Main analysis

Case Detection Scenario Main Analysis

14 October, 2024

## 
## > errors<-c(
## +   ERR_INCORRECT_SETTING_VARIABLE=-1,
## +   ERR_INCORRECT_VECTOR_SIZE=-2,
## +   ERR_INCORRECT_INPUT_VAR=-3,
## +   ERR_EVENT_STACK_FULL=-4,
## +   .... [TRUNCATED] 
## 
## > record_mode<-c(
## +   record_mode_none=0,
## +   record_mode_agent=1,
## +   record_mode_event=2,
## +   record_mode_some_event=3
## + )
## 
## > agent_creation_mode<-c(
## +   agent_creation_mode_one=0,
## +   agent_creation_mode_all=1,
## +   agent_creation_mode_pre=2
## + )
## 
## > medication_classes<-c(
## +   MED_CLASS_SABA=1,
## +   MED_CLASS_LABA=2,
## +   MED_CLASS_LAMA=4,
## +   MED_CLASS_ICS=8,
## +   MED_CLASS_MACRO=16
## + )
## 
## > events<-c(
## +     event_start=0,
## +     event_fixed=1,
## +     event_birthday=2,
## +     event_smoking_change=3,
## +     event_COPD=4,
## +     event_exacerbat .... [TRUNCATED]
# CHANGE: Add a timer (will see addition below to print time too)
# Start timer
start.time <- Sys.time()
# CHANGE: Add save paths (will see later, we also add lines to save to csv)
outputs <- "../outputs/"
files <- list(
  s1 = "s1.csv",
  s2 = "s2.csv",
  s3 = "s3.csv",
  sall = "sall.csv",
  ceplane = "ceplane.csv",
  clinical = "clinicalresults.csv"
)

# Apply to each element in list to create path to file in outputs
paths <- lapply(files, function(filename) paste0(outputs, filename))
## Initializing the session

## [1] 0

Global inputs:

  • Medication adherence is 0.7
  • Smoking adherence is 0.7
  • Cost discounting: 0.015
  • QALY discounting: 0.015
  • Time horizon: 20
  • The WTP threshold for NMB is 50000

Case detection inputs:

  • Case detection occurs at 3 year intervals.
  • An outpatient diagnosis costs 61.18
  • The utility gain due to symptom relief from treatment is 0.0367

S1 All patients scenario

All patients are eligible. The cost of case detection is:

None CDQ17 FlowMeter FlowMeter_CDQ
0 11.56 30.46 42.01

S1NoCD: No Case detection

## [1] 0

## Terminating the session

## [1] 0

S1NoCD2: No Case detection- Other time interval

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0

S1A: CDQ ≥17 points

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0

S1B: Screening Spirometry with BD

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0

S1C: CDQ ≥17 points and Screening Spirometry with BD

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0
Scenario Agents PatientYears CopdPYs NCaseDetections DiagnosedPYs OverdiagnosedPYs SABA LAMA LAMALABA ICSLAMALABA Mild Moderate Severe VerySevere MildPY ModeratePY SeverePY VerySeverePY NoCOPD GOLD1 GOLD2 GOLD3 GOLD4 Cost CostpAgent QALY QALYpAgent NMB IncrementalCosts IncrementalQALY ICER IncrementalNMB
S1NoCD 74388747 1251903576 142277086 381929878 26336153 26747209 0.017 0.135 0.151 0.080 30809289 5766720 9701609 839538.0 0.217 0.041 0.068 0.006 1054811684 57697202 61465410 13763906 2389153 159789813678 2148.037 933216569 12.545 625108.5 0.000 0.000 NaN 0.000
S1NoCD2 74388425 1251968458 142302175 249329256 26636736 32661650 0.021 0.136 0.151 0.080 30801067 5759155 9700407 837363.0 0.216 0.040 0.068 0.006 1054852003 57672835 61488796 13791895 2388663 160061317736 2151.697 933263557 12.546 625139.1 0.000 0.000 NaN 0.000
S1NoCDAvg 74388586 1251936017 142289630 315629567 26486444 29704430 0.019 0.136 0.151 0.080 30805178 5762938 9701008 838450.5 0.216 0.041 0.068 0.006 1054831844 57685018 61477103 13777900 2388908 159925565707 2149.867 933240063 12.545 625123.8 0.000 0.000 NaN 0.000
S1a 74380275 1252107231 142568770 372100831 66270673 26745802 0.026 0.159 0.310 0.094 29815042 5625494 9500837 824680.0 0.209 0.039 0.067 0.006 1054730269 57758498 61574433 13835312 2423951 181401075128 2438.833 934239602 12.560 625576.9 290.796 0.015 19152.73 468.354
S1b 74383024 1252030978 142410670 376764647 47607118 26748888 0.022 0.148 0.241 0.088 30192660 5683507 9596337 830158.0 0.212 0.040 0.067 0.006 1054810413 57710159 61499603 13827904 2405886 175747140584 2362.732 933787724 12.554 625326.0 214.694 0.009 24838.03 217.495
S1c 74393892 1252166867 142379318 378416895 41063274 26758496 0.020 0.144 0.214 0.085 30350312 5702044 9621386 828456.0 0.213 0.040 0.068 0.006 1054965444 57726777 61483651 13803995 2400849 177409072797 2384.726 933746980 12.551 625184.9 236.689 0.006 37796.71 76.419

