DOBAD: Analysis of Discretely Observed Linear Birth-and-Death(-and-Immigration) Markov Chains
Version 1.0.5

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

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AuthorCharles Doss, Vladimir Minin, Marc Suchard
Date of publication2016-03-24 23:29:52
MaintainerCharles Doss <cdoss@umn.edu>
LicenseGPL (>= 2)
Version1.0.5
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DOBAD")

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

ARsim Man page Source code
ARsimTime Source code
ARsimTime1 Source code
BD.MCMC.SC Man page Source code
BD.MCMC.SC.CTMC_PO_1 Source code
BD.MCMC.SC.CTMC_PO_many Source code
BDMC-class Man page
BDMC_many-class Man page
BDPOloglikeGradSqr.CTMC_PO_1 Source code
BDPOloglikeGradSqr.CTMC_PO_many Man page Source code
BDloglikelihood.PO Man page Source code
BDloglikelihood.PO.CTMC_PO_1 Man page Source code
BDloglikelihood.PO.CTMC_PO_many Man page Source code
BDloglikelihood.PO.list Man page Source code
BDsummaryStats Man page
BDsummaryStats,BDMC-method Man page
BDsummaryStats,BDMC_many-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
CTMC-class Man page
CTMC.simulate Man page Source code
CTMC.simulate.piecewise Man page Source code
CTMC2list Man page Source code
CTMCPO2indepIntervals Man page Source code
CTMCPO2indepIntervals.CTMC_PO_1 Man page Source code
CTMCPO2indepIntervals.CTMC_PO_many Man page Source code
CTMC_PO_1-class Man page
CTMC_PO_many-class Man page
E.step Source code
E.step.SC Man page Source code
E.step.SC.CTMC_PO_1 Source code
E.step.SC.CTMC_PO_many Source code
E.step.SC.list Source code
EM.BD Source code
EM.BD.1.CTMC_PO_1 Source code
EM.BD.1.CTMC_PO_many Source code
EM.BD.SC Man page Source code
EM.BD.SC.1 Man page Source code
H Source code
M.step Source code
M.step.SC Man page Source code
NRrootfinder Source code
Nij Man page Source code
NijBD Man page Source code
NijBD.CTMC_many Man page Source code
Nminus Man page Source code
Nminus.CTMC_PO_many Man page Source code
Nplus Man page Source code
Nplus.CTMC_PO_many Man page Source code
Pij.C Source code
Pij.D Source code
Pij.E Source code
Pij.F Source code
Qexact Source code
[,CTMC_PO_many,ANY,ANY,ANY-method Man page
[,CTMC_PO_many-method Man page
[,CTMC_many,ANY,ANY,ANY-method Man page
[,CTMC_many-method Man page
[[,CTMC_PO_many,ANY,ANY,ANY-method Man page
[[,CTMC_PO_many-method Man page
[[,CTMC_many,ANY,ANY,ANY-method Man page
[[,CTMC_many-method Man page
acceptcounts Source code
acceptcounts.1 Source code
add.cond.mean.many Man page Source code
add.cond.mean.one Man page Source code
add.cond.meanSq.one Man page Man page Source code
add.generator Man page Source code
add.joint.mean.many Man page Source code
add.joint.mean.one Man page Source code
add.joint.meanSq.one Man page Man page Source code
add.uncond.mean.one Man page Source code
add.uneven Source code
add.uneven.list Source code
add.uneven.matrix Source code
add.uneven.vector Source code
addhold.cond.mean.one Man page Source code
addhold.generator Man page Source code
addhold.joint.mean.one Man page Source code
addrem.cond.mean.one Man page Source code
addrem.generator Man page Source code
addrem.joint.mean.one Man page Source code
addremhold.generator Man page Source code
all.cond.mean.PO Man page Source code
all.cond.mean2.PO Man page Source code
avgNis Source code
bdARsimCondEnd Man page Source code
bdARsimCondEnd.1 Man page Source code
birth.death.simulant Man page Source code
chooseSim.condBD.1 Source code
chooseSim.condBD.1.CTMC_PO_1 Source code
chooseSim.condBD.CTMC_PO_1 Source code
combineCTMC Man page Source code
condIndices Source code
derivType Man page Source code
exactSimTime Source code
exactSimTime1 Source code
f.i Man page Source code
f.i.notNormalized Source code
firstJtimeCond Source code
genDoneSided Man page Source code Source code
getBDMCsPOlist Man page
getBDMCsPOlist,CTMC_PO_many-method Man page
getBDMCsPOlist-methods Man page
getBDinform.PO Man page
