Man pages for jasonxu90/bdsem
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 |
