## ----include = FALSE----------------------------------------------------------
Sys.setenv(R_USER_LIBS = tempdir())  #Just in case for CRAN
library(biodosetools)
knitr::opts_chunk$set(
  fig.dpi = 96,
  collapse = TRUE,
  comment = "#>"
)

## ----sc-dic-estimate-01, echo=FALSE, out.width='100%', fig.align='center', fig.cap="'Curve fitting data options' box and 'Results' tabbed box in the dose estimation module when loading curve from an `.rds` file."----
knitr::include_graphics("figures/screenshot-dicentrics-estimate-01.png")

## ----sc-dic-estimate-01b, echo=FALSE, out.width='100%', fig.cap="'Curve fitting data options' box and 'Results' tabbed box in the dose estimation module when inputting curve coefficients manually. Note that if no variance-covariance matrix is provided, only the variances calculated from the coefficients' standard errors will be used in calculations."----
knitr::include_graphics("figures/screenshot-dicentrics-estimate-01b.png")

## ----load-fitting-results, tidy=TRUE, tidy.opts=list(width.cutoff=60)---------
fit_results <- system.file("extdata", "dicentrics-fitting-results.rds", package = "biodosetools") %>%
  readRDS()

## ----fit-results--------------------------------------------------------------
fit_results$fit_coeffs

## ----sc-dic-estimate-02, echo=FALSE, out.width='100%', fig.align='center', fig.cap="'Data input options' and 'Data input' boxes in the dose estimation module."----
knitr::include_graphics("figures/screenshot-dicentrics-estimate-02.png")

## ----dic-case-data------------------------------------------------------------
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

## ----sc-dic-estimate-03, echo=FALSE, out.width='60%', fig.align='center', fig.cap="'Dose estimation options' box in the dose estimation module."----
knitr::include_graphics("figures/screenshot-dicentrics-estimate-03.png")

## ----sc-dic-estimate-04, echo=FALSE, out.width='100%', fig.align='center', fig.cap="'Results' tabbed box, 'Curve plot' and 'Save results' boxes in the dose estimation module."----
knitr::include_graphics("figures/screenshot-dicentrics-estimate-04.png")

## ----dic-parse-fit-results----------------------------------------------------
fit_coeffs <- fit_results[["fit_coeffs"]]
fit_var_cov_mat <- fit_results[["fit_var_cov_mat"]]

## ----dic-dose-estimation-whole------------------------------------------------
results_whole_merkle <- estimate_whole_body_merkle(
  num_cases = 2,
  case_data,
  fit_coeffs,
  fit_var_cov_mat,
  conf_int_yield = 0.95,
  conf_int_curve = 0.95,
  protracted_g_value = 1,
  aberr_module = "dicentrics"
)
#Parse results for multiple cases
est_doses_whole <- list()
for (i in seq_along(results_whole_merkle)) {
      est_doses_whole[[i]] <- results_whole_merkle[[i]][["est_doses"]]
          }

    est_doses_whole <- do.call(rbind, est_doses_whole)
    est_doses_whole <- cbind(ID = case_data$ID, est_doses_whole)
    

## ----dic-dose-estimation-partial----------------------------------------------

results_partial <- estimate_partial_body_dolphin(
  num_cases = 2,
  case_data,
  fit_coeffs,
  fit_var_cov_mat,
  conf_int = 0.95,
  gamma = 1 / 2.7,
  aberr_module = "dicentrics"
)
#Parse results for multiple cases
est_doses_partial <- list()
for (i in seq_along(results_partial)) {
    est_doses_partial[[i]] <- results_partial[[i]][["est_doses"]]
 }
    est_doses_partial <- do.call(rbind, est_doses_partial)
    est_doses_partial <- cbind(ID = case_data$ID, est_doses_partial)


## ----dic-estimated-dose-curve-multiple, fig.width=6, fig.height=3.5, fig.align='center', fig.cap="Plot of estimated doses generated by \\{biodosetools\\}. The grey shading indicates the uncertainties associated with the calibration curve."----

plot_triage(
  num_cases = 2, 
  est_doses_whole, 
  est_doses_partial, 
  assessment = "partial",
  place = "UI"
  )