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Calculate risk scores

Source: R/calc_risk.R
calc_risk.Rd

Calculate generalized concentration addition (GCA) and independent action (IA) risk scores and hazard quotients (HQ) based on in vitro concentration data and Hill parameters.

Usage

calc_risk(
  GT,
  max_mult = 1.5,
  fixed = FALSE,
  overwrite = FALSE,
  risk_name = "risk"
)

Arguments

GT

GeoTox object.

max_mult

Upper bound multiplier for max response (default 1.5).

fixed

Logical indicating whether to set standard deviation parameters of Hill fit to zero (default FALSE). Used in sensitivity analysis.

overwrite

Logical indicating whether to overwrite existing risk table (default FALSE).

risk_name

Table name to store risk results (default "risk"). Values other than "risk" are used in sensitivity analysis.

Value

The same GeoTox object, invisibly.

Details

This function requires that the 'concentration', 'sample', and 'hill_params' tables are present in the GeoTox object. Typically these tables will have been created by prior calls to calc_invitro_concentration() and add_hill_params().

The risk scores are calculated for each sample and assay combination and stored in the 'risk' table in the GeoTox object, unless a different risk_name is provided. Supplying a different risk_name shouldn't be done directly by the user, but rather by calling calc_sensitivity().

See also

add_hill_params(), calc_invitro_concentration(), calc_response()

Examples

# Setup required tables
sample_df <- tibble::tribble(
  ~FIPS, ~age, ~weight,
  10000, 25, "Normal",
  10000, 35,  "Obese",
  20000, 50, "Normal"
)
exposure_df <- tibble::tribble(
  ~FIPS, ~casn, ~route, ~mean, ~sd,
  10000, "00-00-1", "inhalation", 10, 1,
  10000, "00-00-2", "inhalation", 20, 1,
  20000, "00-00-1", "inhalation", 30, 1,
  20000, "00-00-2", "inhalation", 40, 1
)
css_df <- tibble::tribble(
  ~casn, ~age_lb, ~age_ub, ~weight, ~css,
  "00-00-1",  0, 49, "Normal", 21,
  "00-00-1", 50, 99, "Normal", 22,
  "00-00-1",  0, 49,  "Obese", 61,
  "00-00-1", 50, 99,  "Obese", 62,
  "00-00-2",  0, 49, "Normal", 11,
  "00-00-2", 50, 99, "Normal", 12,
  "00-00-2",  0, 49,  "Obese", 31,
  "00-00-2", 50, 99,  "Obese", 32
)
hill_df <- tibble::tribble(
  ~assay, ~casn, ~logc, ~resp,
  "a1", "00-00-1",    0,  10,
  "a1", "00-00-1",    1,  20,
  "a1", "00-00-1",    2,  80,
  "a1", "00-00-1",    3, 100,
  "a1", "00-00-2", -0.5,   5,
  "a1", "00-00-2",  0.5,  20,
  "a1", "00-00-2",  1.5,  55,
  "a1", "00-00-2",  2.5,  60
)
GT <- GeoTox() |>
  set_sample(sample_df) |>
  set_simulated_css(css_df) |>
  add_exposure_rate_params() |>
  add_hill_params(fit_hill(hill_df, assay = "assay", substance = "casn")) |>
  simulate_population(exposure = exposure_df) |>
  calc_internal_dose() |>
  calc_invitro_concentration()

# Calculate risk
GT <- GT |> calc_risk()

# Open a connection to GeoTox database
con <- get_con(GT)

# Look at relevant table
dplyr::tbl(con, "risk") |> dplyr::collect()
#> # A tibble: 3 × 6
#>   assay_id sample_id GCA.Eff IA.Eff GCA.HQ.10 IA.HQ.10
#>      <int>     <int>   <dbl>  <dbl>     <dbl>    <dbl>
#> 1        1         1    63.5   68.9      90.7     90.7
#> 2        1         2    64.2   67.9     209.     209. 
#> 3        1         3    68.9   75.9     215.     215. 

# Clean up example
DBI::dbDisconnect(con)
file.remove(GT$db_info$dbdir)
#> [1] TRUE