dyngen (version 0.4.0)

generate_gold_standard: Simulate the gold standard

Description

generate_gold_standard() runs simulations in order to determine the gold standard of the simulations. gold_standard_default() is used to configure parameters pertaining this process.

Usage

generate_gold_standard(model)
gold_standard_default(tau = 30/3600, census_interval = 10/60)

Arguments

model

A dyngen intermediary model for which the kinetics of the feature network has been generated with generate_kinetics().

tau

The time step of the ODE algorithm used to generate the gold standard.

census_interval

A granularity parameter of the gold standard time steps. Should be larger than or equal to tau.

Value

A dyngen model.

Examples

# NOT RUN {
model <- 
  initialise_model(
    backbone = backbone_bifurcating(),
    gold_standard = gold_standard_default(tau = .01, census_interval = 1)
  )
  
# }
# NOT RUN {
model <- model %>%
  generate_tf_network() %>%
  generate_feature_network() %>%
  generate_kinetics() %>%
  generate_gold_standard()
  
plot_gold_simulations(model)
plot_gold_mappings(model)
plot_gold_expression(model)
  
model <- model %>%
  generate_cells() %>%
  generate_experiment

dataset <- wrap_dataset(model)
# }