Partial-body dose estimation (Dolphin's method)

Method based on the paper by Dolphin, G. W. (1969). Biological Dosimetry with Particular Reference to Chromosome Aberration Analysis: A Review of Methods. International Atomic Energy Agency (IAEA) Retrieved from https://inis.iaea.org/search/search.aspx?orig_q=RN:45029080.

Usage

estimate_partial_body_dolphin(
  num_cases,
  case_data,
  fit_coeffs,
  fit_var_cov_mat,
  conf_int = 0.95,
  protracted_g_value = 1,
  genome_factor = 1,
  gamma,
  aberr_module = c("dicentrics", "translocations", "micronuclei")
)

Arguments

num_cases

number of cases.

case_data

Case data in data frame form.

fit_coeffs

Fitting coefficients matrix.

fit_var_cov_mat

Fitting variance-covariance matrix.

conf_int

Confidence interval, 95% by default.

protracted_g_value

Protracted \(G(x)\) value.

genome_factor

Genomic conversion factor used in translocations, else 1.

gamma

Survival coefficient of irradiated cells.

aberr_module

Aberration module.

Value

List containing estimated doses data frame, observed fraction of cells scored which were irradiated, estimated fraction of irradiated blood data frame, AIC, and conf_int_* used.

Examples

#The fitting RDS result from the fitting module is needed. Alternatively, manual data
#frames that match the structure of the RDS can be used:
fit_coeffs <- data.frame(
    estimate   = c(0.001280319, 0.021038724, 0.063032534),
    std.error  = c(0.0004714055, 0.0051576170, 0.0040073856),
    statistic  = c(2.715961, 4.079156, 15.729091),
    p.value    = c(6.608367e-03, 4.519949e-05, 9.557291e-56),
    row.names =  c("coeff_C", "coeff_alpha", "coeff_beta")
  )


fit_var_cov_mat <- data.frame(
  coeff_C      = c(2.222231e-07, -9.949044e-07,  4.379944e-07),
  coeff_alpha  = c(-9.949044e-07, 2.660101e-05, -1.510494e-05),
  coeff_beta   = c(4.379944e-07, -1.510494e-05, 1.605914e-05),
  row.names =  c("coeff_C", "coeff_alpha", "coeff_beta")
)


case_data <- data.frame(
  ID= "example1",
  N = 361,
  X = 100,
  C0 = 302,
  C1 = 28,
  C2 = 22,
  C3 = 8,
  C4 = 1,
  C5 = 0,
  y = 0.277,
  y_err = 0.0368,
  DI = 1.77,
  u = 10.4
)

#FUNCTION ESTIMATE_PARTIAL_BODY_DOLPHIN
estimate_partial_body_dolphin(
  num_cases = 1,
  case_data = case_data,
  fit_coeffs = as.matrix(fit_coeffs),
  fit_var_cov_mat = as.matrix(fit_var_cov_mat),
  conf_int = 0.95,
  gamma = 1 / 2.7,
  aberr_module = "dicentrics"
)
#> [[1]]
#> [[1]]$est_doses
#>      lower estimate    upper
#> 1 3.493143 4.137905 4.782667
#> 
#> [[1]]$est_yield
#>       lower estimate    upper
#> 1 0.8347555  1.16761 1.500465
#> 
#> [[1]]$est_frac
#>       lower  estimate     upper
#> 1 0.5137142 0.5901794 0.6666446
#> 
#> [[1]]$est_metaphases_frac
#>   pi_estimate pi_std_err
#> 1   0.2372438 0.03360268
#> 
#> [[1]]$AIC
#> [1] 8.132597
#> 
#> [[1]]$conf_int
#> [1] 0.95
#> 
#>