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GeoTox Introduction

introduction.Rmd

This vignette covers basic use of package functions. Package data, geo_tox_data, is used throughout the examples and details on how it was created can be found in the “GeoTox Package Data” vignette.

library(GeoTox)
library(dplyr)

n <- 250 # Sample size

NOTE: The sample size here is the size of the simulated population in each region. This is different than the sample size in the “package_data” vignette, which is used to generate C_ss values for each chemical at specified age and weight combinations.

Analysis of single assay

Create GeoTox object, run simulations and computations

set.seed(2357)
geoTox <- GeoTox() |> 
  # Set region and group boundaries (for plotting)
  set_boundaries(region = geo_tox_data$boundaries$county,
                 group  = geo_tox_data$boundaries$state) |> 
  # Simulate populations for each region
  simulate_population(age           = split(geo_tox_data$age, ~FIPS),
                      obesity       = geo_tox_data$obesity,
                      exposure      = split(geo_tox_data$exposure, ~FIPS),
                      simulated_css = geo_tox_data$simulated_css,
                      n             = n) |> 
  # Estimated Hill parameters
  set_hill_params(geo_tox_data$dose_response |>
                    filter(endp == "TOX21_H2AX_HTRF_CHO_Agonist_ratio") |>
                    fit_hill(chem = "casn") |> 
                    filter(!tp.sd.imputed, !logAC50.sd.imputed)) |>
  # Calculate response
  calculate_response() |>
  # Perform sensitivity analysis
  sensitivity_analysis()

geoTox
#> GeoTox object
#> Assays: 1
#> Chemicals: 5
#> Regions: 100
#> Population: 250
#> Data Fields:
#>      Name            Class               Dim
#>       age    list(integer)       100 x (250)
#>        IR    list(numeric)       100 x (250)
#>   obesity  list(character)       100 x (250)
#>     C_ext     list(matrix)  100 x (250 x 21)
#>      C_ss     list(matrix)  100 x (250 x 21)
#> Computed Fields:
#>          Name             Class               Dim
#>         D_int      list(matrix)  100 x (250 x 21)
#>     C_invitro      list(matrix)  100 x (250 x 21)
#>          resp  list(data.frame)   100 x (250 x 5)
#>   sensitivity        list(list)         5 x (100)
#> Other Fields: par, boundaries, exposure, css_sensitivity, hill_params

Plot outputs

plot(geoTox)

plot(geoTox, type = "hill")

plot(geoTox, type = "sensitivity")
#> Picking joint bandwidth of 0.139

Analysis of multiple assay

Create GeoTox object, run simulations and computations

set.seed(2357)
geoTox <- GeoTox() |> 
  # Set region and group boundaries (for plotting)
  set_boundaries(region = geo_tox_data$boundaries$county,
                 group  = geo_tox_data$boundaries$state) |> 
  # Simulate populations for each region
  simulate_population(age           = split(geo_tox_data$age, ~FIPS),
                      obesity       = geo_tox_data$obesity,
                      exposure      = split(geo_tox_data$exposure, ~FIPS),
                      simulated_css = geo_tox_data$simulated_css,
                      n             = n) |> 
  # Estimated Hill parameters
  set_hill_params(geo_tox_data$dose_response |>
                    fit_hill(assay = "endp", chem = "casn") |> 
                    filter(!tp.sd.imputed, !logAC50.sd.imputed)) |>
  # Calculate response
  calculate_response() |>
  # Perform sensitivity analysis
  sensitivity_analysis()

geoTox
#> GeoTox object
#> Assays: 13
#> Chemicals: 20
#> Regions: 100
#> Population: 250
#> Data Fields:
#>      Name            Class               Dim
#>       age    list(integer)       100 x (250)
#>        IR    list(numeric)       100 x (250)
#>   obesity  list(character)       100 x (250)
#>     C_ext     list(matrix)  100 x (250 x 21)
#>      C_ss     list(matrix)  100 x (250 x 21)
#> Computed Fields:
#>          Name             Class               Dim
#>         D_int      list(matrix)  100 x (250 x 21)
#>     C_invitro      list(matrix)  100 x (250 x 21)
#>          resp  list(data.frame)  100 x (3250 x 6)
#>   sensitivity        list(list)         5 x (100)
#> Other Fields: par, boundaries, exposure, css_sensitivity, hill_params

Plot outputs

plot(geoTox)
#> Warning: Multiple assays found, using first assay 'APR_HepG2_p53Act_24h_up'

plot(geoTox, assays = "TOX21_H2AX_HTRF_CHO_Agonist_ratio")

plot(geoTox, type = "hill")

plot(geoTox, type = "sensitivity")
#> Warning: Multiple assays found, using first assay 'APR_HepG2_p53Act_24h_up'
#> Warning: Removed 93000 NA values
#> Picking joint bandwidth of 0.133

plot(geoTox, type = "sensitivity", assay = "TOX21_H2AX_HTRF_CHO_Agonist_ratio")
#> Picking joint bandwidth of 0.139

Exposure Map

The exposure map is the same for both single and multiple assay analyses. The map shows the distribution of chemical exposure across regions for all chemicals, not just those used in a particular analysis.

plot(geoTox, type = "exposure", ncol = 5)

If other facet labels are present they can be specified using the chem_label argument.

plot(geoTox, type = "exposure", chem_label = "chnm", ncol = 5)