getBDinform.PO.0term.CTMC_1 Source code
getBDinform.PO.0term.CTMC_PO_many Source code
getBDinform.PO.SC Man page Source code
getBDinform.PO.SC.manual Man page Source code
getBDinform.full.SC.manual Man page Source code
getBDinform.lost.SC.manual Man page Source code
getBDinform.numeric Source code
getBDjTimes Man page Source code
getBDsummaryExpecs Man page Source code
getBDsummaryProdExpecs Man page Source code
getCommonTerms Source code
getDataSummary Man page
getDataSummary.CTMC_PO_many Man page Source code
getInitParams Man page Source code
getIthJumpTime Man page Source code
getIthJumpTimes Man page Source code
getIthState Man page Source code
getLhat Source code
getMCstate Man page Source code
getNewParams.CTMC_PO_1 Source code
getNewParams.CTMC_PO_many Source code
getNewParams.SC Man page Source code
getNewParams.SC.CTMC_PO_1 Source code
getNewParams.SC.CTMC_PO_many Source code
getNewParams.SC.list Source code
getNuHat Source code
getPartialData Man page Source code
getStates Man page
getStates,BDMC-method Man page
getStates,CTMC-method Man page
getStates,CTMC_PO_1-method Man page
getSubMC Man page Source code
getSumTerm Source code
getT Man page
getT,BDMC-method Man page
getT,BDMC_many-method Man page
getT,CTMC-method Man page
getT,CTMC_PO_1-method Man page
getT,CTMC_PO_many-method Man page
getT,CTMC_many-method Man page
getT-methods Man page
getTimes Man page
getTimes,BDMC-method Man page
getTimes,CTMC-method Man page
getTimes,CTMC_PO_1-method Man page
getTs Man page
getTs,BDMC_many-method Man page
getTs,CTMC_PO_many-method Man page
getTs,CTMC_many-method Man page
getTs-methods Man page
graph.CTMC Man page Source code
graph.CTMC.PO Man page Source code
hessianOneSided Man page Source code Source code
hold.cond.mean.one Man page
hold.cond.meanSq.one Man page Source code
hold.generator Man page Source code
hold.joint.meanSq.one Man page Source code
hold.uncond.mean.one Man page Source code
holdTime Man page Source code
indicesCondSuffStats Source code
list2CTMC Man page Source code
logL.birth Source code
logL.birth.d2Nu2.MLE Source code
logL.birth.dNu.MLE Source code
logL.birth.nu.MLE Source code
logLvec Source code
num.2deriv Source code Source code
num.deriv Man page Source code Source code
num.deriv2 Source code Source code
p.i Man page Source code
pi.j.C Source code
pi.j.D Source code
pi.j.E Source code
pi.j.F Source code
plot,CTMC,missing-method Man page
plot,CTMC_PO_1,missing-method Man page
plot-methods Man page
poch Source code
power.coef.many Man page Source code
power.coef.one Man page Source code
prec.error.handler Source code
process.generator Man page Source code
process.generator.ratesEqual Source code
process.prob.many Man page Source code
process.prob.one Man page Source code
process.prob.one.fft Source code
process.prob.one.singlearg Source code
rem.cond.mean.many Man page Source code
rem.cond.mean.one Man page Source code
rem.cond.meanSq.one Man page Source code
rem.generator Man page Source code
rem.joint.mean.many Man page Source code
rem.joint.mean.one Man page Source code
rem.joint.meanSq.one Man page Source code
rem.uncond.mean.one Man page Source code
remhold.cond.mean.one Man page Source code
remhold.generator Man page Source code
remhold.joint.mean.one Man page Source code
sampleJumpTime2 Man page Source code
sim.condBD Man page Source code
sim.condBD.1 Man page Source code
sim.condBD.main Man page Source code
sim.condBD.main.CTMC_PO_1 Man page Source code
sim.condBD.main.default Man page
sim.condBD.main.list Man page Source code
simplify Man page Source code
solveNuHat Source code
template.cond.factorialmean.one Source code
template.cond.mean.one Source code
template.cond.prodmean.one Source code
timeave.cond.mean.many Man page Source code
timeave.cond.mean.one Man page
timeave.joint.mean.many Man page Source code
timeave.joint.mean.one Man page Source code
timeave.laplace Man page Source code
waitTimes Man page Source code

