simulate_exposure: Simulate exposure concentrations

In GeoTox: Spatiotemporal Mixture Risk Assessment

Simulate exposure concentrations

Description

Simulate external exposure (C_ext) values to be stored in the 'concentration' table of a GeoTox database.

Usage

simulate_exposure(
  GT,
  n = 1000,
  overwrite = FALSE,
  expos_mean = NULL,
  expos_sd = NULL,
  sensitivity = FALSE
)

Arguments

GT	GeoTox object.
n	Number of individuals to simulate per location (default 1000). Ignored if 'sample' table already exists.
overwrite	Logical indicating whether to overwrite existing 'C_ext' values in the 'concentration' table (default FALSE).
expos_mean	Column name of exposure concentration mean in the 'exposure' table (default "mean").
expos_sd	Column name of exposure concentration standard deviation in the 'exposure' table (default "sd").
sensitivity	Logical indicating whether to simulate exposures for sensitivity analysis (default FALSE).

Details

An 'external' table containing simulation data must already exist in the GeoTox database, which is added using add_exposure().

The inputs expos_mean and expos_sd will be assigned default values of "mean" and "sd", respectively, if not provided and not already set in the GeoTox object's parameters, GT$par. If not NULL, the provided values will also be saved to GT$par.

If sensitivity = TRUE, exposure concentrations will be simulated for sensitivity analysis. Typically this shouldn't be used directly by the user, but rather called by calc_sensitivity(). In this case, the function will use the 'concentration_sensitivity' table instead of the 'concentration' table, and will assume that the 'sample' table already exists.

Value

The updated GeoTox object, invisibly.

See Also

add_exposure(), simulate_population()

Examples

# Example exposure simulation data
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
)

# Simulate C_ext values
GT <- GeoTox() |>
  add_exposure(exposure_df) |>
  simulate_exposure(n = 3)

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

# Look at created tables

dplyr::tbl(con, "concentration") |> dplyr::collect()

dplyr::tbl(con, "sample") |> dplyr::collect()

dplyr::tbl(con, "location") |> dplyr::collect()

dplyr::tbl(con, "substance") |> dplyr::collect()

dplyr::tbl(con, "route") |> dplyr::collect()

# Replace 'exposure' table with different column names
names(exposure_df)[4:5] <- c("mu", "sigma")
DBI::dbRemoveTable(con, "exposure")
GT |> add_exposure(exposure_df)

# Overwrite 'C_ext' values in existing 'concentration' table
# Must specify new 'exposure' column names
# Notice how the column names are added to GT$par
str(GT$par)
GT <- GT |>
  simulate_exposure(expos_mean = "mu", expos_sd = "sigma", overwrite = TRUE)
str(GT$par)

# Look at updated 'concentration' table
dplyr::tbl(con, "concentration") |> 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.