CTS_add_rule {ruminate}R Documentation

Add Rule to Element

Description

Takes the ui elements in the state and element and attempts to add a rule.

Usage

CTS_add_rule(state, element)

Arguments

state

CTS state from CTS_fetch_state()

element

Element list from CTS_fetch_current_element()

Details

This depends on the following UI values in the state and element

Value

Element with the results of adding the rule. The rares list element can be used to determine the exit status of the function.

Examples

# For more information see the Clinical Trial Simulation vignette:
# https://ruminate.ubiquity.tools/articles/clinical_trial_simulation.html
# None of this will work if rxode2 isn't installed:

library(formods)
if( Sys.getenv("ruminate_rxfamily_found") == "TRUE"){

# This will populate the session variable with the model building (MB) module
sess_res = MB_test_mksession()
session = sess_res[["session"]]

id     = "CTS"
id_ASM = "ASM"
id_MB  = "MB"
input  = list()

# Configuration files
FM_yaml_file  = system.file(package = "formods", "templates", "formods.yaml")
MOD_yaml_file = system.file(package = "ruminate", "templates", "CTS.yaml")

state = CTS_fetch_state(id              = id,
                        id_ASM          = id_ASM,
                        id_MB           = id_MB,
                        input           = input,
                        session         = session,
                        FM_yaml_file    = FM_yaml_file,
                        MOD_yaml_file   = MOD_yaml_file,
                        react_state     = NULL)


# Fetch a list of the current element
current_ele = CTS_fetch_current_element(state)

# You can modify the element
current_ele[["element_name"]] = "A more descriptive name"

# Defining the source model
state[["CTS"]][["ui"]][["source_model"]] = "MB_obj_1_rx"
current_ele = CTS_change_source_model(state, current_ele)

# Single visit
current_ele[["ui"]][["visit_times"]]                 = "0"
current_ele[["ui"]][["cts_config_nsteps"]]           = "5"

# Creating a dosing rule
state[["CTS"]][["ui"]][["rule_condition"]]           = "time == 0"
state[["CTS"]][["ui"]][["rule_type"]]                = "dose"
state[["CTS"]][["ui"]][["action_dosing_state"]]      = "central"
state[["CTS"]][["ui"]][["action_dosing_values"]]     = "c(1)"
state[["CTS"]][["ui"]][["action_dosing_times"]]      = "c(0)"
state[["CTS"]][["ui"]][["action_dosing_durations"]]  = "c(0)"
state[["CTS"]][["ui"]][["rule_name"]]                = "Single_Dose"

# Adding the rule:
current_ele = CTS_add_rule(state, current_ele)

# Appending the plotting details as well
current_ele[["ui"]][["fpage"]]             = "1"
current_ele[["ui"]][["dvcols"]]            = "Cc"

# Reducing the number of subjects and steps to speed things up on CRAN
current_ele[["ui"]][["nsub"]]              = "2"
current_ele[["ui"]][["cts_config_nsteps"]] = "5"

# Putting the element back in the state forcing code generation
state = CTS_set_current_element(
  state   = state,
  element = current_ele)

# Now we pull out the current element, and simulate it
current_ele = CTS_fetch_current_element(state)
#current_ele = CTS_simulate_element(state, current_ele)

# Next we plot the element
current_ele = CTS_plot_element(state, current_ele)

# Now we save those results back into the state:
state = CTS_set_current_element(
  state   = state,
  element = current_ele)

# This will extract the code for the current module
code = CTS_fetch_code(state)
code

# This will update the checksum of the module state
state = CTS_update_checksum(state)


# Access the datasets generated from simulations
ds = CTS_fetch_ds(state)

# CTS_add_covariate
state[["CTS"]][["ui"]][["covariate_value"]]            = "70, .1"
state[["CTS"]][["ui"]][["covariate_type_selected"]]    = "cont_lognormal"
state[["CTS"]][["ui"]][["selected_covariate"]]         = "WT"
current_ele = CTS_add_covariate(state, current_ele)

# Creates a new empty element
state = CTS_new_element(state)

# Delete the current element
state = CTS_del_current_element(state)
}


[Package ruminate version 0.3.1 Index]