NEWS

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isobxr 2021-09-02

• first released version

isobxr 2.1.0

Bug fixes

• sim.single_run(): with dplyr >= 1.1, the initial sizes and deltas could be assigned to the wrong boxes in sim.scenario() runs after the first one (boxes sorted in a different order). Initial state and box metadata are now matched to the box list.
• sim.single_run(): FORCING_SIZE and FORCING_RAYLEIGH were checked against the wrong list.
• Plot data summaries updated for dplyr >= 1.1 (multi-row summarise).
• In the LOG, SIZE.t0 and DELTA.t0 are now listed in the order of BOXES_ID_list.

sweep.final_nD()

• sweep.final_nD.2() is removed: sweep.final_nD() runs chunks in parallel (mc.cores, default all cores but one; one core on Windows).
• New ask_confirmation argument.
• Each chunk is checked for failed workers and missing runs.
• Each chunk's runs are appended to 1_LOG.csv instead of rewriting the whole file, and the temporary LOG header is written once (fixes a possible silent loss of LOG rows).

sim.scenario(), sweep.dyn_2D()

• Runs no longer read 1_LOG.csv, which makes them much faster in folders with a large LOG. sim.single_run() returns its LOG row (invisibly) when return_data = FALSE.

fit.final_space()

• fit.final_space_2() and fit.final_space_3() (development versions) are merged into fit.final_space(), which is faster and uses less memory.
• parameter_subsets are now applied before selecting the fitted runs: the fit searches the best combination of boxes among the runs within the subsets. Numerical limits are inclusive.
• The observation file may not list a box twice for the same delta.ref; observed boxes absent from the simulated system are ignored with a message.
• Custom expressions keep their written form in reports (e.g. custom.100*f.A_B/f.B_C).
• The LDA page is drawn again when print_lda = TRUE.
• export_fit_data only writes the RDS file when save_outputs = TRUE.

Dependencies

• ggplot2 >= 3.4.0 (linewidth); parallel added to Imports.

isobxr 2.0.0 (2023-08-23)

This is a new major release introducing new data management protocols and new functions. Old functions are replaced for sake of clarity.

The following exported functions were replaced as follows:

• ana_slvr() is replaced by solve_analytically()

• num_slvr() is replaced by solve_numerically()

• compose_isobxr() is replaced by sim.scenario()

• run_isobxr() is replaced by sim.single_run()

• sweep_dyn() is replaced by sweep.dyn_2D()

• sweep_steady() is replaced by sweep.final_nD()

The shinobxr_app() function was removed and replaced by new plotting functions:

• plot_dyn_2D()

• plot_scenario()

Additionally, the following functions are now exported:

• plot_relaxation()

• plot_single_run()

• read.dyn_2D_master()

• read.isobxr_master()

• read.scenario_master()

• read.final_nD_master()

• merge_FINnD_chunks()

• fit.final_space()

isobxr 1.0.1 (2021-09-07)

bug fixes

• prevent writing of (pdf) files outside tempdir in all examples/vignettes/tests (debian systems issue)

• fixed addressing of tempdir, ensuring proper post-run clearing of tempdir including in windows systems