Treatment rate: SABA is expressed per all patient-years, LAMA, LAMA/LABA, ICS/LAMA/LABA are per COPD patient-years Exacerbations: Total exacerbations and rate per COPD patient-year: GOLD Stage: Cumulative patient-years Cost/QALY: Total cost and QALYs NMB: Net Monetary Benefit is calculated as QALY per patient-year * Lamba - Cost per patient-year

S2 Symptomatic patients scenario

Patients with symptoms at year 1 are eligible. The cost of case detection is:

## Initializing the session

## [1] 0
None FlowMeter
0 24.33

S2NoCD: No Case detection

## [1] 0

## Terminating the session

## [1] 0

S2a: Screening Spirometry without BD

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0
Scenario Agents PatientYears CopdPYs NCaseDetections DiagnosedPYs OverdiagnosedPYs SABA LAMA LAMALABA ICSLAMALABA Mild Moderate Severe VerySevere MildPY ModeratePY SeverePY VerySeverePY NoCOPD GOLD1 GOLD2 GOLD3 GOLD4 Cost CostpAgent QALY QALYpAgent NMB IncrementalCosts IncrementalQALY ICER IncrementalNMB
S2NoCD 44156404 729084497 100330760 221928932 19330952 15481473 0.017 0.142 0.159 0.087 22917076 4253860 7098458 609501 0.228 0.042 0.071 0.006 597619551 37246010 44990133 11123560 2050468 117605933755 2663.395 541859031 12.271 610904.5 0.000 0.000 NaN 0.000
S2a 44164773 729329891 100492049 217625447 37010683 15485858 0.023 0.157 0.269 0.097 22383331 4181008 7006346 603148 0.223 0.042 0.070 0.006 597700094 37284225 45068617 11147317 2064302 127735308298 2892.244 542449119 12.282 611227.4 228.849 0.011 20737.2 322.935

Treatment rate: SABA is expressed per all patient-years, LAMA, LAMA/LABA, ICS/LAMA/LABA are per COPD patient-years Exacerbations: Total exacerbations and rate per COPD patient-year: GOLD Stage: Cumulative patient-years Cost/QALY: Total cost and QALYs NMB: Net Monetary Benefit is calculated as QALY per patient-year * Lamba - Cost per patient-year

S3 Smoking history scenario

Ever smokers ≥50 years of age are eligible. The cost of case detection is:

