Biodose Tools 3.7.1

New module for criticality accidents dose estimation.
New module for calculating chacaracteristic limits.
New module for interlaboratory comparisons.

Improvements
Now multiple dose calculations can be done at the same time.
.xlsx save.
Error message when missing fields
Error message when there are no C2 cells for partial body assessment.
Separated micronucleus assay.

Biodose Tools 3.6.1

biodosetools 3.6.1

• Removed {pkgload} and {htmltools} as package dependencies.
• Server modules now use moduleServer(), as recommended in {shiny} >= 1.5.0 (see https://shiny.rstudio.com/articles/modules.html).
• Updated golem_utils_ui.R and related unit tests to match {golem} 0.3.x (see ThinkR-open/golem@61b9063).
• Updated CITATION file.
• Updated vignettes.

Improvements

• Updated LQ and L formulas to use lambda instead of Y for yield in parse_model_formula(), list_fitting_formulas(), and help dialogues.
• Removed unnecessary {base} namespace in solve() call.
• Removed legacy gardner_confidence_table data (deprecated in 585e7b4).
• Updated get_cov_ZIP_ML() to match expressions on manuscript, introducing minor calculation optimisation.
• Improved fit_maxlik_method() by removing unused local variables and redundant calls.
• Switched message() to cli::cli_alert_warning() in fit() function when switching from glm() to ML optimization.
• Updated match_names() to return input x, akin to match.arg() from {base}.
• Updated default values for assessment and whole-body error method selection in mod_estimation_micro_ui().
• Added mean and std_err column renaming to calculate_aberr_table() when type = "case" depending on new aberr_module parameter.
• Added aberr_module validation using match.arg() in *_aberr_table(), estimate_*(), prepare_maxlik_count_data(), fit*() functions.
• Updated unit tests for names_from_model_formula() and parse_model_formula().
• Updated app_config.R and test-golem-recommended.R unit tests.
• Added unit test for load_rmd_report().
• Added basic testServer() unit tests for all mod_*_server() modules.

UI Improvements

• Updated "Irradiation conditions" boxes so they are no longer collapsed by default in mod_fitting_*_ui.R modules.

Bug fixes

• Return case data as_tibble() in calculate_aberr_table() for consistency with count data.
• Minor formatting fix in cli::cli_alert_info() call.
• Fixed pi_estimate value in est_metaphases_frac data frame in estimate_partial_body_dolphin(), as pointed out by Gaëtan.
• Fixed issue with match_names() not correctly stopping, and added unit tests for it.
• Fixed misconstructed column selection in calculate_aberr_table() when type = "case".
• Added est_metaphases_frac data frame to explicitly return f (1 - pi_est) in estimate_partial_body_dolphin() (closes #29).
• Updated deprecated .data calls inside {tidyselect} selections (see https://www.tidyverse.org/blog/2022/10/tidyselect-1-2-0/).

Deprecations

• Removed unused files in data-raw.
• Deprecated model_formula with no intercept in parse_model_formula(), names_from_model_formula(), prepare_maxlik_count_data(), fit_maxlik_method(), and mod_estimation_fit_curve_hot_server().
• Removed golem_utils_server.R.
• Purged calculate_decision_threshold*() functions and mentions in UI and server modules, as this will be rewritten from scratch.
• Removed calculate_decision_threshold from _pkgdown.yml.

Biodose Tools 3.6.0

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.

Bug fixes

• 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.

New functions

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

Improvements

• 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().

UI Improvements

• 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.

Biodose Tools 3.5.0

biodosetools 3.5.0 (2021-05-26)

• Added unit tests for to check code coverage and to validate that the code performs as expected.
• Major revision of the fitting and dose estimation pipelines, introducing new auxiliary functions to reduce duplicated code.
• Major simplification of report rendering process; abandoned HTML output.
• Added custom {pkgdown} theme for more consistent branding.
• Added preliminary citation to README.
• Moved packages required only for reports to Suggests field in DESCRIPTION file.

