daisiecontinental - DAISIEcontinental v0.3.0

The third minor release of the DAISIEcontinental R package includes various minor updates.

New features

• The plot_vicariance_loglik_diff() function is added.
• plot_vicariance_scatter() can now plot both the probability of initial presence and the loglikelihood.

Updates

• Species sink island parameter sets have been added to simulation performance analysis (data/ and data-raw/).
• Volant mammals are removed from the profile likelihood analysis as they no longer fit the continental DAISIE model in the Madagascar communities analysis.
• Plots have been updated.
• The R CMD check GitHub action workflow has been updated.
• renv.lock is updated.
• The test-continental-daisie.Rmd vignette has been updated.

- R
Published by joshwlambert over 1 year ago

daisiecontinental - DAISIEcontinental v0.2.0

Second minor release of DAISIEcontinental R package contains a range of updates and new functionality.

New features

• A new vicariance analysis is added to the package, this includes:

  • A plot_vicariance_scatter() function
  • A post_process_vicariance_results() function
  • A run_vicariance_analysis.R R script
  • A run_vicariance_analysis.sh bash script
  • A vicariance_scatter.png plot

• Markdown formatting is enabled for roxygen2 documentation.

Updated features

• sim_continental_island() now has an epss argument for colonisation max ages of vicariant species. Default is 0.
• GitHub actions continuous integration now installs from renv lock file (using r-lib/actions/setup-r@v2) instead of installing the newest version of required dependencies (using r-lib/actions/setup-r-dependencies@v2).
• ggplot2::annotate(geom = "point") is used over ggplot2::geom_point() when plotting a single point in plot_param_diffs().
• plot_vicariance_scatter() call is added to data_vis.R script.
• post_process_vicariance_results() call is added to post_process.R script.
• Analyses use simplex optimisation method instead of subplex.
• The test-continental-daisie.Rmd vignette is updated.
• Parameter estimate plots and empirical plots are updated.
• Post processed data in inst/ is updated.
• Default plot DPI is changed to 300.

- R
Published by joshwlambert about 2 years ago

daisiecontinental - DAISIEcontinental v0.1.0

DAISIEcontinental 0.1.0

The initial release of DAISIEcontinental R package contains functions, scripts, documentation and data for analysing the continental DAISIE inference model. This first release has developed and used functions and scripts for the manuscript Lambert et al. (in prep) on Madagascar tetrapod fauna.

- R
Published by joshwlambert about 2 years ago