Changes in version 3.7.1 (2025-10-22)                  

  - 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.

                       Changes in version 3.6.1.1                       

  - Updated citation details for {biodosetools} after publication in Int
    J Radiat Biol (doi:10.1080/09553002.2023.2176564).
  - Improvements in deploy-shiny.yml CI workflow.
  - Added dev/shiny-redirect shiny app to redirect biodosetools-v3 at
    shinyapps.io to version hosted by Bundesamt für Strahlenschutz.

                 Changes in version 3.6.1 (2022-11-16)                  

  - 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
    https://github.com/ThinkR-open/golem/commit/61b9063f65006bc9b15dd2f1e535466c45d25424).
  - 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.

                 Changes in version 3.6.0 (2022-01-27)                  

  - 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.

                        Changes in version 3.5.0                        

  - 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
    https://github.com/r-lib/tidyselect/issues/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() function 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 assay.
  - 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.

                        Changes in version 3.4.0                        

  - Removed all non-ASCII characters.
  - Major overhaul of reports.
  - Added "Report bug" button on home screen and cleaned up
    dashboard_*() code.
  - Removed dependencies on {stringr} package.
  - Initial utils::citation() support via CITATION file.
  - Minimal version of R bumped to 3.5.0.
  - Minimal version of {dplyr} bumped to 1.0.0.

Bug fixes

  - Replaced C, α, β variables (and derivatives) by coeff_C,
    coeff_alpha, coeff_beta.
  - Fixed error in genome_fraction parsing for translocations in
    estimate_partial_dolphin().
  - Fixed count/case data standard error column names replacements.
  - Fixed minipage issue when using more than 12 columns in {knitr}
    tables with column name replacements, by using format = "latex",
    escape = FALSE parameters in kable() call.
  - Suppress YAML warning when using !expr in PDF reports. See
    https://github.com/rstudio/rstudio/issues/7545.

New functions

  - 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.

Reports improvements

  - New PDF reports, which are now the default output format.
  - Improved HTML reports styling.
  - Added explicit M-FISH usage in translocation reports.
  - Added assay name in report titles.

                        Changes in version 3.3.1                        

Bug fixes

  - Count and case data calculations are performed using
    calculate_aberr_*() functions. Fixes #8.
  - Fixed missing {dplyr} namespace in n() function call.
  - Fixed mismatched use of awesomeCheckbox() and switchInput() in
    confounders input.

New functions

  - 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().

                        Changes in version 3.3.0                        

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.

New features

  - App is now a {golem} R package.
  - Migrated UI from {shinydashboard} to {bs4Dash}.
  - Modals are now built with {bsplus} instead of {shinyBS}.
  - Functions and internal data are documented using {roxygen2}.
  - Added {pkgdown} support to build {biodosetools}'s website
    automatically.
  - All custom theming is done through SASS and CSS instead of R code
    injection.

New functions

  - New include_help() for help dialogues
  - New help_modal_button() function to help build modal trigger buttons
    on boxes' titles.
  - New load_rmd_report() function to use in server downloadHandler().
  - Moved get_genome_fraction() as its own exported function.

Fixes

  - Fixed #7. Overestimate error of lambda when dispersion is smaller
    than 1.
  - Fixed missing icon on sidebar.
  - Fixes in collapse button paddings.
  - Fixed tabBox parameters.
  - Using rlang::.data$ to avoid "no visible binding for global
    variable" warnings.
  - Fixed bsplus::bs_modal() calls in output$estimate_results_ui.
  - Removed input as parameter in calculation functions.
  - Fixed style of help button on box/tabBox headers.
  - Updated old "biodosimetry-uab" URLs to "biodosetools-team".

Improvements

  - Stop exporting auxiliary include*() functions used on the app only.
  - Moved widget_label() to widgets.R.
  - Refactored inner_column() function.
  - Refactored UI modules names.
  - Refactored server functions and renamed R scripts.
  - Updated reports.
  - Using load_rmd_report() on mod_estimate_results_server() module.
  - Added DNA Content Fractions of Human Chromosomes (IHGSC) data.
  - Updated dna_content_fractions call on
    mod_trans_fraction_to_full_genome_server() module.
  - Added support for tabBox on help_modal_button() widget.
  - Added indentation to all module rhandsontable() calls.
  - Stop exporting get_decision_threshold() function temporarily.
  - "Stains color options" boxes don't use inner_column() anymore.
  - Updated NEWS.md headers so they can be parsed by {pkgdown}.

