Package: biodosetools 3.7.2

Anna Frances-Abellan

biodosetools: 'shiny' Application for Biological Dosimetry

A tool to perform all different statistical tests and calculations needed by Biological dosimetry Laboratories. Detailed documentation is available in <https://biodosetools-team.github.io/documentation/>.

Authors:Alfredo Hernández [aut], Anna Frances-Abellan [aut, cre], David Endesfelder [aut], Pere Puig [aut]

biodosetools_3.7.2.tar.gz
biodosetools_3.7.2.zip(r-4.7)biodosetools_3.7.2.zip(r-4.6)biodosetools_3.7.2.zip(r-4.5)
biodosetools_3.7.2.tgz(r-4.6-any)biodosetools_3.7.2.tgz(r-4.5-any)
biodosetools_3.7.2.tar.gz(r-4.7-any)biodosetools_3.7.2.tar.gz(r-4.6-any)
biodosetools_3.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
biodosetools/json (API)

# Install 'biodosetools' in R:
install.packages('biodosetools', repos = c('https://biodosetools-team.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/biodosetools-team/biodosetools/issues

Pkgdown/docs site:https://biodosetools-team.github.io

Datasets:

On CRAN:

Conda:

biological-datadosimetryshiny-app

7.20 score 5 stars 44 scripts 327 downloads 34 exports 110 dependencies

Last updated from:e4fa67e8bd. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK207
source / vignettesOK206
linux-release-x86_64OK224
macos-release-arm64OK167
macos-oldrel-arm64OK290
windows-develOK199
windows-releaseOK169
windows-oldrelOK171
wasm-releaseOK158

Exports:%>%bar_plotscalc.zValue.newcalculate_aberr_tablecalculate_characteristic_limitscalculate_genome_factorcalculate_trans_rate_manualcalculate_trans_rate_sigurdsoncurves_plotDI_plotdose_boxplotestimate_hetero_mixed_poissonestimate_partial_body_dolphinestimate_whole_body_deltaestimate_whole_body_merklefitfun.estimate.criticalityM_estimateplot_deviation_allplot_estimated_dose_curveplot_estimated_dose_curve_mxplot_fit_dose_curveplot_interlab_deviationplot_interlab_v2plot_triageplot_triage_interlabplot_zscore_allproject_yieldprotracted_g_functionQHampelrun_appsummary_curve_tablesu_test_plotyield_boxplot

Dependencies:askpassattemptbase64encbitbit64bslibbspluscachemclicliprcommonmarkconfigcpp11crayoncrosstalkcurldata.tabledigestdplyrevaluateexpmfarverfastmapfontawesomefsgenericsggplot2gluegolemgridExtragtableherehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmaxLikmemoisemimemiscToolsmixtoolsmsmmvtnormnlmeopensslopenxlsxotelpdftoolspillarpkgconfigplotlyprettyunitsprogresspromisespurrrqpdfR6rappdirsRColorBrewerRcppreadrrhandsontablerlangrmarkdownrprojrootS7sandwichsassscalessegmentedshinyshinydashboardshinyWidgetssourcetoolsstringistringrsurvivalsystibbletidyrtidyselecttimechangetinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableyamlzipzoo

Micronuclei dose-effect fitting
Input count data | Irradiation conditions | Perform fitting
Rendered frommicro-fitting.Rmdusingknitr::rmarkdown

Last update: 2025-12-16
Started: 2025-07-28

Dicentrics dose estimation criticality accidents
Load pre-calculated curves | Input case data | Perform dose estimation
Rendered fromdicent-mixed.Rmdusingknitr::rmarkdown

Last update: 2025-10-21
Started: 2025-07-28

Interlaboratory comparison
Load estimation results | Plot data input | Performe Z-score
Rendered frominterlab.Rmdusingknitr::rmarkdown

Last update: 2025-10-21
Started: 2025-07-28

Translocations dose-effect fitting
Calculate genomic conversion factor | Input count data | Irradiation conditions | Perform fitting
Rendered fromtrans-fitting.Rmdusingknitr::rmarkdown

Last update: 2025-08-19
Started: 2022-01-23

Dicentrics characteristic limits
Compare proband vs. control | Characteristic limits
Rendered fromdicent-limits.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2025-07-28

