Package index • GeoTox

GeoTox

Initialize a GeoTox object.

GeoTox() get_con(): GeoTox S3 object

Wrapper functions

Call a single function for each major step of the workflow. Ordered by workflow sequence.

simulate_population(): Simulate population characteristics and exposures
calc_response(): Calculate concentrations and risks
sensitivity_analysis(): Perform sensitivity analysis

Simulate population

Generate population characteristics and exposures using Monte Carlo simulation.

add_age(): Add age simulation data
add_exposure(): Add exposure simulation data
add_exposure_rate_params(): Add exposure rate simulation data
add_obesity(): Add obesity simulation data
simulate_age(): Simulate age values
simulate_exposure(): Simulate exposure concentrations
simulate_exposure_rate(): Simulate exposure rates
simulate_obesity(): Simulate obesity values

Pre-simulated C_ss

Set and sample from pre-simulated steady-state plasma concentrations C_ss.

sample_simulated_css(): Sample from pre-simulated steady-state plasma concentrations
set_fixed_css(): Prepare steady-state plasma concentrations for sensitivity analysis
set_simulated_css(): Set pre-simulated steady-state plasma concentrations

Set ‘sample’ table

Set population characteristics directly instead of simulating them.

set_sample(): Set sample data

Calculate response

Calculate risk scores using population characteristics, exposures, and concentration-response data.

calc_internal_dose(): Calculate internal dose
calc_invitro_concentration(): Calculate in vitro concentration
calc_risk(): Calculate risk scores

Sensitivity analysis

calc_sensitivity(): Calculate risk sensitivity to a single variable

Hill model

add_hill_params(): Add Hill model parameters
fit_hill(): Fit 2- or 3-parameter Hill model

Boundary information

set_boundary() get_boundary(): Store and retrieve boundary geometries

Utility

Extract information from a GeoTox object.

get_assay_table() get_risk_quantiles() get_risk_sensitivity() get_risk_values(): Get risk metric results
get_concentration_mean(): Get concentration mean values

Datasets

geo_tox_data: GeoTox Data