calc_risk: Calculate risk scores

In GeoTox: Spatiotemporal Mixture Risk Assessment

Calculate risk scores

Description

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.

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().

Value

The same GeoTox object, invisibly.

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()

# Clean up example
DBI::dbDisconnect(con)
file.remove(GT$db_info$dbdir)

GeoTox documentation built on May 20, 2026, 1:07 a.m.