UI Improvements

  - Removed experiment_select selectInput() from sidebar. Every assay is
    listed on the "Aberration assays" sidebarMenu().
  - Loading all UI modules in dashboard_body().
  - Navbar now uses rightUi and leftUi parameters, as well as skin =
    "light".
  - Switched from shinyBS::bsButton() to shiny::actionButton() for
    calling modal dialogues.
  - New CSS style sheet for {shinydashboard}.
  - Deleted old CSS files for {bs4Dash}.
  - New fonts CSS stylesheet.
  - New CSS stylesheets for fixes of existing classes and definition of
    custom classes.
  - Added hot-improved CSS class for rHandsontableOutput().
  - Moved custom widgets classes from theming.R to custom.css.
  - Tweaks in box, awesome-checkbox, and sidebar submenus CSS styles.
  - Replaced theme_button_status() function by proper SASS to CSS
    compilation.
  - Finished SASS box header colors.
  - Using SASS modules to reconstruct biodose_style.css.
  - Moved treeview-menu style to sidebar.scss.
  - Added checkboxes SASS style.
  - Added missing col-inner-* CSS classes.
  - Added app version on sidebar footer with custom sticky-footer CSS
    class.
  - Switched to a single stylesheet, being everything built by SASS
    modules.
  - Added custom style to radiobuttons.

                        Changes in version 3.2.1                        

Bug fixes

  - Added required {pander} package to generate DOCX reports.

                        Changes in version 3.2.0                        

All calculations functions previously provided in inst/app/calcs have
been made proper functions on the package.

New functions

  - 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.

"New" 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().

                        Changes in version 3.1.0                        

Unofficial release (wasn't changed on DESCRIPTION file). This includes
some of the changes discussed with David in Stockholm (ERPW19).

New features

  - Made var-cov matrix optional on dose estimation inputs.
  - Fixed calculations to make var-cov matrix optional on dose
    estimation inputs.

Fixes

  - Added additional package dependencies to DESCRIPTION file.
  - Following the ISO, renamed detection limits to decision threshold.

Changes

  - Disabled decision thresholds (for now).
  - Hide AIC as a relative quality statistic of the dose estimation.
  - Added mean and variance to count data tables in fitting module.

                        Changes in version 3.0.0                        

The app is now available as an R package on GitHub (not submitted to
CRAN yet).

New functions

  - runApp() for launching Biodose Tools.
  - %>% imported from {magrittr}.

Fixes

  - Fixed variance calculation for count data.
  - Provide fallback method for NB2 when using
    constraint-maxlik-optimization.

                        Changes in version 2.1.0                        

New features

  - Initial implementation of micronuclei, adding support in UI and
    server functions.
  - Implemented negative binomial fitting calculation for micronuclei
    count data.
  - Initial detection limit implementation for translocations.
  - Added DOCX support for dicentrics and translocations.

New functions

  - New bs4MyTabPanel() widget to remove unnecessary padding on
    tabCards' panels.

Fixes

  - Fixed colwidths for detection limits.
  - Fixed unnecessary recalculation of num_cols for chromosome tables in
    translocations modules.
  - New subdirectory structure for help dialogues.
  - Added buttons and example tables in help dialogues.
  - Updated documentation link.

Improvements

  - Added button_fit dependency for detection limits calculation.
  - Updated fitting reports (new hot structures & dynamic widths).
  - Moved calculation functions from fitting and estimation modules to
    their own files in a new calcs directory.
  - Translocations reports are complete now.

Changes

  - Disable sourcing translations.R for now (until {shiny-i18n} is
    implemented).

                        Changes in version 2.0.0                        

New features

  - Added manual input of translocations name.
  - Implemented dynamic calculation of hot width for counts, cases, and
    chromosome data tables.
  - Implemented manual input of translocation frequency to be subtracted
    from the observed yield.
  - Started detection limit calculation in fitting module.
  - Implemented Delta method for whole-body estimation.
  - Added calculation of standard error of Fg for translocations' dose
    estimation module.

Fixes

  - Fixed dependency of the "Calculate fitting" button in the
    translocation module.
  - Fixed calculations for whole and partial body estimations for
    translocations module.
  - Fixed colors on chromosome hot table example.
  - Fix genomic conversion factor not being read when doing fitting.
  - Fix Fp -> y when using dicentrics in dose estimation module.
  - Fixed detection limit calculation.
  - Fixed dose estimation in detection limits function.
  - Corrected correction of FISH to Full genome when inputting manual
    fitting curve in dose estimation modules.
  - Corrected reading of translocations fit curve values in dose
    estimation module.

