# 'shiny' Application for Biological Dosimetry

## Documentation for package ‘biodosetools’ version 3.7.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

AIC_from_data | Calculate AIC (Akaike's 'An Information Criterion')
bar_plots | Bar plots dosimetry
calc.zValue.new | Calculate ZScore
calculate_aberr | Aberration calculation functions
calculate_aberr_disp_index | Aberration calculation functions
calculate_aberr_IRR | Calculate IRR (this is the same as the Odds-Ratio calculation in IAEA2011)
calculate_aberr_mean | Aberration calculation functions
calculate_aberr_power | Aberration calculation functions
calculate_aberr_table | Calculate aberrations table
calculate_aberr_u_value | Aberration calculation functions
calculate_aberr_var | Aberration calculation functions
calculate_characteristic_limits | Characteristic limits function---
calculate_genome_factor | Calculate genomic conversion factor
calculate_model_stats | Calculate model statistics
calculate_table | Calculate the characteristic limits table
calculate_trans_rate_manual | Calculate manual translocation rate
calculate_trans_rate_sigurdson | Calculate Sigurdson's translocation rate
calculate_yield | Calculate yield from dose
calculate_yield_infimum | Calculate theoretical yield infimum
correct_boundary | Correct boundary of irradiated fractions to be bounded by 0 and 1
correct_conf_int | Correct yield confidence interval
correct_negative_vals | Correct negative values
correct_yield | Correct yields if they are below the curve
curves_plot | Plot curves
DI_plot | Dispersion index
dna_content_fractions_ihgsc | DNA Content Fractions of Human Chromosomes (IHGSC)
dna_content_fractions_morton | DNA Content Fractions of Human Chromosomes (Morton 1991)
dose_boxplot | Boxplot dose estimates
dose_estimation_mx | Prepare data to dose estimate using mixed fields manual
estimate_hetero_mixed_poisson | Heterogeneous dose estimation (Mixed Poisson model)
estimate_partial_body_dolphin | Partial-body dose estimation (Dolphin's method)
estimate_whole_body_delta | Whole-body dose estimation (delta method)
estimate_whole_body_merkle | Whole-body dose estimation (Merkle's method)
fit | Perform dose-effect fitting algorithm
fit_glm_method | Perform GLM (Generalised Linear Model) fitting
fit_maxlik_method | Perform max-likelihood optimization fitting
fun.curve | Calculate curve
fun.estimate.criticality | Calculate absorbed dose for mixed fields exposure
generate_plot_and_download | Plot at the UI and save
get_deltamethod_std_err | Get standard errors using delta method
include_help | Include Markdown help
init_aberr_table | Aberration calculation functions
load_manual_data | Load manual data
load_rds_data | Load and show rds files
load_rmd_report | Load RMarkdown report
M_estimate | Calculate algB
plot_deviation_all | Plot Deviaition from ref dose all blind samples
plot_estimated_dose_curve | Plot dose estimation curve
plot_estimated_dose_curve_mx | Criticality Plot
plot_fit_dose_curve | Plot fit dose curve
plot_interlab_deviation | Plot deviation
plot_interlab_v2 | Plot zscore v2
plot_triage | Plot triage
plot_triage_interlab | Plot triage interlab
plot_zscore_all | Plot Z-scores all blind samples
prepare_maxlik_count_data | Prepare count data for max-likelihood optimization fitting
project_yield | Project yield into dose-effect fitting curve
protracted_g_function | Calculate protracted function G(x)
QHampel | Calculate QHampel
run_app | Run the Shiny Application
R_factor | Calculate R regression confidence factor
summary_curve_tables | Summary and curve tables
update_outputs | Update dose estimation box with yield values
u_test_plot | U-test
yield_boxplot | Boxplot yield
yield_error_fun | Calculate yield error
yield_fun | Calculate yield