Main analysis

Case Detection Scenario Main Analysis

10 September, 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 file.path 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 371579 6251100 706693.3 1907271 131040.9 133904 0.017 0.136 0.152 0.081 152231 28857 48565 4210 0.215 0.041 0.069 0.006 5270314 287267 304912 67938.0 12088 798567288 2149.118 4660359 12.542 624953.0 0.000 0.000 NaN 0.000
S1NoCD2 371849 6258006 711427.5 1245925 134326.9 162900 0.021 0.138 0.153 0.081 153957 28983 48765 4194 0.216 0.041 0.069 0.006 5272466 288303 307998 68401.0 11986 803320692 2160.341 4664958 12.545 625104.8 0.000 0.000 NaN 0.000
S1NoCDAvg 371714 6254553 709060.4 1576598 132683.9 148402 0.019 0.137 0.152 0.081 153094 28920 48665 4202 0.216 0.041 0.069 0.006 5271390 287785 306455 68169.5 12037 800943990 2154.732 4662659 12.544 625028.9 0.000 0.000 NaN 0.000
S1a 371902 6259940 715671.7 1860288 332259.1 133758 0.027 0.157 0.308 0.093 148736 27895 46953 4074 0.208 0.039 0.066 0.006 5270381 290230 309289 68990.0 12196 900481317 2421.287 4670660 12.559 625521.0 272.168 0.017 16195.98 568.066
S1b 372140 6259675 712868.5 1884251 237934.2 133471 0.021 0.149 0.242 0.088 150400 28799 48224 4222 0.211 0.040 0.068 0.006 5272825 288870 308796 68640.0 11651 882188218 2370.582 4668622 12.545 624896.3 221.463 0.003 67189.32 -56.658
S1c 371919 6260241 706186.6 1892166 204936.3 134248 0.020 0.144 0.214 0.086 150938 28202 47543 4054 0.214 0.040 0.067 0.006 5279621 286590 304912 68525.0 11555 878053058 2360.872 4668922 12.554 625319.1 211.753 0.012 18321.20 366.138

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 219759 3629137 502614.4 1104519 96571.85 76657 0.017 0.142 0.159 0.088 114918 21470 35762 3125 0.229 0.043 0.071 0.006 2971512 185231 226774 55920 10059 592355610 2695.478 2696622 12.271 610845.2 0.000 0.000 NaN 0.000
S2a 221233 3655045 504163.3 1090071 187694.30 76886 0.023 0.161 0.273 0.100 111819 21267 35379 3000 0.222 0.042 0.070 0.006 2994733 187473 224775 56946 10292 644478701 2913.122 2718304 12.287 611440.1 217.644 0.016 13391.77 594.959

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 172154 2596453 416267.8 799855 76852.85 57928 0.018 0.136 0.152 0.085 97495 17657 29861 2619 0.234 0.042 0.072 0.006 2071385 153396 185269 48874 8728 494403150 2871.866 1934054 11.234 558850.2 0.000 0.000 NaN 0.000
S3a 172660 2605291 417975.1 794584 109412.00 58149 0.021 0.142 0.202 0.091 97401 17791 29901 2514 0.233 0.043 0.072 0.006 2078316 153154 186348 48897 9539 527017592 3052.343 1941269 11.243 559113.0 180.478 0.009 20354.54 262.857
S3b 172336 2597409 414801.3 776924 169415.85 58485 0.027 0.156 0.292 0.098 93305 17249 29154 2538 0.225 0.042 0.070 0.006 2073562 151906 185791 48390 8665 542053886 3145.332 1937179 11.241 558890.3 273.466 0.006 43606.19 40.097
S3c 172314 2601178 413310.6 785238 140563.81 58308 0.024 0.152 0.253 0.097 94971 17967 29976 2568 0.230 0.043 0.073 0.006 2078632 152348 184613 47450 9041 535046632 3105.068 1939341 11.255 559629.4 233.202 0.020 11516.85 779.237
S3d 172882 2607172 418585.2 790887 126089.76 58037 0.022 0.148 0.229 0.093 96041 18109 30257 2592 0.229 0.043 0.072 0.006 2079272 153348 187559 48917 8624 542727747 3139.296 1943060 11.239 558821.9 267.430 0.005 55904.12 -28.244

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
S3c 172314 535046632 3105.068 1939341 11.255 11516.85 779.237
S2a 221233 644478701 2913.122 2718304 12.287 13391.77 594.959
S1a 371902 900481317 2421.287 4670660 12.559 16195.98 568.066
S1c 371919 878053058 2360.872 4668922 12.554 18321.20 366.138
S3a 172660 527017592 3052.343 1941269 11.243 20354.54 262.857
S3b 172336 542053886 3145.332 1937179 11.241 43606.19 40.097
S1NoCD 371579 798567288 2149.118 4660359 12.542 NaN 0.000
S2NoCD 219759 592355610 2695.478 2696622 12.271 NaN 0.000
S3NoCD 172154 494403150 2871.866 1934054 11.234 NaN 0.000
S3d 172882 542727747 3139.296 1943060 11.239 55904.12 -28.244
S1b 372140 882188218 2370.582 4668622 12.545 67189.32 -56.658

