Create or add to the 'exposure_rate_params' table in a GeoTox database.
Arguments
- GT
GeoTox object.
- route
Exposure route (default "inhalation").
- params
Data frame with exposure rate parameters. If
NULL, default parameters for the specifiedroutewill be used (defaultNULL).- overwrite
Logical indicating whether to overwrite existing exposure rate parameters for the specified
route(defaultFALSE).
Details
There are two routes with built-in default exposure rate parameters:
"inhalation" and "drinking". If params is not provided (NULL), the
default parameters for the specified route will be used. If params is
provided, it must contain columns "age_lb", "age_ub", "mean", and "sd". The
exposure rate parameters are used by simulate_exposure_rate() to generate
exposure rate samples for each individual in the population.
The build-in parameters come from the following sources:
Inhalation: EPA Exposure Factors Handbook (2015), Table 6.7 in m\(^3\)/kg-day. The "mean" and "sd" values are the average of male and female values.
Drinking: EPA Exposure Factors Handbook (2019), Table 3-30 in mL/kg-day.
Examples
# Add both default params to GeoTox database
GT <- GeoTox() |>
add_exposure_rate_params() |>
add_exposure_rate_params(route = "drinking")
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmplZTgWH/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmplZTgWH/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmplZTgWH/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
# Open a connection to GeoTox database
con <- get_con(GT)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmplZTgWH/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
# Look at relevant tables
params_tbl <- dplyr::tbl(con, "exposure_rate_params") |> dplyr::collect()
params_tbl |> dplyr::filter(route_id == 1)
#> # A tibble: 10 × 6
#> id route_id age_lb age_ub mean sd
#> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 1 1 0 1 0.488 0.0775
#> 2 2 1 1 2 0.465 0.07
#> 3 3 1 2 5 0.44 0.055
#> 4 4 1 5 7 0.41 0.05
#> 5 5 1 7 11 0.36 0.06
#> 6 6 1 11 23 0.285 0.05
#> 7 7 1 23 30 0.24 0.04
#> 8 8 1 30 40 0.24 0.035
#> 9 9 1 40 65 0.22 0.04
#> 10 10 1 65 150 0.18 0.035
params_tbl |> dplyr::filter(route_id == 2)
#> # A tibble: 10 × 6
#> id route_id age_lb age_ub mean sd
#> <int> <int> <dbl> <dbl> <dbl> <dbl>
#> 1 11 2 0 1 43.5 42.5
#> 2 12 2 1 4 46.8 28.1
#> 3 13 2 4 7 37.9 21.8
#> 4 14 2 7 11 26.9 15.3
#> 5 15 2 11 15 20.2 11.6
#> 6 16 2 15 20 16.4 9.6
#> 7 17 2 20 45 18.6 10.7
#> 8 18 2 45 65 22 10.8
#> 9 19 2 65 75 21.9 9.9
#> 10 20 2 75 150 21.6 9.5
dplyr::tbl(con, "route") |> dplyr::collect()
#> # A tibble: 2 × 2
#> id route
#> <int> <chr>
#> 1 1 inhalation
#> 2 2 drinking
# Add custom params with new column (gender), assign to route "custom"
params_df <- tibble::tribble(
~age_lb, ~age_ub, ~gender, ~mean, ~sd,
0, 49, "male", 10, 1,
50, 99, "male", 20, 1,
0, 49, "female", 30, 1,
50, 99, "female", 40, 1
)
GT |> add_exposure_rate_params(params_df, route = "custom")
# Look at updated tables
params_tbl <- dplyr::tbl(con, "exposure_rate_params") |> dplyr::collect()
params_tbl |> dplyr::filter(route_id == 1)
#> # A tibble: 10 × 7
#> id route_id age_lb age_ub mean sd gender
#> <int> <int> <dbl> <dbl> <dbl> <dbl> <chr>
#> 1 1 1 0 1 0.488 0.0775 NA
#> 2 2 1 1 2 0.465 0.07 NA
#> 3 3 1 2 5 0.44 0.055 NA
#> 4 4 1 5 7 0.41 0.05 NA
#> 5 5 1 7 11 0.36 0.06 NA
#> 6 6 1 11 23 0.285 0.05 NA
#> 7 7 1 23 30 0.24 0.04 NA
#> 8 8 1 30 40 0.24 0.035 NA
#> 9 9 1 40 65 0.22 0.04 NA
#> 10 10 1 65 150 0.18 0.035 NA
params_tbl |> dplyr::filter(route_id == 2)
#> # A tibble: 10 × 7
#> id route_id age_lb age_ub mean sd gender
#> <int> <int> <dbl> <dbl> <dbl> <dbl> <chr>
#> 1 11 2 0 1 43.5 42.5 NA
#> 2 12 2 1 4 46.8 28.1 NA
#> 3 13 2 4 7 37.9 21.8 NA
#> 4 14 2 7 11 26.9 15.3 NA
#> 5 15 2 11 15 20.2 11.6 NA
#> 6 16 2 15 20 16.4 9.6 NA
#> 7 17 2 20 45 18.6 10.7 NA
#> 8 18 2 45 65 22 10.8 NA
#> 9 19 2 65 75 21.9 9.9 NA
#> 10 20 2 75 150 21.6 9.5 NA
params_tbl |> dplyr::filter(route_id == 3)
#> # A tibble: 4 × 7
#> id route_id age_lb age_ub mean sd gender
#> <int> <int> <dbl> <dbl> <dbl> <dbl> <chr>
#> 1 21 3 0 49 10 1 male
#> 2 22 3 50 99 20 1 male
#> 3 23 3 0 49 30 1 female
#> 4 24 3 50 99 40 1 female
dplyr::tbl(con, "route") |> dplyr::collect()
#> # A tibble: 3 × 2
#> id route
#> <int> <chr>
#> 1 1 inhalation
#> 2 2 drinking
#> 3 3 custom
# Clean up example
DBI::dbDisconnect(con)
file.remove(GT$db_info$dbdir)
#> [1] TRUE