Files

inst
inst/doc
inst/doc/BD_MCMC.Rnw
inst/doc/BD_EM_wImmig.R
inst/doc/BD_MCMC.R
inst/doc/BD_MCMC.pdf
inst/doc/sim_condBD.Rnw
inst/doc/BD_EM.R
inst/doc/sim_condBD.R
inst/doc/sim_condBD.pdf
inst/doc/BD_EM_wImmig.Rnw
inst/doc/BD_EM.pdf
inst/doc/BD_EM.Rnw
inst/doc/BD_EM_wImmig.pdf
NAMESPACE
R
R/CTMCutils_helpers.R
R/accRejSim_helpers.R
R/numDeriv_helpers.R
R/CTMC.simulate.R
R/BD_chooseSim_helpers.R
R/OPS_helpers.R
R/numDeriv.R
R/BD_EM_inference.R
R/CTMCPO2indepIntervals_helpers.R
R/BD_chooseSim.R
R/accRejSim.R
R/sim.condBD.R
R/BD_EM_inference_helpers.R
R/BD_calc_helpers.R
R/BD_exactSim_helpers.R
R/BD_calc.R
R/BD_EM.R
R/BD_sim.R
R/combineCTMC.R
R/BD_MCMC_helpers.R
R/CTMCutils.R
R/CTMCPO2indepIntervals.R
R/BD.MCMC.SC.R
R/OPS.R
R/BD_EM_helpers.R
R/getDataSummary_helpers.R
R/BDclasses.R
R/ARsim.R
R/CTMC.simulate.piecewise.R
vignettes
vignettes/DOBADbiblio.bib
vignettes/BD_MCMC.Rnw
vignettes/versions.sty
vignettes/sim_condBD.Rnw
vignettes/BD_EM_wImmig.Rnw
vignettes/BD_EM.Rnw
vignettes/biom.bst
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getMCstate.Rd
man/combineCTMC.Rd
man/CTMCPO2indepIntervals.Rd
man/Nij.Rd
man/CTMC-class.Rd
man/doublebracket-methods.Rd
man/plot-methods.Rd
man/CTMC_PO_1-class.Rd
man/add.generator.Rd
man/process.prob.one.Rd
man/BD.EMInference.prodExpecs.Rd
man/birth.death.simulant.Rd
man/derivType.Rd
man/getNewParams.SC.Rd
man/getIthJumpTime.Rd
man/getPartialData.Rd
man/power.coef.one.Rd
man/Nplus.Rd
man/BDMC_many-class.Rd
man/CTMC_PO_many-class.Rd
man/num.deriv.Rd
man/getDataSummary.CTMC_PO_many.Rd
man/EM.BD.SC.Rd
man/BD.MCMC.SC.Rd
man/sub-methods.Rd
man/getSubMC.Rd
man/list2CTMC.Rd
man/getTs-methods.Rd
man/sampleJumpTime.Rd
man/ARsim.Rd
man/getT-methods.Rd
man/add.joint.mean.many.Rd
man/BDsummaryStats.Rd
man/getBDinform.PO.Rd
man/CTMC.simulate.piecewise.Rd
man/getBDMCsPOlist-methods.Rd
man/bracket-methods.Rd
man/getInitParams.Rd
man/CTMC2list.Rd
man/BDloglikelihood.PO.Rd
man/simplify.Rd
man/getBDinform.Rd
man/getStates.Rd
man/BDMC-class.Rd
man/bdARsimCondEnd.Rd
man/getBDjTimes.Rd
man/getTimes.Rd
man/sim.condBD.Rd
man/EMutilities.Rd
man/graph.CTMC.Rd
man/BDPOloglikeGradSqr.CTMC_PO_many.Rd
man/CTMC.simulate.Rd
man/add.uncond.mean.one.Rd
DOBAD documentation built on May 20, 2017, 3:13 a.m.