## Initializing the session

## [1] 0
None CDQ195 CDQ165 FlowMeter FlowMeter_CDQ
0 11.56 11.56 24.33 42.01

S3NoCD: No Case detection

## [1] 0

## Terminating the session

## [1] 0

S3a: CDQ ≥19.5 points

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0

S3b: CDQ ≥16.5 points

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0

S3c: Screening spirometry without BD

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0

S3d: Screening Spirometry with BD + CDQ ≥17 points

## Initializing the session

## [1] 0

## [1] 0

## Terminating the session

## [1] 0
Scenario Agents PatientYears CopdPYs NCaseDetections DiagnosedPYs OverdiagnosedPYs SABA LAMA LAMALABA ICSLAMALABA Mild Moderate Severe VerySevere MildPY ModeratePY SeverePY VerySeverePY NoCOPD GOLD1 GOLD2 GOLD3 GOLD4 Cost CostpAgent QALY QALYpAgent NMB IncrementalCosts IncrementalQALY ICER IncrementalNMB
S3NoCD 34500334 520264617 83469550 160191877 15617539 11630123 0.018 0.137 0.154 0.086 19525292 3631989 6073558 522424 0.234 0.044 0.073 0.006 415002016 30608834 37422882 9624470 1788687 99842281258 2893.951 387517176 11.232 558719.7 0.000 0.000 NaN 0.000
S3a 34507415 520428951 83482576 158676520 22030098 11639538 0.021 0.144 0.204 0.091 19287934 3609226 6045313 521405 0.231 0.043 0.072 0.006 415152628 30610103 37407716 9641236 1794702 106095806862 3074.580 387796823 11.238 558829.0 180.629 0.006 31147.82 109.325
S3b 34499539 520396932 83618002 155590263 34428826 11625591 0.027 0.156 0.293 0.099 18988453 3564625 5980823 516662 0.227 0.043 0.072 0.006 414988556 30607762 37472866 9688489 1813970 110363699543 3198.991 388038736 11.248 559183.5 305.039 0.015 19837.73 463.797
S3c 34496334 520227370 83568351 157099275 28171361 11622564 0.024 0.150 0.249 0.095 19145218 3585036 6010150 518449 0.229 0.043 0.072 0.006 414875686 30589301 37479876 9661353 1804425 107627143927 3119.959 387776879 11.241 558935.2 226.008 0.009 25592.92 215.536
S3d 34507664 520495018 83555471 157877292 25364366 11630839 0.023 0.147 0.229 0.093 19209915 3595849 6028084 520340 0.230 0.043 0.072 0.006 415141325 30594930 37472224 9653084 1805226 108255487965 3137.143 387911628 11.241 558928.8 243.192 0.009 26887.15 209.054

Treatment rate: SABA is expressed per all patient-years, LAMA, LAMA/LABA, ICS/LAMA/LABA are per COPD patient-years Exacerbations: Total exacerbations and rate per COPD patient-year GOLD Stage: Cumulative patient-years Cost/QALY: Total cost and QALYs NMB: Net Monetary Benefit is calculated as QALY per patient-year * Lamba - Cost per patient-year

All Scenarios

Ordered by descending Net Monetary Benefit

Scenario Agents Cost CostpAgent QALY QALYpAgent ICER IncrementalNMB
S1a 74380275 181401075128 2438.833 934239602 12.560 19152.73 468.354
S3b 34499539 110363699543 3198.991 388038736 11.248 19837.73 463.797
S2a 44164773 127735308298 2892.244 542449119 12.282 20737.20 322.935
S1b 74383024 175747140584 2362.732 933787724 12.554 24838.03 217.495
S3c 34496334 107627143927 3119.959 387776879 11.241 25592.92 215.536
S3d 34507664 108255487965 3137.143 387911628 11.241 26887.15 209.054
S3a 34507415 106095806862 3074.580 387796823 11.238 31147.82 109.325
S1c 74393892 177409072797 2384.726 933746980 12.551 37796.71 76.419
S1NoCD 74388747 159789813678 2148.037 933216569 12.545 NaN 0.000
S2NoCD 44156404 117605933755 2663.395 541859031 12.271 NaN 0.000
S3NoCD 34500334 99842281258 2893.951 387517176 11.232 NaN 0.000

Cost Effectiveness Plane

Adjusted to the total population

Scenario Agents PropAgents Cost CostpAgent CostpAgentExcluded CostpAgentAll QALY QALYpAgent QALYpAgentExcluded QALYpAgentAll IncrementalCosts IncrementalQALY ICERAdj ICER INMB
S1NoCDAvg 74388586 1.0000000 159925565707 2149.867 0.000 2149.867 933240063 12.54547 0.00000 12.54547 0.00000 0.0000000 NaN NaN 0.00000
S1a 74380275 1.0000000 181401075128 2438.833 0.000 2438.833 934239602 12.56031 0.00000 12.56031 288.96609 0.0148400 19472.10 19152.73 453.03421
S1b 74383024 1.0000000 175747140584 2362.732 0.000 2362.732 933787724 12.55377 0.00000 12.55377 212.86487 0.0083008 25643.89 24838.02 202.17518
S1c 74393892 1.0000000 177409072797 2384.726 0.000 2384.726 933746980 12.55139 0.00000 12.55139 234.85933 0.0059192 39677.70 37796.70 61.09955
S2NoCD 44156404 0.5935911 117605933755 2663.395 1399.821 2149.867 541859031 12.27136 12.94584 12.54547 0.00000 0.0000000 NaN NaN 0.00000
S2a 44164773 0.5937036 127735308298 2892.244 1399.821 2285.878 542449119 12.28239 12.94584 12.55195 136.01091 0.0064761 21002.14 20737.20 187.79161
S3NoCD 34500334 0.4637853 99842281258 2893.951 1506.290 2149.867 387517176 11.23227 13.68129 12.54547 0.00000 0.0000000 NaN NaN 0.00000
S3a 34507415 0.4638805 106095806862 3074.580 1506.290 2233.789 387796823 11.23807 13.68129 12.54793 83.92228 0.0024570 34156.94 31147.82 38.92579
S3b 34499539 0.4637746 110363699543 3198.991 1506.290 2291.322 388038736 11.24765 13.68129 12.55263 141.45471 0.0071575 19763.12 19837.73 216.42072
S3c 34496334 0.4637315 107627143927 3119.959 1506.290 2254.599 387776879 11.24110 13.68129 12.54970 104.73230 0.0042268 24777.92 25592.93 106.60970
S3d 34507664 0.4638839 108255487965 3137.143 1506.290 2262.817 387911628 11.24132 13.68129 12.54943 112.94966 0.0039545 28562.49 26887.15 84.77408

