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

Share:

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

Author
Charles Doss, Vladimir Minin, Marc Suchard
Date of publication
2016-03-24 23:29:52
Maintainer
Charles Doss <cdoss@umn.edu>
License
GPL (>= 2)
Version
1.0.5

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