v1.1.1 - Conditioning and trait parameter space

DAISIErobustness 1.1.1

• Pipeline now conditions all simulations and MLE on a minimum of 5 colonising lineages.
• Removed sim_constraints().
• New traits parameter space.

v1.1.0 - Traits, Peregrine submissions

DAISIErobustness 1.1.0

• Rework Peregrine HPC job submission. Job submissions done by calling sbatch on /DAISIErobustness/bash/submit_run_robustness_peregrine.sh.
• run_robustness_peregrine.R is no longer a function, but an R script that runs the pipeline on Peregrine.
• Include improved DAISIE traits parameter space.
• Depend on rsetienne/[email protected] (which is also the CRAN release).

v1.0.3 - Fix DD bug in calc_ml()

DAISIErobustness 1.0.3

• Use correct diversity-dependence settings when estimating using calc_ml(). See #43.
• Depend on rsetienne/DAISIE@25d0285, which is DAISIE v3.0.0 but prior to CRAN release.

v1.0.2 - Finalize parameter sets

DAISIErobustness 1.0.2

• Finalize nonoceanic land bridge parameter space.
• Improve Peregrine HPCC job submission scripts simulation_run_script and add analysis_run_script.
• Can now choose number of max concurrent jobs. Improvements to parameter set range selection.
• Remove deprecated code from scripts folder.
• Move and add images to /pics/.

v1.0.1 - Fix save bug on cluster when ml_constraints fail

DAISIErobustness 1.0.1

• Fix bug in ml_constraints() when one of the initpars attempts in run_analysis() does not converge, which prevented some failed_cond_ results from being saved on Peregrine.
• Depend on rsetienne/DAISIE@dd54db2.
• Add revised geodynamics parameter spaces for robustness study.
• Slightly better test coverage in the pipeline when ML convergence fails.
• Vignette is in correct location.

See attached source for rsetienne/DAISIE@dd54db2.

v1.0.0 - Geodynamics and traits studies

DAISIErobustness 1.0.0

• Package to test the robustness of island biogeography models.
• Simulate new geodynamics and trait dependent models using the DAISIE model.
• Pipeline to analyse the robustness of the DAISIE ML inference to the newly implemented models.
• Can read any new model input in the DAISIE format regardless of generating model from a file.
• Store intermediate simulation output and read said output to finish analyses and save to file.
• Interact and submit jobs to the Pergrine HPCC at the RUG.
• Generate parameter spaces used for geodynamics and trait dependence robustness studies.
• Contains DAISIE v3.0.0 version that DAISIErobustness depends on, for the geodynamics and traits studies.