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

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... |

EM.BD.SC.cov.1sv | Expectation-Maximization on Linear Birth Death (and... |

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 |

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