v4.1.0

DAISIE 4.1.0

• Rework IW simulation code to:
  • Produces full stt tables.
  • Can run with conditioning on number of surviving species to the present.
• Added DAISIE_CS_max_steps() to manually change the maximum number of integration steps for the CS C++ integrators.
• Renamed and reworked simulation architecture.
• Renamed totaltime to total_time.
• Integrators from package 'deSolve' are reinstated as the default ODE solvers.
• Added stac_key vignette detailing possible statuses of colonist lineages.
• Use LazyData.

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.

v4.0.2

DAISIE 4.0.2

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.

• Suggest ggtree >= 3.0.0.

v4.0.1

DAISIE 4.0.1

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.

• Fix possibility of fitting CS model with IW likelihood on simulated data by setting CS_version = 0. Improve CS_version documentation.

v4.0.0

DAISIE 4.0.0

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.

• Fix bug when calculating conditional probabilities, which are now correctly calculated from island age to the present.
• Fix bug when calculating probabilities upon migration, which assumed no recolonisation was possible in the CS model. Handling recolonisation in the same manner is not possible for the IW model, so an approximation is now made. The influence of the bug and of the approximation in the IW model is expected to be minimal, particularly in cases where the colonisation rate is low. Such cases of low colonisation are the norm.
• Add num_cycles argument to ML functions, allowing to specify how many cycles the optimizer should take. Defaults to 1.
• Minor vignette corrections.
• Improve README.md documentation.

v3.2.1

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.

• Minor documentation improvements.

v3.2.0

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.

Changes

• DAISIE_loglikg_IW() is now more efficient and numerically stable. Numerical integration is now done via C++ with package odeint.
• Add relaxed rate capabilities (both inference and simulations). Relaxed rate models allow for parameters to not be static, but to be sampled by specific probability distributions.
• Introduce MinAge data status in DAISIE data objects. A status containing MinAge sets a lower boundary for colonization in situations when the precise colonization time is unknown. This is interpreted by DAISIE_dataprep() so that the information is passed on to the likelihood optimization functions. See the DAISIE_dataprep() help page for more details. In the back-end this results in new stac values 8 and 9.
• Bug fix of "bug 2" in the bug report manuscript. This bug was present in DAISIE_ONEcolonist() when recolonization occurs. It has now been fixed so that the colonization and branching times are stored in the way that we now think is the best for it to be dealt with in the likelihood code. In recolonization cases, $other_clades_same_ancestor renamed to $all_colonisations. #125
• Fix bug which occurs rarely, when computing log conditional probabilities. Only applicable to ML code running with cond.
• Removed deprecated legacy functions. Removed all functions named DAISIE_*_VERSION_NUMBER() and all DAISIE_calc_*_rate() funcions and get_brts_mya(). #126
• Made some functions internal, as they should be. DAISIE_make_global() and create_island() are now internal. #127
• @HHildenbrandt is now an author.
• Added @xieshu95's and @joshwlambert's ORCIDs.
• Added a NEWS.md file to track changes to the package.

v3.1.0

• Expands the possibility of conditioning simulations and MLE of the CS model on the number of colonizing lineages.

• In simulation and ML functions, the cond argument can now be greater than one. A non-zero cond signifies that the ML or simulation is conditioned on having at least cond colonizations on the island.

• Implements #121, at sim and ML level.

• Add BugReports, Website and missing ORCID in DESCRIPTION.

v3.0.1

• Correct @joshwlambert's name in DESCRIPTION.
• DAISIE_sim_relaxed_rate() input is closer to DAISIE_ML() input.
• Documentation improvements.
• Tweak Makevars.

v3.0.0

• Major revamp to simulation code. Simulations now accessed using DAISIE_sim_*() syntax.
• Constant rate, time-dependent, trait-dependent, and (multiple) split-rate available.
• Relaxed-rate inference available in DAISIE_ML_CS().
• Improved vignettes documenting CS and IW cases.
• Full stt can be returned by setting sample_freq = Inf in DAISIE_sim_*() functions.
• Optional plotting with DAISIE_plot_input(). (Requires additional dependencies).
• Back-end architecture improvements.