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 371714 1.0000000 800943990 2154.732 0.000 2154.732 4662659 12.54367 0.00000 12.54367 0.00000 0.0000000 NaN NaN 0.00000
S1a 371902 1.0000000 900481317 2421.287 0.000 2421.287 4670660 12.55885 0.00000 12.55885 266.55473 0.0151739 17566.70 16195.98 492.13863
S1b 372140 1.0000000 882188218 2370.582 0.000 2370.582 4668622 12.54534 0.00000 12.54534 215.84971 0.0016653 129616.17 67189.32 -132.58475
S1c 371919 1.0000000 878053058 2360.872 0.000 2360.872 4668922 12.55360 0.00000 12.55360 206.13991 0.0099270 20765.54 18321.20 290.21108
S2NoCD 219759 0.5912045 592355610 2695.478 1372.698 2154.732 2696622 12.27081 12.93828 12.54367 0.00000 0.0000000 NaN NaN 0.00000
S2a 221233 0.5951699 644478701 2913.122 1372.698 2289.512 2718304 12.28707 12.93828 12.55070 134.78032 0.0070259 19183.27 13391.77 216.51625
S3NoCD 172154 0.4631356 494403150 2871.866 1536.084 2154.732 1934054 11.23444 13.67310 12.54367 0.00000 0.0000000 NaN NaN 0.00000
S3a 172660 0.4644969 527017592 3052.343 1536.084 2240.382 1941269 11.24331 13.67310 12.54447 85.64968 0.0007989 107210.07 20354.54 -45.70489
S3b 172336 0.4636253 542053886 3145.332 1536.084 2282.172 1937179 11.24071 13.67310 12.54539 127.43983 0.0017135 74374.40 43606.19 -41.76530
S3c 172314 0.4635661 535046632 3105.068 1536.084 2263.411 1939341 11.25469 13.67310 12.55201 108.67955 0.0083369 13035.89 11516.85 308.16789
S3d 172882 0.4650941 542727747 3139.296 1536.084 2281.728 1943060 11.23922 13.67310 12.54112 126.99637 -0.0025512 -49778.54 55904.12 -254.55773

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 0.0190669 0.1369635 0.1524877 0.0811388 0.4118597 0.0778018 0.1309205 0.0113044 0.8428084 0.0460121 0.0489971 0.0108992 0.0019245 0.1871263
S1a 1.0000000 1.0000000 1.0000000 0.0265445 0.1570223 0.3084907 0.0926510 0.3999333 0.0750063 0.1262510 0.0109545 0.8419219 0.0463631 0.0494077 0.0110209 0.0019483 0.4642618
S1b 1.0000000 1.0000000 1.0000000 0.0214586 0.1491594 0.2417213 0.0881407 0.4041490 0.0773875 0.1295856 0.0113452 0.8423480 0.0461478 0.0493310 0.0109654 0.0018613 0.3337701
S1c 1.0000000 1.0000000 1.0000000 0.0203173 0.1442037 0.2142410 0.0858433 0.4058357 0.0758283 0.1278316 0.0109002 0.8433575 0.0457794 0.0487061 0.0109461 0.0018458 0.2902014
S2NoCD 0.5912045 0.5802392 0.7088457 0.0190669 0.1369635 0.1524877 0.0811388 0.4118597 0.0778018 0.1309205 0.0113044 0.8428084 0.0460121 0.0489971 0.0108992 0.0019245 0.1871263
S2a 0.5951699 0.5843814 0.7110301 0.0224588 0.1502763 0.2333607 0.0900274 0.4025264 0.0770612 0.1295535 0.0109400 0.8428925 0.0462087 0.0485518 0.0110439 0.0019587 0.3152558
S3NoCD 0.4631356 0.4151300 0.5870696 0.0190669 0.1369635 0.1524877 0.0811388 0.4118597 0.0778018 0.1309205 0.0113044 0.8428084 0.0460121 0.0489971 0.0108992 0.0019245 0.1871263
S3a 0.4644969 0.4165431 0.5894774 0.0201971 0.1407461 0.1823544 0.0846326 0.4112275 0.0780854 0.1308999 0.0110111 0.8426805 0.0459215 0.0491228 0.0108954 0.0020529 0.2325859
S3b 0.4636253 0.4152828 0.5850013 0.0226724 0.1487887 0.2343546 0.0889405 0.4004511 0.0766765 0.1289724 0.0110826 0.8430228 0.0457682 0.0490755 0.0108210 0.0019143 0.3180639
S3c 0.4635661 0.4158854 0.5828990 0.0212574 0.1466240 0.2115343 0.0882504 0.4049496 0.0786114 0.1311894 0.0111638 0.8433063 0.0458168 0.0488672 0.0106675 0.0019739 0.2777743
S3d 0.4650941 0.4168438 0.5903378 0.0207322 0.1440997 0.1979824 0.0857580 0.4074024 0.0789072 0.1318013 0.0112162 0.8425703 0.0459414 0.0493065 0.0108970 0.0019063 0.2559428

Time elapsed

Run time for this notebook:

end.time <- Sys.time()
time.taken <- end.time - start.time
time.taken
## Time difference of 8.587178 mins