Analysis of discretely observed Birth-Death-Shift processes

de.birth | Expected births ODE |

de.death | Expected deaths ODE |

de.particleT | Expected particle time ODE |

de.shift | Expected shifts ODE |

de.trans | Transition probability ODE |

EM.run | Inference via EM algorithm |

ESTEP | Perform one accelerated E-step of the EM algorithm |

ESTEP.slow | Perform one E-step of the EM algorithm |

FFT.optim | Maximize the log-likelihood in 'logFFT' |

FFT.pat.optim | Optimizes the function 'logFFT.patients' using 'optim'... |

FFT.replicate | Replicate the function 'FFT.run' |

FFT.run | Generate synthetic data from simple BSD process and infer... |

FM.data | Finds all intervals compatible under frequent monitoring... |

FM.optim | Optimizes the frequent monitoring log-likelihood |

FM.replicate | Replicate 'FM.run' |

FM.run | Main function for generating observations from... |

getBirthMeans.initList | Compute expected births over a grid at a list of initial... |

getBirthMeans.timeList | Compute expected birth over a grid at a list of evaluation... |

getCover | Calculates coverage indicators for estimated parameters |

getDeathMeans.initList | Compute expected deaths over a grid at a list of initial... |

getDeathMeans.timeList | Compute expected deaths over a grid at a list of evaluation... |

getEst | Get coefficient estimate from optim object |

getParticleT.initList | Compute expected particle time over a grid at a list of... |

getParticleT.timeList | Compute expected particle time over a grid at a list of... |

getShiftMeans.initList | Compute expected shifts over a grid at a list of initial... |

getShiftMeans.timeList | Compute expected shifts over a grid at a list of evaluation... |

getStandardErrors | Calculate numerical standard errors of estimated coefficients |

getTrans.FreqMon | Calculates the four transition probabilities defined under... |

getTrans.initList | Compute transition probabilites over a grid at a list of... |

getTrans.MC | Calculate empirical transition probabilities |

getTrans.timeList | Compute transition probabilities over a grid at a list of... |

logFFT | Calculate log-likelihood using generating function technique |

logFFT.patients | Log likelihood for BSD process with covariates |

logFM | Calculate approximate log-likelihood based on Frequent... |

makedata.simple | Generate synthetic dataset for BSD process with simple rates |

makeGrid.birth.partial | Evaluates partial derivative of expected births ODE over 2D... |

makeGrid.birth.r1 | Evaluates expected births ODE over 2D grid of arguments |

makeGrid.death.partial | Evaluates partial derivative of expected deaths ODE over 2D... |

makeGrid.death.r1 | Evaluates expected deaths ODE over 2D grid of arguments |

makeGrid.particleT.partial | Evaluates partial derivative of expected particle time ODE... |

makeGrid.particleT.r0 | Evaluates expected particle time ODE over 2D grid of... |

makeGrid.shift.partial | Evaluates partial derivative of expected shifts ODE over 2D... |

makeGrid.shift.r1 | Evaluates expected shifts ODE over 2D grid of arguments |

makeGrid.trans | Evaluates transition probability ODE over 2D grid of... |

MakePatientData | Generates synthetic patient data for inference in discretely... |

MakePatientRates | Makes matrix of patient-specific birth, shift, and death... |

MSTEP | Execute a Newton-Raphson step within M-step of the EM... |

PatientDesignExample | Create example design matrix in the format required for... |

ransim.N.true | Simulate N realizations from the BSD process, each with... |

sim.eventcount | Simulate a BSD process and return sufficient statistics |

sim.N.eventcount | Simulate N BSD processes and return sufficient statistics |

sim.N.true | Simulate N realizations from the BSD process |

sim.one.eventcount | Simulate a BSD process and return sufficient statistics with... |

sim.one.ran | Simulate a BSD process, returning initial number as well as... |

sim.one.true | Simulate a BSD process with error catch |

simulate.true | Simulate a birth-shift-death-process |

solve.birth | Expected births ODE solver |

solve.death | Expected deaths ODE solver |

solve.particleT | Expected births ODE solver |

solve.shift | Expected shifts ODE solver |

solve.trans | Transition ODE solver |

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