GeoTox S3 object

An S3 object that can be used to help organize the data and results of a GeoTox analysis.

Usage

GeoTox()

# S3 method for class 'GeoTox'
plot(x, type = c("resp", "hill", "exposure", "sensitivity"), ...)

Arguments

x

GeoTox object.

type

type of plot.

...

arguments passed to subsequent methods.

Value

a GeoTox S3 object

See also

plot_resp, plot_hill, plot_exposure, plot_sensitivity

Examples

# See the vignette for a full example:
#   vignette("introduction", package = "geotox")

if (FALSE) { # \dontrun{
# Use a subset of the package data for demonstration purposes
set.seed(2357)
n <- 10 # Population size
m <- 2 # Number of regions
idx <- if (m < 100) sample(1:100, m) else 1:100

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$age, ~FIPS)[idx],
                      obesity       = geo_tox_data$obesity[idx, ],
                      exposure      = split(geo_tox_data$exposure, ~FIPS)[idx],
                      simulated_css = geo_tox_data$simulated_css,
                      n             = n) |>
  # Estimated Hill parameters
  set_hill_params(geo_tox_data$dose_response |>
                    fit_hill(assay = "endp", chem = "casn") |>
                    dplyr::filter(!tp.sd.imputed, !logAC50.sd.imputed)) |>
  # Calculate response
  calculate_response() |>
  # Perform sensitivity analysis
  sensitivity_analysis()

# Print GeoTox object
geoTox

# Plot hill fits
plot(geoTox, type = "hill")
# Plot exposure data
plot(geoTox, type = "exposure", ncol = 5)
# Plot response data
plot(geoTox, assays = "TOX21_H2AX_HTRF_CHO_Agonist_ratio")
# Plot sensitivity data
plot(geoTox,
     type = "sensitivity",
     assay = "TOX21_H2AX_HTRF_CHO_Agonist_ratio")
} # }