In biodosimetry-uab/biodosetools: An R Shiny Application for Biological Dosimetry

library(biodosetools)
knitr::opts_chunk$set(
  fig.dpi = 96,
  collapse = TRUE,
  comment = "#>"
)

Load pre-calculated curve

The first step is to either load the pre-calculated curve in .rds format obtained in the dose-effect fitting module or input the curve coefficients manually in case the user wants to use a pre-existing curve calculated outside of Biodose Tools. Clicking on "Preview data" will load the curve into the app and display it on the "Results" tabbed box.

knitr::include_graphics("figures/screenshot-dicentrics-estimate-01.png")

knitr::include_graphics("figures/screenshot-dicentrics-estimate-01b.png")

This step is accomplished in R by either using the results from fit() or by loading an existing .rds object via readRDS():

fit_results <- system.file("extdata", "dicentrics-fitting-results.rds", package = "biodosetools") %>%
  readRDS()

fit_results$fit_coeffs

Input case data

Next we can choose to either load the case data from a file (supported formats are .csv, .dat, and .txt) or to input the data manually. Once the table is generated and filled, the "Calculate parameters" button will calculate the total number of cells ($N$), total number of aberrations ($X$), as well as mean ($\bar{y}$), standard error ($\sigma$), dispersion index ($\sigma^{2}/\bar{y}$), and $u$-value.

knitr::include_graphics("figures/screenshot-dicentrics-estimate-02.png")

This step is accomplished in R by calling the calculate_aberr_table() function:

case_data <- system.file("extdata", "cases-data-partial.csv", package = "biodosetools") %>%
  utils::read.csv(header = TRUE) %>%
  calculate_aberr_table(
    type = "case",
    assessment_u = 1,
    aberr_module = "dicentrics"
  )

case_data

Perform dose estimation

The final step is to select the dose estimation options. In the "Dose estimation options" box we can select type of exposure (acute, protracted, and highly protracted), type of assessment (whole-body, partial-body, or heterogeneous), and error methods for each type of assessment.

knitr::include_graphics("figures/screenshot-dicentrics-estimate-03.png")

knitr::include_graphics("figures/screenshot-dicentrics-estimate-04.png")

To perform the dose estimation in R we can call the adequate estimate_*() functions. In this example, we will use estimate_whole_body_merkle() and estimate_partial_body_dolphin(). First of all, however, we will need to load the fit coefficients and variance-covariance matrix:

fit_coeffs <- fit_results[["fit_coeffs"]]
fit_var_cov_mat <- fit_results[["fit_var_cov_mat"]]

After that is done, we can simply call estimate_whole_body_merkle() and estimate_partial_body_dolphin():

results_whole_merkle <- estimate_whole_body_merkle(
  case_data,
  fit_coeffs,
  fit_var_cov_mat,
  conf_int_yield = 0.83,
  conf_int_curve = 0.83,
  protracted_g_value = 1,
  aberr_module = "dicentrics"
)

results_partial <- estimate_partial_body_dolphin(
  case_data,
  fit_coeffs,
  fit_var_cov_mat,
  conf_int = 0.95,
  gamma = 1 / 2.7,
  aberr_module = "dicentrics"
)

To visualise the estimated doses, we call the plot_estimated_dose_curve() function:

r. The grey shading indicates the uncertainties associated with the calibration curve."} plot_estimated_dose_curve( est_doses = list( whole = results_whole_merkle, partial = results_partial ), fit_coeffs, fit_var_cov_mat, protracted_g_value = 1, conf_int_curve = 0.95, aberr_name = "Dicentrics" )

biodosimetry-uab/biodosetools documentation built on Jan. 26, 2024, 5:36 p.m.