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Changelog

Source: NEWS.md

DAISIE 4.4.1

CRAN release: 2023-10-21

  • Fix bug in the calculation of shift loglikelihoods.
  • Fix bug where parameters being optimized could incorrectly be Inf #159 #160 (@joshwlambert).
  • DAISIE_SR_loglik_CS_M1() is now DAISIE_loglik_CS_shift().
  • New pkgdown website.
  • Several improvements to the relaxed rate code.

DAISIE 4.4.0

CRAN release: 2023-04-02

  • No longer include patched version of boost/numeric/odeint/stepper/bulirsch_stoer.hpp, address the issue by passing previously uninitialised variable as boost::units::quantity<boost::units::si::dimensionless, double>.
  • Document return type of exported Rcpp functions.
  • Move all internal non-error printing to console message() and warning(). Add internal functions to address this. verbose variable is now numeric, varying from 0 to 3. Increasing values increase amount of messages to be printed. Change default of printing some output to golden rule of silence verbose == 0. To print again, set verbose >= 1.
  • Remove calls to options(warn = -1) that suppress warnings in non standard way. Use suppressWarnings() where appropriate.
  • Safely restore graphics settings after plot.
  • Fix references in DESCRIPTION.
  • Remove internal (unnecessary) calls to internal functions via :::.
  • No longer use roxygen2 tag internal to document without index but use noRd instead. are_area_pars() is now internal.
  • Replace \dontrun examples in documentation with \donttest. Speed up examples.
  • License package C++ source files as BSL-1.0 (c) Hanno Hildenbrandt, FORTRAN files as BSL-1.0 (c) Rampal S. Etienne.
  • Add LICENSE.note, inst/COPYRIGHTS to clarify license and copyrights. Pipe such files in DESCRIPTION.

DAISIE 4.3.4

  • Require C++17 via CXX_STD flag on Makevars[.win].
  • Add SystemRequirements: C++17 to DESCRIPTION as for that standard “Writing R Extensions” requires it be explicitly stated.
  • Depends on R (>= 4.2.0) due to C++17 requirement on Windows due to Rtools 4.0, which is used for R 4.0-4.1. Toolchain for Rtools 4.0 is gcc 8.3 but “GCC 9.1 was the first release with non-experimental C++17 support”. as per https://gcc.gnu.org/.

DAISIE 4.3.3

  • Address problem detected by valgrind: unitialized member variable bulirsch_stoer<>::m_dt_last.
    • Patched version of boost/numeric/odeint/stepper/bulirsch_stoer.hpp. This is done by including the patched header file src/patched_bulrisch_stoer.h before boost/numeric/odeint to shadow boost/numeric/odeint/stepper/bulrisch_stoer.hpp The issue is not fixed in BOOST_VERSION == 1.81.0. Must check for fixes in upcomming boost (BH) releases.
  • Fix tab spacing in src/DAISIE_loglik_rhs_FORTRAN.f95.
  • Re-implement clang16 -D_HAS_AUTO_PTR_ETC flag fix via Makevars[.win] to comply with CRAN requests and to force C++ standard C++14 without using SystemRequirements line in DESCRIPTION, at CRAN’s request.
  • Skip plotting tests that cause problems in headless systems. These should be run manually.
  • Skip tests of as-of-now experimental steppers from ODEINT rosenbrock4 and adams bashfort moulton 1 because they are too slow.

DAISIE 4.3.2

  • Apply CRAN suggested fixes to clang16 issues with deprecated C++ functions included the Boost library, which are used in some of the stepper functions.
    • Add config.h in a macro, checking for, and setting, _HAS_AUTO_PTR_ETC and BOOST_NO_AUTO_PTR.
    • Change SystemRequirements in DESCRIPTION from C++17 to C++14. This same fix was applied in package 'DDD' version 5.2.1.

DAISIE 4.3.1

CRAN release: 2023-02-13

  • Fix issue that prevented ‘covr’ from running correctly.
  • Depend on R >= 4.1.0, C++17.
  • Tests of DAISIE_ML_*() and integration tests don’t run on CRAN due to too long runtime.