Clinical Results for all scenarios

Adjusted to the total population

Scenario PropAgents ProppPatientYears ProppCopdPYs SABAAll LAMAAll LAMALABAAll ICSLAMALABAAll MildpAgentAll ModeratepAgentAll SeverepAgentAll VerySeverepAgentAll NoCOPDpPYAll GOLD1pPYAll GOLD2pPYAll GOLD3pPYAll GOLD4pPYAll DiagnosedpPYAll
S1NoCDAvg 1.0000000 1.0000000 1.0000000 0.0190054 0.1355252 0.1513708 0.0796683 0.4141116 0.0774707 0.1304099 0.0112712 0.8425605 0.0460767 0.0491056 0.0110053 0.0019082 0.1861446
S1a 1.0000000 1.0000000 1.0000000 0.0264033 0.1593018 0.3099946 0.0940914 0.4008461 0.0756315 0.1277333 0.0110873 0.8423642 0.0461290 0.0491766 0.0110496 0.0019359 0.4648330
S1b 1.0000000 1.0000000 1.0000000 0.0216398 0.1482342 0.2406521 0.0877947 0.4059079 0.0764087 0.1290125 0.0111606 0.8424795 0.0460932 0.0491199 0.0110444 0.0019216 0.3342946
S1c 1.0000000 1.0000000 1.0000000 0.0201517 0.1441110 0.2141912 0.0851720 0.4079678 0.0766467 0.1293303 0.0111361 0.8425119 0.0461015 0.0491018 0.0110241 0.0019174 0.2884076
S2NoCD 0.5935911 0.5823656 0.7051165 0.0190054 0.1355252 0.1513708 0.0796683 0.4141116 0.0774707 0.1304099 0.0112712 0.8425605 0.0460767 0.0491056 0.0110053 0.0019082 0.1861446
S2a 0.5937036 0.5825616 0.7062500 0.0223572 0.1465203 0.2287835 0.0867962 0.4069072 0.0764858 0.1291620 0.0111850 0.8424534 0.0460995 0.0491621 0.0110233 0.0019191 0.3102030
S3NoCD 0.4637853 0.4155681 0.5866172 0.0190054 0.1355252 0.1513708 0.0796683 0.4141116 0.0774707 0.1304099 0.0112712 0.8425605 0.0460767 0.0491056 0.0110053 0.0019082 0.1861446
S3a 0.4638805 0.4156993 0.5867088 0.0201156 0.1395918 0.1808230 0.0824771 0.4108939 0.0771596 0.1300215 0.0112568 0.8425660 0.0460728 0.0490892 0.0110179 0.0019129 0.2311946
S3b 0.4637746 0.4156737 0.5876605 0.0227032 0.1471017 0.2332507 0.0873282 0.4068980 0.0765657 0.1291642 0.0111939 0.8424573 0.0460719 0.0491421 0.0110558 0.0019283 0.3181560
S3c 0.4637315 0.4155383 0.5873116 0.0213262 0.1432680 0.2074859 0.0848645 0.4090175 0.0768424 0.1295624 0.0112182 0.8424856 0.0460621 0.0491521 0.0110349 0.0019208 0.2742435
S3d 0.4638839 0.4157521 0.5872211 0.0207546 0.1415673 0.1954816 0.0837051 0.4098442 0.0769796 0.1297896 0.0112424 0.8425108 0.0460587 0.0491390 0.0110271 0.0019212 0.2545329

Time elapsed

Run time for this notebook:

end.time <- Sys.time()
time.taken <- end.time - start.time
time.taken
## Time difference of 20.64576 hours