rsetienne/DAISIE: v4.0.5

DAISIE 4.0.5

N.B.: MacOS users may experience issues when installing DAISIE, especially when on MacOS Big Sur. If that is you case, please see here for detailed installation instructions.

• CS model can be fit with C++ code, similarly to the IW model since version v3.2.0. To do so, set methode to:
  • "odeint::runge_kutta_cash_karp54"
  • "odeint::runge_kutta_fehlberg78" [default]
  • "odeint::runge_kutta_dopri5"
  • "odeint::bulirsch_stoer"

without the odeint::-prefix, the deSolve::ode method is assumed. deSolve::ode using "lsodes" is still the default, as before. Make sure CS_version = 0 (default) to use C++ ODEINT numerical integration.

• Better handling of number of threads to use with DAISIE_IW_num_threads() for ML estimation of the IW model when more threads are available.
• Fixes to numerical instability in conditional probability calculation in the IW model when the probability of extinction is very close to 1.
• Introduce an approximation when the log conditional likelihood cannot be computed and add message when this is triggered.