WARDEN (version 0.99.1)

run_sim: Run the simulation

Description

Run the simulation

Usage

run_sim(
  arm_list = c("int", "noint"),
  sensitivity_inputs = NULL,
  common_all_inputs = NULL,
  common_pt_inputs = NULL,
  unique_pt_inputs = NULL,
  init_event_list = NULL,
  evt_react_list = evt_react_list,
  util_ongoing_list = NULL,
  util_instant_list = NULL,
  util_cycle_list = NULL,
  cost_ongoing_list = NULL,
  cost_instant_list = NULL,
  cost_cycle_list = NULL,
  other_ongoing_list = NULL,
  other_instant_list = NULL,
  npats = 500,
  n_sim = 1,
  psa_bool = NULL,
  sensitivity_bool = FALSE,
  sensitivity_names = NULL,
  n_sensitivity = 1,
  input_out = NULL,
  ipd = 1,
  timed_freq = NULL,
  debug = FALSE,
  accum_backwards = FALSE,
  continue_on_error = FALSE,
  seed = NULL
)

Value

A list of data frames with the simulation results

Arguments

arm_list

A vector of the names of the interventions evaluated in the simulation

sensitivity_inputs

A list of sensitivity inputs that do not change within a sensitivity in a similar fashion to common_all_inputs, etc

common_all_inputs

A list of inputs common across patients that do not change within a simulation

common_pt_inputs

A list of inputs that change across patients but are not affected by the intervention

unique_pt_inputs

A list of inputs that change across each intervention

init_event_list

A list of initial events and event times. If no initial events are given, a "Start" event at time 0 is created automatically

evt_react_list

A list of event reactions

util_ongoing_list

Vector of QALY named variables that are accrued at an ongoing basis (discounted using drq)

util_instant_list

Vector of QALY named variables that are accrued instantaneously at an event (discounted using drq)

util_cycle_list

Vector of QALY named variables that are accrued in cycles (discounted using drq)

cost_ongoing_list

Vector of cost named variables that are accrued at an ongoing basis (discounted using drc)

cost_instant_list

Vector of cost named variables that are accrued instantaneously at an event (discounted using drc)

cost_cycle_list

Vector of cost named variables that are accrued in cycles (discounted using drc)

other_ongoing_list

Vector of other named variables that are accrued at an ongoing basis (discounted using drq)

other_instant_list

Vector of other named variables that are accrued instantaneously at an event (discounted using drq)

npats

The number of patients to be simulated (it will simulate npats * length(arm_list))

n_sim

The number of simulations to run per sensitivity

psa_bool

A boolean to determine if PSA should be conducted. If n_sim > 1 and psa_bool = FALSE, the differences between simulations will be due to sampling

sensitivity_bool

A boolean to determine if Scenarios/DSA should be conducted.

sensitivity_names

A vector of scenario/DSA names that can be used to select the right sensitivity (e.g., c("Scenario_1", "Scenario_2")). The parameter "sens_name_used" is created from it which corresponds to the one being used for each iteration.

n_sensitivity

Number of sensitivity analysis (DSA or Scenarios) to run. It will be interacted with sensitivity_names argument if not null (n_sensitivityitivity = n_sensitivity * length(sensitivity_names)). For DSA, it should be as many parameters as there are. For scenario, it should be 1.

input_out

A vector of variables to be returned in the output data frame

ipd

Integer taking value 1 for full IPD data returned, and 2 IPD data but aggregating events (returning last value for numeric/character/factor variables. For other objects (e.g., matrices), the IPD will still be returned as the aggregation rule is not clear). Other values mean no IPD data returned (removes non-numerical or length>1 items)

timed_freq

If NULL, it does not produce any timed outputs. Otherwise should be a number (e.g., every 1 year)

debug

If TRUE, will generate a log file

accum_backwards

If TRUE, the ongoing accumulators will count backwards (i.e., the current value is applied until the previous update). If FALSE, the current value is applied between the current event and the next time it is updated.

continue_on_error

If TRUE, on error it will attempt to continue by skipping the current simulation

seed

Starting seed to be used for the whole analysis. If null, it's set to 1 by default.

Details

This function is slightly different from run_sim_parallel. run_sim_parallel only runs multiple-core at the simulation level. run_sim uses only-single core. run_sim can be more efficient if using only one simulation (e.g., deterministic), while run_sim_parallel will be more efficient if the number of simulations is >1 (e.g., PSA).