Improvements

  - Tweaked variable names and order in cases data for translocations
    dose estimation.
  - Updated help_colors_dialog for translocations modules.
  - New module for auxiliary rhandsontable() tables used in help
    dialogues.
  - New help dialogues for translocations modules.
  - Consistent use of genome_fraction in variables related to the
    genomic conversion factor/fraction of genome hybridised.
  - ggplot2 curve generation is now wrapped inside a function on the
    dose estimation modules.
  - Finished confounders help dialogue.
  - New aberration calculation method using purrr::map_df() instead of a
    nested loops, which is about 10 times faster.
  - Make clear in translocations dose estimation module that the
    coefficients are from the full genome.
  - Added highly protracted exposure.
  - Implemented calculation of detection limits from data.
  - Added dose calculation to detection limits section.
  - Changed σ to \sigma in help dialogues.
  - Added units to result tables.
  - Code clean-up on delta method for whole-body dose estimation.
  - Updated plot CI text generation on legend to account for new Delta
    method and for separate whole-body & heterogeneous error method
    selection.
  - CONTRIBUTORS.md is now displayed as a modal.
  - Using ORCID for authors when possible.
  - Updated institution links in contributors files.

UI Improvements

  - Improved side-widget-tall bottom margins.
  - Moved translocation frequency selectInput() next to Calculate
    Fitting button for better UX.
  - New hot-improved CSS class for better hot tables' formatting.
  - All hot tables are using hot-improved class now.
  - New contributors list style and custom CSS style for tables.
  - Added experiment/aberration name on tab body title to avoid
    confusions.
  - Improved "About" tab paddings.
  - Improve widths of color columns in chromosome tables.
  - Narrower color columns in chromosome tables.
  - All hot tables' widths are dynamic or exact now.
  - Improved small action buttons style on help dialogues.
  - New results color to differentiate from main color.
  - Updated UI to adapt for new Delta method for whole-body estimation.
  - Updated translocations UI to adapt for new Delta method for
    whole-body estimation.
  - Added CI for Dolphin dose estimation UI.
  - Added (work in progress) Micronuclei into UI.
  - Hide language selector until shiny-i18n is implemented.

                        Changes in version 1.2.0                        

New features

  - Start translocations dose estimation module and report.
  - Allow using M-Fish color scheme in translocations fitting module.
  - Added method to convert from translocations measured by FISH to full
    genome.
  - Implemented confounders modifications for translocations in
    generalEstimateCaseHotTable() module.

Improvements

  - New chromosome table structure. transChromosomeTable() and
    transFractionToFullGenomeCalc() have been moved to
    transGeneralModule.R, as they are reused in the dose estimation
    module.
  - Using new chromosome table UI and server modules for translocations
    dose estimation.
  - Merged "repeated" fitting modules into a generalFittingModules.R
    file.
  - Merged *FittingResults() modules into generalFittingResults()
    module.
  - Updated translocations fitting report to new chromosome table
    structure.
  - New generalEstimateFittingCurveHotTables() and
    generalEstimateFittingCurve() modules.
  - New globalVariables.R with global_fitting_formulas list.
  - Added translocations-specific code in generalEstimateFittingCurve()
    module to take into account used translocation frequency.
  - New inputs for used translocation frequency and genomic conversion
    factor in manual fitting input in dose estimation module.
  - Moved dose estimation to generalEstimateResults() module.
  - Modify translocations (X - Xt) for whole-body and partial-body dose
    estimation.
  - Added readOnly status to Xt, yt, yt_err variables on rhandsontable()
    for translocations case data.

UI improvements

  - New innerColumn to use inside cards/boxes.
  - New widgetLabel() function for labels above widgets without default
    label.
  - Replaced old labels by new widgetLabel() function.
  - Finished confounders UI in translocations dose estimation module.
  - New mySwichInput() function based on shinyWidgets::switchInput()
    with sideLabel and custom status colors.
  - Moved from awesomeCheckbox() to mySwitchInput() in all UI modules.
  - Moved fitting curve input in translocations' dose estimation module
    to the top.

Fixes

  - Fix minor error in calculation of infimum yield values.
  - Fixed "Color options" card and color_list object for chromosome
    table generation.
  - Fixed missing type argument in get_model_statistics() in dose
    estimation module.
  - Deleted heterogeneous estimation for translocations.

