD/man/CTMC_PO_1-class.Rd DOBAD/man/add.generator.Rd DOBAD/man/process.prob.one.Rd DOBAD/man/BD.EMInference.prodExpecs.Rd DOBAD/man/birth.death.simulant.Rd DOBAD/man/derivType.Rd DOBAD/man/getNewParams.SC.Rd DOBAD/man/getIthJumpTime.Rd DOBAD/man/getPartialData.Rd DOBAD/man/power.coef.one.Rd DOBAD/man/Nplus.Rd DOBAD/man/BDMC_many-class.Rd DOBAD/man/CTMC_PO_many-class.Rd DOBAD/man/num.deriv.Rd DOBAD/man/getDataSummary.CTMC_PO_many.Rd DOBAD/man/EM.BD.SC.Rd DOBAD/man/BD.MCMC.SC.Rd DOBAD/man/sub-methods.Rd DOBAD/man/getSubMC.Rd DOBAD/man/list2CTMC.Rd DOBAD/man/getTs-methods.Rd DOBAD/man/sampleJumpTime.Rd DOBAD/man/ARsim.Rd DOBAD/man/getT-methods.Rd DOBAD/man/add.joint.mean.many.Rd DOBAD/man/BDsummaryStats.Rd DOBAD/man/getBDinform.PO.Rd DOBAD/man/CTMC.simulate.piecewise.Rd DOBAD/man/getBDMCsPOlist-methods.Rd DOBAD/man/bracket-methods.Rd DOBAD/man/getInitParams.Rd DOBAD/man/CTMC2list.Rd DOBAD/man/BDloglikelihood.PO.Rd DOBAD/man/simplify.Rd DOBAD/man/getBDinform.Rd DOBAD/man/getStates.Rd DOBAD/man/BDMC-class.Rd DOBAD/man/bdARsimCondEnd.Rd DOBAD/man/getBDjTimes.Rd DOBAD/man/getTimes.Rd DOBAD/man/sim.condBD.Rd DOBAD/man/EMutilities.Rd DOBAD/man/graph.CTMC.Rd DOBAD/man/BDPOloglikeGradSqr.CTMC_PO_many.Rd DOBAD/man/CTMC.simulate.Rd DOBAD/man/add.uncond.mean.one.Rd

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