Dicentrics dose estimation
Load pre-calculated curve | Input case data | Perform dose estimation
Rendered fromdicent-estimation.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2022-01-23

Dicentrics dose-effect fitting
Input count data | Irradiation conditions | Perform fitting
Rendered fromdicent-fitting.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2022-01-23

Micronuclei dose estimation
Load pre-calculated curve | Input case data | Perform dose estimation
Rendered frommicro-estimation.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2025-07-28

Translocations dose estimation
Load pre-calculated curve | Calculate genomic conversion factor | Input case data | Perform dose estimation
Rendered fromtrans-estimation.Rmdusingknitr::rmarkdown

Last update: 2025-07-29
Started: 2022-01-23

Readme and manuals

Help Manual

Help pageTopics
Calculate AIC (Akaike's 'An Information Criterion')AIC_from_data
Bar plots dosimetrybar_plots
Calculate ZScorecalc.zValue.new
Aberration calculation functionscalculate_aberr calculate_aberr_disp_index calculate_aberr_mean calculate_aberr_power calculate_aberr_u_value calculate_aberr_var init_aberr_table
Calculate IRR (this is the same as the Odds-Ratio calculation in IAEA2011)calculate_aberr_IRR
Calculate aberrations tablecalculate_aberr_table
Characteristic limits function----------------calculate_characteristic_limits
Calculate genomic conversion factorcalculate_genome_factor
Calculate model statisticscalculate_model_stats
Calculate the characteristic limits tablecalculate_table
Calculate manual translocation ratecalculate_trans_rate_manual
Calculate Sigurdson's translocation ratecalculate_trans_rate_sigurdson
Calculate yield from dosecalculate_yield
Calculate theoretical yield infimumcalculate_yield_infimum
Correct boundary of irradiated fractions to be bounded by 0 and 1correct_boundary
Correct yield confidence intervalcorrect_conf_int
Correct negative valuescorrect_negative_vals
Correct yields if they are below the curvecorrect_yield
Plot curvescurves_plot
Dispersion indexDI_plot
DNA Content Fractions of Human Chromosomes (IHGSC)dna_content_fractions_ihgsc
DNA Content Fractions of Human Chromosomes (Morton 1991)dna_content_fractions_morton
Boxplot dose estimatesdose_boxplot
Prepare data to dose estimate using mixed fields manualdose_estimation_mx
Heterogeneous dose estimation (Mixed Poisson model)estimate_hetero_mixed_poisson
Partial-body dose estimation (Dolphin's method)estimate_partial_body_dolphin
Whole-body dose estimation (delta method)estimate_whole_body_delta
Whole-body dose estimation (Merkle's method)estimate_whole_body_merkle
Perform dose-effect fitting algorithmfit
Perform GLM (Generalised Linear Model) fittingfit_glm_method
Perform max-likelihood optimization fittingfit_maxlik_method
Calculate curvefun.curve
Calculate absorbed dose for mixed fields exposurefun.estimate.criticality
Plot at the UI and savegenerate_plot_and_download
Get standard errors using delta methodget_deltamethod_std_err
Include Markdown helpinclude_help
Load manual dataload_manual_data
Load and show rds filesload_rds_data
Load RMarkdown reportload_rmd_report
Calculate algBM_estimate
Plot Deviaition from ref dose all blind samplesplot_deviation_all
Plot dose estimation curveplot_estimated_dose_curve
Criticality Plotplot_estimated_dose_curve_mx
Plot fit dose curveplot_fit_dose_curve
Plot deviationplot_interlab_deviation
Plot zscore v2plot_interlab_v2
Plot triageplot_triage
Plot triage interlabplot_triage_interlab
Plot Z-scores all blind samplesplot_zscore_all
Prepare count data for max-likelihood optimization fittingprepare_maxlik_count_data
Project yield into dose-effect fitting curveproject_yield
Calculate protracted function G(x)protracted_g_function
Calculate QHampelQHampel
Calculate R regression confidence factorR_factor
Run the Shiny Applicationrun_app
Summary and curve tablessummary_curve_tables
U-testu_test_plot
Update dose estimation box with yield valuesupdate_outputs
Boxplot yieldyield_boxplot
Calculate yield erroryield_error_fun
Calculate yieldyield_fun