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.

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).

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.

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().

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.

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.