                        Changes in version 1.1.0                        

New features

  - Conditional tabs in sidebar by implementing
    bs4MyConditionalSidebarMenuItem() function.
  - Implemented AIC calculation for different dose estimation
    assessments.
  - Added ZIP archive with sample data for testing.
  - New dynamic bs4TabCard() using renderUI() and session$ns() to show
    different tabs depending on user input.
  - Implemented manual calculation of case parameters (N, X, y, y_est,
    DI, u) in dose estimation module.

Improvements

  - Disabled automatic calculation of N, X, DI, u to avoid broken input
    issues when running the deployed app.
  - Added CONTRIBUTORS.md file.
  - Removed {fontawesome} package requirement.
  - Added translocation frequency and genomic conversion factor to
    translocations fitting report.
  - Chromosome table included in reports.
  - Major rewrite of {ggplot2} plot in dose estimation module.
  - Added Dolphin CI info into plot when using partial-body assessment.
  - Changed display of CI in plot for dose estimation.
  - Genomic conversion factor is used in transFittingResults() module
    for calculations instead of modifying the value of N in
    transFittingHotTable().
  - Added theoretical calculation of model-specific statistics (glm
    method) on fitting module.
  - Added renormalisation of data for proper calculation of
    model-specific statistics in fitting module.
  - Added theoretical model-specific statistics calculation for
    constraint maxlik optimization method in fitting module.
  - Added global get_model_statistics() to translocations fitting
    module.

UI improvements

  - Cleaner version of topButton() for help button and help modals on
    fitting and dose estimation modules..
  - More informative model summary dialogue in fitting module.
  - Better output of genomic conversion factor.
  - "Partial" is now "Partial-body". Better titles in dose estimation
    results card.
  - New bs4MyTabCard() function with topButton and noPadding
    capabilities.

Fixes

  - Fixed problem with fit_formula_raw when using linear model. Disabled
    *-no-int models until Dolphin can deal with them.
  - Fixed rendering problem in Firefox (and potentially other browsers)
    with count data rhandsontable() using 100% of the card's height.
  - Fixed dose estimation rhandsontables() divs on Firefox having height
    = 100% of the card's own height.
  - Fixed height error in cases data table in dose estimation module in
    Firefox.
  - Fixed glm_results object issue in get_model_statistics() function.

                        Changes in version 1.0.0                        

First public beta for laboratories and research centres.

New features

  - Initial support of reports.
  - Implemented selection of CI for dose estimation (83%-83% & 95%-95%).
  - Added method selection for partial body exposure estimation.
  - Fixed formatting of variance covariance matrices when rendered by
    rHandsontableOutput().
  - Linear models compatibility for partial-body (Dolphin) and
    heterogeneous dose estimation.
  - Experimental version of new Maximum Likelihood Estimation method for
    dose-effect fitting.
  - Manual input of fitting coefficients and var/cov matrix for dose
    estimation.

Improvements

  - Added format/MIME type validation for file inputs.
  - Render fitting formula using MathJax.
  - Format curve depending on selected assessment/method (use
    appropriate CI) on dose estimation.
  - Check if yield projection into dose is mathematically possible.
    Negative values of yield or dose are changed to zero as well.
  - Added modification to Merkle's yield error function when using
    protracted exposures.
  - Implemented protracted exposure for partial body dose estimation.
  - Added automatic Poisson/quasi-Poisson selection on fitting.
  - Correct p-values depending on fitting model dispersion.
  - Added automatic correction of confidence intervals to use
    "simplified" Merkle's method if necessary.

Fixes

  - Fixed calculation of full genome.
  - Fixed alignment of conditional error/method inputs for dose
    estimation.
  - Changed "base" to "estimate" on CI tables for dose estimation.
  - Fixed bs4TabCard() bug.

                        Changes in version 0.2.0                        

Version presented in second Team Meeting at Munich.

New features

  - Migrated UI from {shinydashboard} to {bs4Dash}.
  - Added data, plot, and results export options.
  - Added modal dialogues using {shinyBS}.
  - Dose estimation modules for dicentrics.
  - Complete implementation of dicentrics analysis.
  - Experimental fitting for translocations assay.

                        Changes in version 0.1.0                        

First draft and proof of concept presented to the RENEB team at
Barcelona.

Features

  - UI built using {shinydashboard}.
  - Fitting modules for dicentrics.
  - Dynamic input tables powered by {rhandsontable}.