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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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.