Package: biodosetools 3.6.1.9000

Alfredo Hernández

biodosetools: An R 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/> and the paper by Hernández et al. (2023) <doi:10.1080/09553002.2023.2176564>.

Authors:Alfredo Hernández [aut, cre], David Endesfelder [aut], Pere Puig [aut]

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biodosetools.pdf |biodosetools.html✨
biodosetools/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

biological-datadosimetryshiny-app

5.90 score 5 stars 16 scripts 289 downloads 15 exports 98 dependencies

Last updated 10 months agofrom:f349f46a14. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 25 2024
R-4.5-winOKOct 25 2024
R-4.5-linuxOKOct 25 2024
R-4.4-winOKOct 25 2024
R-4.4-macOKOct 25 2024
R-4.3-winOKOct 25 2024
R-4.3-macOKOct 25 2024

Exports:%>%calculate_aberr_tablecalculate_characteristic_limitscalculate_genome_factorcalculate_trans_rate_manualcalculate_trans_rate_sigurdsonestimate_hetero_mixed_poissonestimate_partial_body_dolphinestimate_whole_body_deltaestimate_whole_body_merklefitplot_estimated_dose_curveplot_fit_dose_curveprotracted_g_functionrun_app

Dependencies:askpassattemptbase64encbslibbspluscachemclicolorspacecommonmarkconfigcpp11crayoncrosstalkcurldata.tabledigestdplyrevaluateexpmfansifarverfastmapfontawesomefsgenericsggplot2gluegolemgtableherehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmaxLikmemoisemgcvmimemiscToolsmixtoolsmsmmunsellmvtnormnlmeopensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprhandsontablerlangrmarkdownrprojrootsandwichsassscalessegmentedshinyshinydashboardshinyWidgetssourcetoolsstringistringrsurvivalsystibbletidyrtidyselecttimechangetinytexutf8vctrsviridisLitewithrxfunxtableyamlzoo

Dicentrics dose estimation

Rendered fromdicent-estimation.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2022-11-11
Started: 2022-01-23

Dicentrics dose-effect fitting

Rendered fromdicent-fitting.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2022-05-11
Started: 2022-01-23

Translocations dose estimation

Rendered fromtrans-estimation.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2022-11-11
Started: 2022-01-23

Translocations dose-effect fitting

Rendered fromtrans-fitting.Rmdusingknitr::rmarkdownon Oct 25 2024.

Last update: 2022-05-11
Started: 2022-01-23

Readme and manuals

Help Manual

Help pageTopics
Calculate AIC (Akaike's 'An Information Criterion')AIC_from_data
'biodosetools' packagebiodosetools-package biodosetools
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 aberrations tablecalculate_aberr_table
Calculate characteristic limitscalculate_characteristic_limits
Calculate genomic conversion factorcalculate_genome_factor
Calculate model statisticscalculate_model_stats
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
DNA Content Fractions of Human Chromosomes (IHGSC)dna_content_fractions_ihgsc
DNA Content Fractions of Human Chromosomes (Morton 1991)dna_content_fractions_morton
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
Get standard errors using delta methodget_deltamethod_std_err
Include Markdown helpinclude_help
Load RMarkdown reportload_rmd_report
Plot dose estimation curveplot_estimated_dose_curve
Plot fit dose curveplot_fit_dose_curve
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 R regression confidence factorR_factor
Run the Shiny Applicationrun_app
Calculate yield erroryield_error_fun
Calculate yieldyield_fun