packageVersion("FeatureExtraction")
#> [1] '3.4.0'

# 4283893204 = condition_era group: Sinusitis
temporalCovariateSettings <- FeatureExtraction::createTemporalCovariateSettings(
  useConditionEraGroupOverlap = TRUE,
  temporalStartDays = c(-365, -364),
  temporalEndDays = c(-365, -364),
  includedCovariateConceptIds = 4283893 
)

# Execute the analysis on Eunomia
connectionDetails <- Eunomia::getEunomiaConnectionDetails()
Eunomia::createCohorts(
  connectionDetails = connectionDetails
)
#> Connecting using SQLite driver
#> Creating cohort: Celecoxib
#>   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%
#> Executing SQL took 0.026 secs
#> Creating cohort: Diclofenac
#>   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%
#> Executing SQL took 0.0169 secs
#> Creating cohort: GiBleed
#>   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%
#> Executing SQL took 0.0279 secs
#> Creating cohort: NSAIDs
#>   |                                                                              |                                                                      |   0%  |                                                                              |======================================================================| 100%
#> Executing SQL took 0.0735 secs
#> Cohorts created in table main.cohort
#>   cohortId       name
#> 1        1  Celecoxib
#> 2        2 Diclofenac
#> 3        3    GiBleed
#> 4        4     NSAIDs
#>                                                                                        description
#> 1    A simplified cohort definition for new users of celecoxib, designed specifically for Eunomia.
#> 2    A simplified cohort definition for new users ofdiclofenac, designed specifically for Eunomia.
#> 3 A simplified cohort definition for gastrointestinal bleeding, designed specifically for Eunomia.
#> 4       A simplified cohort definition for new users of NSAIDs, designed specifically for Eunomia.
#>   count
#> 1  1844
#> 2   850
#> 3   479
#> 4  2694

covariateData <- FeatureExtraction::getDbCovariateData(
  connectionDetails = connectionDetails,
  cdmDatabaseSchema = "main",
  cohortDatabaseSchema = "main",
  cohortTable = "cohort",
  covariateSettings = temporalCovariateSettings,
  aggregated = TRUE
)
#> Connecting using SQLite driver
#> Currently in a tryCatch or withCallingHandlers block, so unable to add global calling handlers. ParallelLogger will not capture R messages, errors, and warnings, only explicit calls to ParallelLogger. (This message will not be shown again this R session)
#> Sending temp tables to server
#> Inserting data took 0.0144 secs
#> Inserting data took 0.0312 secs
#> Constructing features on server
#>   |                                                                              |                                                                      |   0%  |                                                                              |=====                                                                 |   8%  |                                                                              |===========                                                           |  15%  |                                                                              |================                                                      |  23%  |                                                                              |======================                                                |  31%  |                                                                              |===========================                                           |  38%  |                                                                              |================================                                      |  46%  |                                                                              |======================================                                |  54%  |                                                                              |===========================================                           |  62%  |                                                                              |================================================                      |  69%  |                                                                              |======================================================                |  77%  |                                                                              |===========================================================           |  85%  |                                                                              |=================================================================     |  92%  |                                                                              |======================================================================| 100%
#> Executing SQL took 0.102 secs
#> Fetching data from server
#> Warning: Low disk space in 'C:/Users/asena5/AppData/Local/Temp/1/Rtmp2fzzCg'. Only 9.5 GB left.
#> Use options(warnDiskSpaceThreshold = <n>) to set the number of bytes for this warning to trigger.
#> This warning will not be shown for this file location again during this R session.
#> Fetching data took 0.177 secs

covariateData$covariates
#> # Source:   table<covariates> [4 x 5]
#> # Database: sqlite 3.41.2 [C:\Users\asena5\AppData\Local\Temp\1\Rtmp2fzzCg\file4085a72dbc.sqlite]
#>   cohortDefinitionId covariateId timeId sumValue averageValue
#>                <dbl>       <dbl>  <dbl>    <dbl>        <dbl>
#> 1                  1  4283893204      1        4      0.00217
#> 2                  1  4283893204      2        4      0.00217
#> 3                  4  4283893204      1        4      0.00148
#> 4                  4  4283893204      2        4      0.00148

FeatureExtraction::computeStandardizedDifference(
  covariateData1 = covariateData,
  covariateData2 = covariateData,
  cohortId1 = 1,
  cohortId2 = 4
)
#> # A tibble: 4 × 8
#>   covariateId   mean1    sd1   mean2    sd2     sd stdDiff covariateName        
#>         <dbl>   <dbl>  <dbl>   <dbl>  <dbl>  <dbl>   <dbl> <chr>                
#> 1  4283893204 0.00217 0.0465 0.00148 0.0385 0.0427 -0.0160 condition_era group:…
#> 2  4283893204 0.00217 0.0465 0.00148 0.0385 0.0427 -0.0160 condition_era group:…
#> 3  4283893204 0.00217 0.0465 0.00148 0.0385 0.0427 -0.0160 condition_era group:…
#> 4  4283893204 0.00217 0.0465 0.00148 0.0385 0.0427 -0.0160 condition_era group:…