biodosetools 3.6.0

Major rewrite of plot_estimated_dose_curve() function.
Delta method calculations are now all done via msm::deltamethod().
Added progress and alert notifications to UI.
Added {markdown} as suggested dependency.
Added {cli} as dependency.
Tweaked references section in {pkgdown} site to only include exported functions organised by topic/usage.
Use consistently genomic conversion factor or genome_factor across all functions, help dialogues, and reports.
Added R-CMD check GitHub Action.
Added vignettes.

New features

Return conf_int in estimate_*() family of functions.
Parse est_full_doses$type in plot_estimated_dose_curve() function so unused assessments are not shown in legend.
Added match_names() function to match est_doses list names when calling plot_estimated_dose_curve().
Updated plot_estimated_dose_curve() to automatically build est_full_doses object from list of dose estimation results, added parse_conf_int_text() auxiliary function.

Correct dispersion index value on estimate_whole_body_delta() when there's no aberrations.
Fixed issue in missing count data in DOCX fitting report.
Removed double calculation of cov_est in estimate_partial_dolphin().
Wrapped mixed Poisson model dose estimation in try() to ensure convergence (up to 5 tries).
Mixed Poisson model estimate_hetero_mixed_poisson() uses exact delta methods for dose and fraction irradiated, as described in paper by Pujol et al. (2016) https://doi.org/10.1667/RR14145.1.
Fixed gamma and gamma_error parsing when calling estimate_hetero_mixed_poisson() in mod_estimation_results_server().
Wrap unicode characters (\uxxxx) in rlang::as_utf8_character() to avoid "unable to translate to native encoding" warning on Windows.

get_deltamethod_std_err(): auxiliary function to wrap all msm::deltamethod() calls.

Fixed order of output case data columns in calculate_aberr_table() so they match the final output in Shiny.
Renamed count-data-IAEA.csv to count-data-barquinero-1995.csv from Barquinero et al. (1995) https://doi.org/10.1016/0027-5107(94)00150-4.
Added count-data-rodriguez-2004.csv for total translocations from Rodriguez et al. (2004) https://doi.org/10.1667/RR3198.
Updated translocations fitting unit tests to use data from Rodriguez et al. (2004) https://doi.org/10.1667/RR3198.
Rewrote calculate_aberr_power() to remove {purrr} dependency and reduce computation time by 4.
Replaced message() calls with appropriate cli::cli_*() calls.
Split quasi-Poisson from automatic fitting in fit_glm_method(), as it is otherwise confusing.
Updated \sigma to \hat{\sigma} in fix_count_data_names() and respective tests.
Updated unit tests to test individual values both in dose-effect fitting and dose estimation.
Use *-fitting-results-*.rds instead of *-fitting-data-*.rds when exporting RDS objects in mod_fitting_results_server().

Added new side-widget-* CSS classes to better style file download/format buttons.
Added widget_sep_vert() function.
Use new sep-widget_* CSS classes in fitting UI modules.
Updated report help modals text.
Using new side-widget-* CSS classes in dose estimation UI modules.
Added progress notifications to calculations via shiny::Progress.
Updated _pkgdown.yml and simplified extra.css thanks to Bootstrap 5 support in {pkgdown} 2.0.0.