v4.4.1

DAISIE 4.4.1

• 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.

v4.4.0

DAISIE 4.4.0

• 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.

v4.3.4

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/.

v4.3.3

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. Bug report opened -> boostorg/odeint#59
  • 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.

v4.3.2

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.

v4.3.1

DAISIE 4.3.1

• 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.

v4.3.0

v4.3.0

• 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 RcppCore/Rcpp#1236 and eddelbuettel/bh#90 respectively. Also require package 'DDD' v(>= 5.0.0).
• Add code for the trait-dependent simulations considering different 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.

v4.2.1

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.

v4.2.0

DAISIE 4.2.0

• 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.

v4.1.1

DAISIE 4.1.1

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