ARsim                   Accept-Reject Simulation
BD.MCMC.SC              MCMC on Linear Birth Death Process
BDMC-class              Class "BDMC"
BDMC_many-class         Class '"BDMC_many"'
BDPOloglikeGradSqr.CTMC_PO_many
                        Gradient-Squared of PartialData likelihood
BDloglikelihood.PO      Calculate log likelihood of Partially Observed
                        BD process
BDsummaryStats          Get summary statistics for EM Algorithm on
                        Linear Birth-Death Process
CTMC-class              Class "CTMC"
CTMC.simulate           Simulate from ("regular") CTMC
CTMC.simulate.piecewise
                        Simulate from piecewise constant/homogeneous
                        CTMC
CTMC2list               Convert Between two representations of a
                        Continuous Time Markov Chain.
CTMCPO2indepIntervals   Converts CTMC_PO (either CTMC_PO_1 or
                        CTMC_PO_many) to independent intervals.
CTMC_PO_1-class         Class "CTMC_PO_1"
CTMC_PO_many-class      Class "CTMC_PO_many"
EM.BD.SC                Expectation-Maximization on Linear Birth Death
                        (_S_pecial _C_ase with constrained immigration)
EM.BD.SC.cov.1sv        Expectation-Maximization on Linear Birth Death
                        (and constrained Immigration) with Covariates
M.step.SC               Functions related to implementing the EM
                        algorithm on partially observed Birth-Death
                        Chain
Nij                     Count transitions in a fully observed CTMC.
Nplus                   Calculate summary statistics for BDMCs and
                        CTMC_POs
[,CTMC_many,ANY,ANY,ANY-method
                        Methods for Function '[' in Package 'DOBAD'
[,CTMC_many-method      Subscripting CTMCs
[[,CTMC_many,ANY,ANY,ANY-method
                        Methods for Function '[[' in Package 'DOBAD'
add.generator           Generating functions for birth-death processes
                        with immigration
add.joint.mean.many     Mean counts and particle time averages for
                        birth-death processes with immigration
add.uncond.mean.one     ENplus, ENminus, Eholdtime, unconditional on
                        ending state.
bdARsimCondEnd          Conditional Simulation of BD via Accept-Reject
birth.death.simulant    Simulation of birth-death processes with
                        immigration
combineCTMC             Combine several CTMCs into one CTMC
derivType               Helper for getting means from generating
                        functions
getBDMCsPOlist-methods
                        Methods for Function 'getBDMCsPOlist' in
                        Package 'DOBAD'
getBDinform.PO          Get Information Matrix for MLE estimates on
                        Partially Observed Linear Birth Death
                        (_S_pecial _C_ase with constrained immigration)
getBDinform.lost.SC.manual
                        Helpers for Getting Information Matrix for MLE
                        estimates on Partially Observed Linear Birth
                        Death (_S_pecial _C_ase with constrained
                        immigration)
getBDjTimes             Get Jump times of a BD process.
getBDsummaryExpecs      Functions That Calculate Product Expectations
                        Needed for Inference via EM Algorithm
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
getT-methods            ~~ Methods for Function getT in Package 'DOBAD'
                        ~~
getTimes                Get list of jump times.
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
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 process.
sampleJumpTime2         Functions for Simulating Conditionally the
                        first Jump of a chain.
sim.condBD              Simulate birth-death process, Conditionally
                        upon observing its state at finite, discrete
                        time points
simplify                Transform Lists to Vectors