Event ties are processed in the order declared within the init_event_list argument (evts argument within the first sublist of that object). To do so, the program automatically adds a sequence from to 0 to the (number of events - 1) times 1e-10 to add to the event times when selecting the event with minimum time. This time has been selected as it's relatively small yet not so small as to be ignored by which.min (see .Machine for more details)

A list of protected objects that should not be used by the user as input names or in the global environment to avoid the risk of overwriting them is as follows: c("arm", "arm_list", "categories_for_export", "cur_evtlist", "curtime", "evt", "i", "prevtime", "sens", "simulation", "sens_name_used","list_env","uc_lists","npats","ipd").

The engine uses the L'Ecuyer-CMRG for the random number generator. Note that the random seeds are set to be unique in their category (i.e., at patient level, patient-arm level, etc.)

If no drc or `drq parameters are passed within any of the input lists, these are assigned value 0.03.

Ongoing items will look backward to the last time updated when performing the discounting and accumulation. This means that the user does not necessarily need to keep updating the value, but only add it when the value changes looking forward (e.g., o_q = utility at event 1, at event 2 utility does not change, but at event 3 it does, so we want to make sure to add o_q = utility at event 3 before updating utility. The program will automatically look back until event 1). Note that in previous versions of the package backward was the default, and now this has switched to forward.

It is important to note that the QALYs and Costs (ongoing or instant or per cycle) used should be of length 1. If they were of length > 1, the model would expand the data, so instead of having each event as a row, the event would have N rows (equal to the length of the costs/qalys to discount passed). This means more processing of the results data would be needed in order for it to provide the correct results.

If the cycle lists are used, then it is expected the user will declare as well the name of the variable pasted with cycle_l and cycle_starttime (e.g., c_default_cycle_l and c_default_cycle_starttime) to ensure the discounting can be computed using cycles, with cycle_l being the cycle length, and cycle_starttime being the starting time in which the variable started counting.

debug = TRUE will export a log file with the timestamp up the error in the main working directory.

continue_on_error will skip the current simulation (so it won't continue for the rest of patient-arms) if TRUE. Note that this will make the progress bar not correct, as a set of patients that were expected to be run is not.

Examples

library(magrittr)
common_all_inputs <-add_item(
util.sick = 0.8,
util.sicker = 0.5,
cost.sick = 3000,
cost.sicker = 7000,
cost.int = 1000,
coef_noint = log(0.2),
HR_int = 0.8,
drc = 0.035, #different values than what's assumed by default
drq = 0.035,
random_seed_sicker_i = sample.int(100000,5,replace = FALSE)
)

common_pt_inputs <- add_item(death= max(0.0000001,rnorm(n=1, mean=12, sd=3))) 

unique_pt_inputs <- add_item(fl.sick = 1,
                             q_default = util.sick,
                             c_default = cost.sick + if(arm=="int"){cost.int}else{0}) 
                             
init_event_list <- 
add_tte(arm=c("noint","int"), evts = c("sick","sicker","death") ,input={
  sick <- 0
  sicker <- draw_tte(1,dist="exp",
   coef1=coef_noint, beta_tx = ifelse(arm=="int",HR_int,1),
    seed = random_seed_sicker_i[i])
  
})   

evt_react_list <-
add_reactevt(name_evt = "sick",
             input = {}) %>%
  add_reactevt(name_evt = "sicker",
               input = {
                 modify_item(list(q_default = util.sicker,
                                  c_default = cost.sicker + if(arm=="int"){cost.int}else{0},
                                  fl.sick = 0)) 
               }) %>%
  add_reactevt(name_evt = "death",
               input = {
                 modify_item(list(q_default = 0,
                                  c_default = 0, 
                                  curtime = Inf)) 
               }) 
               
util_ongoing <- "q_default"
cost_ongoing <- "c_default"
                          

run_sim(arm_list=c("int","noint"),
common_all_inputs = common_all_inputs,
common_pt_inputs = common_pt_inputs,
unique_pt_inputs = unique_pt_inputs,
init_event_list = init_event_list,
evt_react_list = evt_react_list,
util_ongoing_list = util_ongoing,
cost_ongoing_list = cost_ongoing,
npats = 2,
n_sim = 1,
psa_bool = FALSE,
ipd = 1)