NEWS.md

In Neves-P/DAISIErobustness: Test the Robustness of DAISIE to Geodynamics and Traits

DAISIErobustness (development version)

• Remove unused argument replicates from calc_error(). #68, thanks @Yangshen0325

DAISIErobustness 2.6.0

• Depend on DAISIE v4.3.0.
• New traits parameter space considering different carrying capacity among states, as well as the case without asymmetric transitions. The parameter sets are recorded in two files called trait_CES_2K.csv and trait_no_trans.csv.
• Update data analysis files for trait-dependent simulations.

DAISIErobustness 2.5.0

• Suggest 'patchwork' to assist in figure layout. Used in conjunction with previous package 'cowplot' for generating publication ready figures.
• Update layout of faceted plots to comply with journal requirements.

DAISIErobustness 2.4.0

• Update and tweak visuals of figures for publication as requested by journal.
• Minor style and linting.

DAISIErobustness 2.3.0

• Depend on DAISIE v4.1.1.
• Restructured parameter spaces using scripts in /data-raw/.
• Changes to summary metrics.
• Added new diagnostic functions that use generated log files.

DAISIErobustness 2.2.1

• Change plot legend to read "colonisation multiplier" rather than "immigration multiplier".

DAISIErobustness 2.2.0

• Completely rework all plotting functions for Santos Neves, Lambert, Valente, and Etienne 2021. Scripts associated with the paper can be found in the scripts/folder/ and the necessary functions are found in the sub directory scripts/folder/functions.
• Add functions for reading log files and checking checking correlations between error and run time. Functions are calc_ed95_param_set(), read_runtime_log(), read_param_space_log(), read_param_set_log(), get_runtime_params(), calc_runtime_ed95_cor(), and plot_cor().
• Rename calc_stat_diff() to calc_ed_95_for_plot(). This is the function upon which the plotting functions for publications rely. Add tests for this function.
• load_param_space() no longer uses the function read_csv2() from the readr package in favour of base R read.csv2(). This change was prompted by the release of readr v2.0.0, which parses column types in a different way, resulting in the incorrect reading of K from the parameter spaces. Either character vectors or NAs were returned due to a combination of ',' as decimal and Inf in the data set. The change to read.csv() is functionally the same.
• Improve run_robustness() documentation.

DAISIErobustness 2.1.1

• Depend on DAISIE v4.0.2 to make use of all of it's corrections. See here for DAISIE v4.0.0, v4.0.1 and v4.0.2 patch notes for details on the changes.

DAISIErobustness 2.1.0

• RNG is no longer seeded it 1L by default. The seed used for each parameter set is now chosen from the current system time and parameter set index.
• ML runs again fail when computed loglikelihood is Inf.
• Depend on DAISIE v3.2.1.
• Add a number of plotting functions and scripts, which live on scripts/plots/.
• Change traits, nonoceanic (termed continental island on the paper), and nonoceanic sea-level parameter spaces.
• Add better metadata on HPCC log files.
• Move analysis scripts files from scripts/ to scripts/analysis/.

DAISIErobustness 2.0.0

• Rework pipeline flow. pipeline, load_from_file, replicate_range removed as arguments from run_robustness(). No longer possible to run the simulation part of the pipeline separately from the analysis part.
• Failed ML runs will now result in a new generating simulation being run to overcome numerical issues in MLE. This results in the output of run_robustness() directly matching the number of replicates (barring run time constraints).
• New traits parameter space. These are now split into two files called trait_CES.csv and trait_trans.csv.
• Add regular partition job scripts for Peregrine HPCC.
• Improved geodynamics plots in scripts/.
• Add new calc_stat_diff() unexported function in scripts/for data analysis.
• Add new extract_error_metrics() unexported function in scripts/for data analysis.
• Fix bug in calculation of number of mainland species in the traits model.
• Minor documentation improvements.

DAISIErobustness 1.1.2

• Rework decide_best_pars() to intelligently salvage failed ML convergence whenever possible.
• Request less memory from the Peregrine HPCC.

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.

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/DAISIE@v3.0.1 (which is also the CRAN release).

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.

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/.

DAISIErobustness 1.0.1

• Fix bug in ml_constraints when one of the initpars attempts in run_analysis() did 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.

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 Peregrine HPCC at the RUG.
• Generate parameter spaces used for geodynamics and trait dependence robustness studies.

Neves-P/DAISIErobustness documentation built on May 22, 2024, 4:26 p.m.