New features

• Added irradiation conditions input to dose-effect fitting modules.
• Reports include conditional formatting of u-value and other formatting refinements.
• Added biodosetools_version element to Shiny App's exported *-fitting-data-YYY-MM-DD.rds files.
• fit() function allows to optionally select "glm" or "maxlik" algorithms. If "glm" if selected, the original tryCatch() routine will be executed.

Bug fixes

• Fixed unexported calculate_aberr_var() function.
• Stopped using weights in fitting algorithms (glm and glm.nb). Fixes #20, addresses part of #14 as well.
• Fixed aggregated count data column parsing in fix_count_data_names() function.
• Fixed case data parsing issue when .csv file is not perfectly formatted.
• Fixed issue with manual fitting curve input (fixes #23).
• Fixed bug in calculate_yield_infimum() where infima were being calculated for yield estimate only (fixes #26).
• Fixed wrong calculation of aberrations X for Ck when k>=10 (fixes #27).
• Fixed fix_count_data_names() to properly correct Ck>=C10 (related to issue #27).
• Added "where" to global variables (see r-lib/tidyselect#201).

New functions

• inner_column(), to fix padding of boxes inside columns.
• widget_sep(), to insert div(class = "widget-sep", br()) calls.
• widget_sep_vert() to insert div(style = "height: 8px;") calls.
• names_from_model_formula(), to parse rhandsontable() Unicode row and column coefficient names.
• parse_model_formula() to get raw and TeX formulae from model_formula.
• calculate_trans_rate_sigurdson() and calculate_trans_rate_manual() to calculate translocation rates.
• calculate_aberr_table() wrapper, to calculate aberration tables for count and cases data.
• init_aberr_table(), to initialise aberration distribution tables in fitting and estimation server modules.
• list_fitting_formulas(), to replace global global_fitting_formulas object.
• generalise_fit_coeffs() and generalise_fit_var_cov_mat(), used internally in estimation functions instead of using general_fit_* as parameters.

Function refactoring

• Refactored get_decision_threshold() functoin to calculate_decision_threshold(), and added calculate_decision_threshold_table() wrapper function.
• Refactored calculate_decision_threshold_*() functions to remove input argument.
• Refactored get_*() translocation functions to calculate_*() for better consistency.
• Refactored get_*_dose_curve() functions to plot_*_dose_curve() for more clarity.
• Refactored get_model_statistics() to calculate_model_stats().
• Refactored get_fit_*() functions to fit() and fit_*_method().

Improvements

• Added Oliveira citation on get_fit_maxlik_method() function.
• Fixed Gaëtan's name order in citation and contributors list.
• Updated README and About body text.
• Renamed source R files for better naming consistency.
• Changed structure of modules to mod_<calc_type>_<aberration>_*().
• Generalised get_model_statistics() function so that local get_model_statistics() definition could be removed from mod_estimate_fit_curve_server() module.
• Multiple (18 files) <aberration>-<module>-<format>.Rmd report templates have been merged into <module>-<format>.Rmd (4 files).
• Use correct_negative_vals() to ensure correct dose estimation when X < Xc in translocations asay.
• Replaced all *_at() and *_if() occurrences by their {dplyr} 1.0.0 equivalents.

UI Improvements

• Replaced column(width = X) calls by col_X() in UI modules.
• Added tabitem-container class to tabItem() page containers for fixed max-width while keeping responsive UI.
• Added col-inner-textinput-* CSS classes for Irradiation conditions textInput() widgets' containers.
• Added sep-widget-download and sep-widget-format CSS classes to unify download and format select buttons into a single widget.

Biodose Tools 3.4.0

v3.4.0

Version bump to 3.4.0

Biodose Tools 3.3.0

v3.3.0

Added dna_fraction_tests.R script

Version 3.1.0 (2019-10-26)

This is the first version of the app bundled as an R package.

The package consists of runApp() only, which runs the app located on inst/app. This includes some of the changes I discussed with David in Stockholm.