DAISIE 4.3.0

  • Due to recent changes in CRAN policy that result in warnings due to the use of Rcpp related packages that link to libraries that use sprintf (‘Rcpp’ and ‘BH’), ‘DAISIE’ now requires Rcpp v(>= 1.0.10) and BH v(>= 1.81.0-1). See https://github.com/RcppCore/Rcpp/pull/1236 and https://github.com/eddelbuettel/bh/pull/90 respectively. Also require package ‘DDD’ v(>= 5.0.0).
  • Add code for the trait-dependent simulations considering two carrying capacities for each trait state.
  • Improvements to the relaxed rate model fitting procedure.
  • Add DAISIE_count_species() to count the number of species in a datalist or simulated data.
  • Simply printing code by wrapping multiple instances into print_parameters_and_loglik().
  • Overall documentation improvements and updated references.
  • Bug fix in DAISIE_sim_cr_iw(), which wrongly computed number of species at present. #147
  • Improve the likelihood calculation. Fixed incorrect likelihood present for type 2 case CS model inference if the values of lambda were high, in the C++ implementation.
  • Overhaul GHA workflows to be more up to date and more conservative when to run. Feature branches require the tag [run ci] be added to the commit message to run.

DAISIE 4.2.1

  • Bug fixes in DAISIE_loglik_CS()on the likelihood code for the continental sampling (probability of initial presence on the island).
  • Bug fix in the DAISIE_sim_cr_iw() so replication works correctly.

DAISIE 4.2.0

CRAN release: 2022-06-02

  • Important bugfixes on estimation when data contains a lineage or a clade for which (see stac_key vignette for details on each case):
    • The divergence time is unknown but known to have occurred after a specific point in time in the island’s existence.
    • The divergence time is unknown but known to have occurred before a specific point in time in the island’s existence (usually known when dated population level phylogenetic data is available).
  • Improve and finalise the continental island estimation scenario, when there are initially species present on the island on inception.
  • Improve tests related to the two points above.
  • Remove DAISIE time dependent estimation code for now to ease work on the remaining code. Development will proceed separately.
  • Rate computations in simulation are first calculated per lineage, to then be calculated per island. This will be needed for time dependent estimation later on.
  • Improve zenodo metadata.
  • Add methode = "odeint::adams_bashforth_moulton_X" to the list of available numeric integrators for parameter estimation.

DAISIE 4.1.1

  • Correctly use is.data.frame() rather than class(foo) == "data.frame" to satisfy CRAN note.

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.

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.

DAISIE 4.0.2

DOI

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.

DAISIE 4.0.1

DOI

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.

DAISIE 4.0.0

DOI

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.

DAISIE 3.2.1

DOI

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.

DAISIE 3.2.0

DOI

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.

  • 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.

DAISIE 3.1.0

DOI

  • 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.

DAISIE 3.0.1

CRAN release: 2020-08-26

DAISIE 3.0.0

CRAN release: 2020-08-14

  • 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.

DAISIE 2.0.1

Minor update to v2.0: when empty islands are simulated the output list contains only one element instead of two (where the second indicated stac = 0, i.e. no surviving colonization).

DAISIE 2.0

Contains the functions used in:

  • Valente L., Etienne R.S., Garcia-R J.C. (2019) Deep macroevolutionary impact of humans on New Zealand’s unique avifauna. Current Biology , 29, 2563-2569.e4. https://doi.org/10.1016/j.cub.2019.06.058

  • Valente L., Phillimore A.B., Melo M. et al. (2020) A simple dynamic model explains the diversity of island birds worldwide. Nature , 579, 92–96. https://doi.org/10.1038/s41586-020-2022-5

  • Hauffe T, Delicado D, Etienne R.S. and Valente L. (2020) Lake expansion elevates equilibrium diversity via increasing colonisation. Journal of Biogeography. https://doi.org/10.1111/jbi.13914