Run the simulation
run_sim.RdRun 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
)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)
#> Analysis number: 1
#> Simulation number: 1
#> Time to run simulation 1: 0.05s
#> Time to run analysis 1: 0.05s
#> Total time to run: 0.05s
#> [[1]]
#> [[1]][[1]]
#> [[1]][[1]]$sensitivity_name
#> [1] ""
#>
#> [[1]][[1]]$arm_list
#> [1] "int" "noint"
#>
#> [[1]][[1]]$total_lys
#> int noint
#> 9.046874 9.046874
#>
#> [[1]][[1]]$total_qalys
#> int noint
#> 6.207438 6.181151
#>
#> [[1]][[1]]$total_costs
#> int noint
#> 49921.64 41225.25
#>
#> [[1]][[1]]$total_lys_undisc
#> int noint
#> 10.89866 10.89866
#>
#> [[1]][[1]]$total_qalys_undisc
#> int noint
#> 7.501176 7.474146
#>
#> [[1]][[1]]$total_costs_undisc
#> int noint
#> 59831.36 49293.10
#>
#> [[1]][[1]]$c_default
#> int noint
#> 49921.64 41225.25
#>
#> [[1]][[1]]$c_default_undisc
#> int noint
#> 59831.36 49293.10
#>
#> [[1]][[1]]$q_default
#> int noint
#> 6.207438 6.181151
#>
#> [[1]][[1]]$q_default_undisc
#> int noint
#> 7.501176 7.474146
#>
#> [[1]][[1]]$merged_df
#> Index: <arm>
#> evtname evttime prevtime pat_id arm total_lys total_qalys
#> <char> <num> <num> <int> <char> <num> <num>
#> 1: sick 0.0000000 0.0000000 1 int 10.339480 8.271584
#> 2: death 12.7779512 0.0000000 1 int 10.339480 8.271584
#> 3: sick 0.0000000 0.0000000 2 int 7.754267 4.143293
#> 4: sicker 0.9010175 0.0000000 2 int 7.754267 4.143293
#> 5: death 9.0193725 0.9010175 2 int 7.754267 4.143293
#> 6: sick 0.0000000 0.0000000 1 noint 10.339480 8.271584
#> 7: death 12.7779512 0.0000000 1 noint 10.339480 8.271584
#> 8: sick 0.0000000 0.0000000 2 noint 7.754267 4.090719
#> 9: sicker 0.7208140 0.0000000 2 noint 7.754267 4.090719
#> 10: death 9.0193725 0.7208140 2 noint 7.754267 4.090719
#> total_costs total_costs_undisc total_qalys_undisc total_lys_undisc
#> <num> <num> <num> <num>
#> 1: 41357.92 51111.80 10.222361 12.777951
#> 2: 41357.92 51111.80 10.222361 12.777951
#> 3: 58485.35 68550.91 4.779991 9.019372
#> 4: 58485.35 68550.91 4.779991 9.019372
#> 5: 58485.35 68550.91 4.779991 9.019372
#> 6: 31018.44 38333.85 10.222361 12.777951
#> 7: 31018.44 38333.85 10.222361 12.777951
#> 8: 51432.07 60252.35 4.725930 9.019372
#> 9: 51432.07 60252.35 4.725930 9.019372
#> 10: 51432.07 60252.35 4.725930 9.019372
#> lys qalys costs lys_undisc qalys_undisc costs_undisc
#> <num> <num> <num> <num> <num> <num>
#> 1: 10.3394801 8.2715841 41357.920 12.7779512 10.2223609 51111.805
#> 2: 0.0000000 0.0000000 0.000 0.0000000 0.0000000 0.000
#> 3: 0.8871965 0.7097572 3548.786 0.9010175 0.7208140 3604.070
#> 4: 6.8670706 3.4335353 54936.565 8.1183550 4.0591775 64946.840
#> 5: 0.0000000 0.0000000 0.000 0.0000000 0.0000000 0.000
#> 6: 10.3394801 8.2715841 31018.440 12.7779512 10.2223609 38333.854
#> 7: 0.0000000 0.0000000 0.000 0.0000000 0.0000000 0.000
#> 8: 0.7119504 0.5695603 2135.851 0.7208140 0.5766512 2162.442
#> 9: 7.0423168 3.5211584 49296.218 8.2985585 4.1492793 58089.910
#> 10: 0.0000000 0.0000000 0.000 0.0000000 0.0000000 0.000
#> c_default q_default c_default_undisc q_default_undisc nexttime simulation
#> <num> <num> <num> <num> <num> <int>
#> 1: 41357.920 8.2715841 51111.805 10.2223609 12.7779512 1
#> 2: 0.000 0.0000000 0.000 0.0000000 12.7779512 1
#> 3: 3548.786 0.7097572 3604.070 0.7208140 0.9010175 1
#> 4: 54936.565 3.4335353 64946.840 4.0591775 9.0193725 1
#> 5: 0.000 0.0000000 0.000 0.0000000 9.0193725 1
#> 6: 31018.440 8.2715841 38333.854 10.2223609 12.7779512 1
#> 7: 0.000 0.0000000 0.000 0.0000000 12.7779512 1
#> 8: 2135.851 0.5695603 2162.442 0.5766512 0.7208140 1
#> 9: 49296.218 3.5211584 58089.910 4.1492793 9.0193725 1
#> 10: 0.000 0.0000000 0.000 0.0000000 9.0193725 1
#> sensitivity
#> <int>
#> 1: 1
#> 2: 1
#> 3: 1
#> 4: 1
#> 5: 1
#> 6: 1
#> 7: 1
#> 8: 1
#> 9: 1
#> 10: 1
#>
#>
#>