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

Functions

add.cond.mean.many Man page
add.cond.mean.one Man page
add.cond.meanSq.one Man page
add.cond.meanSq.one Man page
add.generator Man page
addhold.cond.mean.one Man page
addhold.generator Man page
addhold.joint.mean.one Man page
add.joint.mean.many Man page
add.joint.mean.one Man page
add.joint.meanSq.one Man page
add.joint.meanSq.one Man page
addrem.cond.mean.one Man page
addrem.generator Man page
addremhold.generator Man page
addrem.joint.mean.one Man page
add.uncond.mean.one Man page
all.cond.mean2.PO Man page
all.cond.mean.PO Man page
ARsim Man page
bdARsimCondEnd Man page
bdARsimCondEnd.1 Man page
BDloglikelihood.PO Man page
BDloglikelihood.PO.CTMC_PO_1 Man page
BDloglikelihood.PO.CTMC_PO_many Man page
BDloglikelihood.PO.list Man page
BDMC-class Man page
BDMC_many-class Man page
BD.MCMC.SC Man page
BDPOloglikeGradSqr.CTMC_PO_many Man page
BDsummaryStats Man page
BDsummaryStats,BDMC_many-method Man page
BDsummaryStats,BDMC-method Man page
BDsummaryStats,list-method Man page
BDsummaryStats.PO Man page
BDsummaryStats.PO,CTMC_PO_1-method Man page
BDsummaryStats.PO,CTMC_PO_many-method Man page
BDsummaryStats.PO,list-method Man page
birth.death.simulant Man page
combineCTMC Man page
CTMC2list Man page
CTMC-class Man page
[,CTMC_many,ANY,ANY,ANY-method Man page
[[,CTMC_many,ANY,ANY,ANY-method Man page
[,CTMC_many-method Man page
[[,CTMC_many-method Man page
CTMC_PO_1-class Man page
CTMCPO2indepIntervals Man page
CTMCPO2indepIntervals.CTMC_PO_1 Man page
CTMCPO2indepIntervals.CTMC_PO_many Man page
[,CTMC_PO_many,ANY,ANY,ANY-method Man page
[[,CTMC_PO_many,ANY,ANY,ANY-method Man page
CTMC_PO_many-class Man page
[,CTMC_PO_many-method Man page
[[,CTMC_PO_many-method Man page
CTMC.simulate Man page
CTMC.simulate.piecewise Man page
derivType Man page
EM.BD.SC Man page
EM.BD.SC.1 Man page
E.step.SC Man page
f.i Man page
genDoneSided Man page
getBDinform.full.SC.manual Man page
getBDinform.lost.SC.manual Man page
getBDinform.PO Man page
getBDinform.PO.SC Man page
getBDinform.PO.SC.manual Man page
getBDjTimes Man page
getBDMCsPOlist Man page
getBDMCsPOlist,CTMC_PO_many-method Man page
getBDMCsPOlist-methods Man page
getBDsummaryExpecs Man page
getBDsummaryProdExpecs Man page
getDataSummary Man page
getDataSummary.CTMC_PO_many Man page
getInitParams Man page
getIthJumpTime Man page
getIthJumpTimes Man page
getIthState Man page
getMCstate Man page
getNewParams.SC Man page
getPartialData Man page
getStates Man page
getStates,BDMC-method Man page
getStates,CTMC-method Man page
getStates,CTMC_PO_1-method Man page
getSubMC Man page
getT Man page
getT,BDMC_many-method Man page
getT,BDMC-method Man page
getT,CTMC_many-method Man page
getT,CTMC-method Man page
getT,CTMC_PO_1-method Man page
getT,CTMC_PO_many-method Man page
getTimes Man page
getTimes,BDMC-method Man page
getTimes,CTMC-method Man page
getTimes,CTMC_PO_1-method Man page
getT-methods Man page
getTs Man page
getTs,BDMC_many-method Man page
getTs,CTMC_many-method Man page
getTs,CTMC_PO_many-method Man page
getTs-methods Man page
graph.CTMC Man page
graph.CTMC.PO Man page
hessianOneSided Man page
hold.cond.mean.one Man page
hold.cond.meanSq.one Man page
hold.generator Man page
hold.joint.meanSq.one Man page
holdTime Man page
hold.uncond.mean.one Man page
list2CTMC Man page
M.step.SC Man page
Nij Man page
NijBD Man page
NijBD.CTMC_many Man page
Nminus Man page
Nminus.CTMC_PO_many Man page
Nplus Man page
Nplus.CTMC_PO_many Man page
num.deriv Man page
p.i Man page
plot,CTMC,missing-method Man page
plot,CTMC_PO_1,missing-method Man page
plot-methods Man page
power.coef.many Man page
power.coef.one Man page
process.generator Man page
process.prob.many Man page
process.prob.one Man page
rem.cond.mean.many Man page
rem.cond.mean.one Man page
rem.cond.meanSq.one Man page
rem.generator Man page
remhold.cond.mean.one Man page
remhold.generator Man page
remhold.joint.mean.one Man page
rem.joint.mean.many Man page
rem.joint.mean.one Man page
rem.joint.meanSq.one Man page
rem.uncond.mean.one Man page
sampleJumpTime2 Man page
sim.condBD Man page
sim.condBD.1 Man page
sim.condBD.main Man page
sim.condBD.main.CTMC_PO_1 Man page
sim.condBD.main.default Man page
sim.condBD.main.list Man page
simplify Man page
timeave.cond.mean.many Man page
timeave.cond.mean.one Man page
timeave.joint.mean.many Man page
timeave.joint.mean.one Man page
timeave.laplace Man page
waitTimes Man page

Files

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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