Calculate concentrations and risks

Calculate internal dose, in vitro concentration, and risk estimates.

Usage

calc_response(GT, overwrite = FALSE, ...)

Arguments

GT

GeoTox object.

overwrite

Logical indicating whether to overwrite existing values (default FALSE).

...

Additional arguments passed to calc_risk().

Value

The same GeoTox object, invisibly.

Details

This is a wrapper around several other functions:

• calc_internal_dose() to calculate internal dose (D_int).

• calc_invitro_concentration() to calculate in vitro concentration (C_invitro).

• calc_risk() to calculate risk estimates.

If a risk_name argument is provided to ... and it is not "risk", then sensitivity analysis is assumed and the sensitivity argument in the internal dose and in vitro concentration calculations is set to TRUE.

See also

calc_internal_dose(), calc_invitro_concentration(), calc_risk()

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)

# Calculate concentrations and risk
GT <- GT |> calc_response()

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

# Look at relevant table

dplyr::tbl(con, "concentration") |> dplyr::collect()
#> # A tibble: 6 × 8
#>      id sample_id substance_id route_id C_ext  C_ss D_int C_invitro
#>   <dbl>     <int>        <int>    <int> <dbl> <dbl> <dbl>     <dbl>
#> 1     1         1            1        1 10.5     21  2.59      54.4
#> 2     2         1            2        1 19.7     11  4.88      53.7
#> 3     3         2            1        1  8.67    61  2.23     136. 
#> 4     4         2            2        1 20.7     31  5.32     165. 
#> 5     5         3            1        1 28.6     22  6.98     154. 
#> 6     6         3            2        1 39.5     12  9.65     116. 

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    65.7   71.9      116.     116.
#> 2        1         2    67.5   70.5      311.     311.
#> 3        1         3    67.2   72.8      218.     218.

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