deploy-shiny.yml CI workflow.dev/shiny-redirect shiny app to redirect biodosetools-v3 at shinyapps.io to version hosted by Bundesamt für Strahlenschutz.moduleServer(), as recommended in {shiny} >= 1.5.0 (see https://shiny.rstudio.com/articles/modules.html).golem_utils_ui.R and related unit tests to match {golem} 0.3.x (see https://github.com/ThinkR-open/golem/commit/61b9063f65006bc9b15dd2f1e535466c45d25424).parse_model_formula(), list_fitting_formulas(), and help dialogues.solve() call.gardner_confidence_table data (deprecated in 585e7b4).get_cov_ZIP_ML() to match expressions on manuscript, introducing minor calculation optimisation.fit_maxlik_method() by removing unused local variables and redundant calls.message() to cli::cli_alert_warning() in fit() function when switching from glm() to ML optimization.match_names() to return input x, akin to match.arg() from {base}.mod_estimation_micro_ui().mean and std_err column renaming to calculate_aberr_table() when type = "case" depending on new aberr_module parameter.aberr_module validation using match.arg() in *_aberr_table(), estimate_*(), prepare_maxlik_count_data(), fit*() functions.names_from_model_formula() and parse_model_formula().app_config.R and test-golem-recommended.R unit tests.load_rmd_report().testServer() unit tests for all mod_*_server() modules.mod_fitting_*_ui.R modules.as_tibble() in calculate_aberr_table() for consistency with count data.cli::cli_alert_info() call.pi_estimate value in est_metaphases_frac data frame in estimate_partial_body_dolphin(), as pointed out by Gaëtan.match_names() not correctly stopping, and added unit tests for it.calculate_aberr_table() when type = "case".est_metaphases_frac data frame to explicitly return f (1 - pi_est) in estimate_partial_body_dolphin() (closes #29)..data calls inside {tidyselect} selections (see https://www.tidyverse.org/blog/2022/10/tidyselect-1-2-0/).data-raw.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().golem_utils_server.R.calculate_decision_threshold*() functions and mentions in UI and server modules, as this will be rewritten from scratch.calculate_decision_threshold from _pkgdown.yml.plot_estimated_dose_curve() function.msm::deltamethod().genome_factor across all functions, help dialogues, and reports.conf_int in estimate_*() family of functions.est_full_doses$type in plot_estimated_dose_curve() function so unused assessments are not shown in legend.match_names() function to match est_doses list names when calling plot_estimated_dose_curve().plot_estimated_dose_curve() to automatically build est_full_doses object from list of dose estimation results, added parse_conf_int_text() auxiliary function.estimate_whole_body_delta() when there's no aberrations.cov_est in estimate_partial_dolphin().try() to ensure convergence (up to 5 tries).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.gamma and gamma_error parsing when calling estimate_hetero_mixed_poisson() in mod_estimation_results_server().\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.calculate_aberr_table() so they match the final output in Shiny.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.count-data-rodriguez-2004.csv for total translocations from Rodriguez et al. (2004) https://doi.org/10.1667/RR3198.calculate_aberr_power() to remove {purrr} dependency and reduce computation time by 4.message() calls with appropriate cli::cli_*() calls.fit_glm_method(), as it is otherwise confusing.\sigma to \hat{\sigma} in fix_count_data_names() and respective tests.*-fitting-results-*.rds instead of *-fitting-data-*.rds when exporting RDS objects in mod_fitting_results_server().side-widget-* CSS classes to better style file download/format buttons.widget_sep_vert() function.sep-widget_* CSS classes in fitting UI modules.side-widget-* CSS classes in dose estimation UI modules.shiny::Progress._pkgdown.yml and simplified extra.css thanks to Bootstrap 5 support in {pkgdown} 2.0.0.Suggests field in DESCRIPTION file.u-value and other formatting refinements.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.calculate_aberr_var() function.glm and glm.nb). Fixes #20, addresses part of #14 as well.fix_count_data_names() function..csv file is not perfectly formatted.calculate_yield_infimum() where infima were being calculated for yield estimate only (fixes #26).X for Ck when k>=10 (fixes #27).fix_count_data_names() to properly correct Ck>=C10 (related to issue #27).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.get_decision_threshold() function to calculate_decision_threshold(), and added calculate_decision_threshold_table() wrapper function.calculate_decision_threshold_*() functions to remove input argument.get_*() translocation functions to calculate_*() for better consistency.get_*_dose_curve() functions to plot_*_dose_curve() for more clarity.get_model_statistics() to calculate_model_stats().get_fit_*() functions to fit() and fit_*_method().get_fit_maxlik_method() function.mod_<calc_type>_<aberration>_*().get_model_statistics() function so that local get_model_statistics() definition could be removed from mod_estimate_fit_curve_server() module.<aberration>-<module>-<format>.Rmd report templates have been merged into <module>-<format>.Rmd (4 files).correct_negative_vals() to ensure correct dose estimation when X < Xc in translocations assay.*_at() and *_if() occurrences by their {dplyr} 1.0.0 equivalents.column(width = X) calls by col_X() in UI modules.tabitem-container class to tabItem() page containers for fixed max-width while keeping responsive UI.col-inner-textinput-* CSS classes for Irradiation conditions textInput() widgets' containers.sep-widget-download and sep-widget-format CSS classes to unify download and format select buttons into a single widget.dashboard_*() code.utils::citation() support via CITATION file.C, α, β variables (and derivatives) by coeff_C, coeff_alpha, coeff_beta.estimate_partial_dolphin().format = "latex", escape = FALSE parameters in kable() call.!expr in PDF reports. See https://github.com/rstudio/rstudio/issues/7545.fix_coeff_names(), to fix coefficient names in reports.fix_count_data_names(), to fix count/case data column names in PDF reports.to_title(), to replace stringr::str_to_title() using base R.calculate_aberr_*() functions. Fixes #8.n() function call.awesomeCheckbox() and switchInput() in confounders input.calculate_aberr_power(), which supersedes internal aberr_calc() function in server modules.calculate_aberr_mean().calculate_aberr_var().calculate_aberr_disp_index().calculate_aberr_u_value().Initial migration of the app into a {golem} R package. This means Biodose Tools is also available as a regular R package in case the user wants to build their own R scripts. This also reduced lots of code redundancies, and made the code a lot more robust.
