'shiny' Application for Biological Dosimetry
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Documentation for package ‘biodosetools’ version 3.7.1
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 |