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Set pre-simulated steady-state plasma concentrations

Source: R/set_simulated_css.R
set_simulated_css.Rd

Create the 'simulated_css' table in a GeoTox database, which contains pre-simulated steady-state plasma concentrations (C\(_{ss}\)).

Usage

set_simulated_css(GT, df, substance = "casn", overwrite = FALSE)

Arguments

GT

GeoTox object.

df

Data frame containing simulated C\(_{ss}\) values for groups of population characteristics.

substance

Column name(s) in df that contain substance identifier(s) (default "casn").

overwrite

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

Value

The same GeoTox object, invisibly.

Details

The 'simulated_css' table is used by sample_simulated_css() to assign C\(_{ss}\) values to individuals. The minimum required columns in the df data frame are "age_lb", "age_ub", "weight", "css", and at least one column with substance information (default "casn").

The values for "age_lb" and "age_ub" should be non-overlapping integers representing age ranges (in years). For example, two subsequent age groups might be c(0, 4) and c(5, 9). The "weight" column should contain the weight category and contain values of either "Normal" or "Obese". The "css" column should contain the pre-simulated C\(_{ss}\) values.

The substance input can be a named vector to specify multiple substance identifier columns in df. For example, c(casn = "casn", name = "chnm") would indicate that df contains both CAS numbers and chemical names for substances. The name = "chnm" part would rename the "chnm" column in df to "name" in the 'substance' table.

See also

sample_simulated_css()

Examples

# Example pre-simulated C_ss data
# Note: normally the css_df would have many more rows for each combination of
# the non-'css' columns to allow for sampling.
css_df <- tibble::tribble(
  ~casn, ~age_lb, ~age_ub, ~weight, ~css,
  "00-00-1",  0, 49, "Normal",  1,
  "00-00-1", 50, 99, "Normal",  2,
  "00-00-1",  0, 49,  "Obese", 11,
  "00-00-1", 50, 99,  "Obese", 12,
  "00-00-2",  0, 49, "Normal", 21,
  "00-00-2", 50, 99, "Normal", 22,
  "00-00-2",  0, 49,  "Obese", 31,
  "00-00-2", 50, 99,  "Obese", 32
)

# Set simulated C_ss values
GT <- GeoTox() |> set_simulated_css(css_df)

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

# Look at relevant tables

dplyr::tbl(con, "simulated_css") |> dplyr::collect()
#> # A tibble: 8 × 6
#>      id substance_id age_lb age_ub weight   css
#>   <int>        <int>  <dbl>  <dbl> <chr>  <dbl>
#> 1     1            1      0     49 Normal     1
#> 2     2            1     50     99 Normal     2
#> 3     3            1      0     49 Obese     11
#> 4     4            1     50     99 Obese     12
#> 5     5            2      0     49 Normal    21
#> 6     6            2     50     99 Normal    22
#> 7     7            2      0     49 Obese     31
#> 8     8            2     50     99 Obese     32

dplyr::tbl(con, "substance") |> dplyr::collect()
#> # A tibble: 2 × 2
#>      id casn   
#>   <int> <chr>  
#> 1     1 00-00-1
#> 2     2 00-00-2

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