include_help() for help dialogueshelp_modal_button() function to help build modal trigger buttons on boxes' titles.load_rmd_report() function to use in server downloadHandler().get_genome_fraction() as its own exported function.tabBox parameters.rlang::.data$ to avoid "no visible binding for global variable" warnings.bsplus::bs_modal() calls in output$estimate_results_ui.box/tabBox headers.include*() functions used on the app only.widget_label() to widgets.R.inner_column() function.load_rmd_report() on mod_estimate_results_server() module.dna_content_fractions call on mod_trans_fraction_to_full_genome_server() module.tabBox on help_modal_button() widget.rhandsontable() calls.get_decision_threshold() function temporarily.inner_column() anymore.NEWS.md headers so they can be parsed by {pkgdown}.experiment_select selectInput() from sidebar. Every assay is listed on the "Aberration assays" sidebarMenu().dashboard_body().rightUi and leftUi parameters, as well as skin = "light".shinyBS::bsButton() to shiny::actionButton() for calling modal dialogues.hot-improved CSS class for rHandsontableOutput().theming.R to custom.css.box, awesome-checkbox, and sidebar submenus CSS styles.theme_button_status() function by proper SASS to CSS compilation.biodose_style.css.sidebar.scss.col-inner-* CSS classes.sticky-footer CSS class.radiobuttons.All calculations functions previously provided in inst/app/calcs have been made proper functions on the package.
calculate_yield() new wrapper of yield_fun(), R_factor(), and yield_error_fun().calculate_yield_infimum() function to calculate infima of yields given a curve.project_yield() merged version of the project_yield_estimate(), project_yield_lower(), and project_yield_upper() functions.get_decision_threshold().get_fit_dose_curve().get_fit_glm_method().get_fit_maxlik_method().get_fit_results().get_model_statistics().prepare_maxlik_count_data().AIC_from_data().correct_boundary().correct_conf_int().correct_negative_vals().correct_yield().get_estimated_dose_curve().protracted_g_function().R_factor().yield_error_fun().yield_fun().estimate_hetero().estimate_partial_dolphin().estimate_whole_body_delta().estimate_whole_body().Unofficial release (wasn't changed on DESCRIPTION file). This includes some of the changes discussed with David in Stockholm (ERPW19).
DESCRIPTION file.The app is now available as an R package on GitHub (not submitted to CRAN yet).
runApp() for launching Biodose Tools.%>% imported from {magrittr}.bs4MyTabPanel() widget to remove unnecessary padding on tabCards' panels.colwidths for detection limits.num_cols for chromosome tables in translocations modules.button_fit dependency for detection limits calculation.calcs directory.translations.R for now (until {shiny-i18n} is implemented).Fg for translocations' dose estimation module.Fp -> y when using dicentrics in dose estimation module.help_colors_dialog for translocations modules.rhandsontable() tables used in help dialogues.genome_fraction in variables related to the genomic conversion factor/fraction of genome hybridised.purrr::map_df() instead of a nested loops, which is about 10 times faster.σ to \sigma in help dialogues.side-widget-tall bottom margins.selectInput() next to Calculate Fitting button for better UX.hot-improved CSS class for better hot tables' formatting.hot-improved class now.generalEstimateCaseHotTable() module.transChromosomeTable() and transFractionToFullGenomeCalc() have been moved to transGeneralModule.R, as they are reused in the dose estimation module.generalFittingModules.R file.*FittingResults() modules into generalFittingResults() module.generalEstimateFittingCurveHotTables() and generalEstimateFittingCurve() modules.globalVariables.R with global_fitting_formulas list.generalEstimateFittingCurve() module to take into account used translocation frequency.generalEstimateResults() module.(X - Xt) for whole-body and partial-body dose estimation.Xt, yt, yt_err variables on rhandsontable() for translocations case data.innerColumn to use inside cards/boxes.widgetLabel() function for labels above widgets without default label.widgetLabel() function.mySwichInput() function based on shinyWidgets::switchInput() with sideLabel and custom status colors.awesomeCheckbox() to mySwitchInput() in all UI modules.get_model_statistics() in dose estimation module.bs4MyConditionalSidebarMenuItem() function.bs4TabCard() using renderUI() and session$ns() to show different tabs depending on user input.N, X, y, y_est, DI, u) in dose estimation module.N, X, DI, u to avoid broken input issues when running the deployed app.CONTRIBUTORS.md file.transFittingResults() module for calculations instead of modifying the value of N in transFittingHotTable().glm method) on fitting module.maxlik optimization method in fitting module.get_model_statistics() to translocations fitting module.topButton() for help button and help modals on fitting and dose estimation modules..bs4MyTabCard() function with topButton and noPadding capabilities.*-no-int models until Dolphin can deal with them.rhandsontable() using 100% of the card's height.rhandsontables() divs on Firefox having height = 100% of the card's own height.glm_results object issue in get_model_statistics() function.First public beta for laboratories and research centres.
rHandsontableOutput().bs4TabCard() bug.Version presented in second Team Meeting at Munich.
First draft and proof of concept presented to the RENEB team at Barcelona.