# Evaluating Output

For this example we take the case of Viral Sinusitis and several treatments as events. We set our `minEraDuration = 7`, `minCombinationDuration = 7` and `combinationWindow = 7`. We treat multiple events of Viral Sinusitis as separate cases by setting `concatTargets = FALSE`. When set to `TRUE` it would append multiple cases, which might be useful for time invariant target cohorts like chronic conditions.

    library(CDMConnector)
    library(dplyr)
    library(TreatmentPatterns)

    cohortSet <- CDMConnector::readCohortSet(
      path = system.file(package = "TreatmentPatterns", "exampleCohorts")
    )

    con <- DBI::dbConnect(
      drv = duckdb::duckdb(),
      dbdir = CDMConnector::eunomiaDir()
    )

    cdm <- CDMConnector::cdmFromCon(
      con = con,
      cdmSchema = "main",
      writeSchema = "main"
    )

    cdm <- CDMConnector::generateCohortSet(
      cdm = cdm,
      cohortSet = cohortSet,
      name = "cohort_table",
      overwrite = TRUE
    )

    ## ℹ Generating 8 cohorts

    ## ℹ Generating cohort (1/8) - acetaminophen✔ Generating cohort (1/8) - acetaminophen [236ms]
    ## ℹ Generating cohort (2/8) - amoxicillin✔ Generating cohort (2/8) - amoxicillin [181ms]
    ## ℹ Generating cohort (3/8) - aspirin✔ Generating cohort (3/8) - aspirin [184ms]
    ## ℹ Generating cohort (4/8) - clavulanate✔ Generating cohort (4/8) - clavulanate [148ms]
    ## ℹ Generating cohort (5/8) - death✔ Generating cohort (5/8) - death [99ms]
    ## ℹ Generating cohort (6/8) - doxylamine✔ Generating cohort (6/8) - doxylamine [133ms]
    ## ℹ Generating cohort (7/8) - penicillinv✔ Generating cohort (7/8) - penicillinv [164ms]
    ## ℹ Generating cohort (8/8) - viralsinusitis✔ Generating cohort (8/8) - viralsinusitis [255ms]

    cohorts <- cohortSet %>%
      # Remove 'cohort' and 'json' columns
      dplyr::select(-"cohort", -"json", -"cohort_name_snakecase") %>%
      dplyr::mutate(
        type = c(
          "event", "event", "event", "event",
          "exit", "event", "event", "target"
        )
      ) %>%
      dplyr::rename(
        cohortId = "cohort_definition_id",
        cohortName = "cohort_name",
      )

    outputEnv <- TreatmentPatterns::computePathways(
      cohorts = cohorts,
      cohortTableName = "cohort_table",
      cdm = cdm,
      minEraDuration = 7,
      combinationWindow = 7,
      minPostCombinationDuration = 7,
      concatTargets = FALSE
    )

    ## -- Qualifying records for cohort definitions: 1, 2, 3, 4, 5, 6, 7, 8
    ##  Records: 14041
    ##  Subjects: 2693
    ## -- Removing records < minEraDuration (7)
    ##  Records: 11347
    ##  Subjects: 2159
    ## >> Starting on target: 8 (viralsinusitis)
    ## -- Removing events outside window (startDate: 0 | endDate: 0)
    ##  Records: 8327
    ##  Subjects: 2142
    ## -- splitEventCohorts
    ##  Records: 8327
    ##  Subjects: 2142
    ## -- Collapsing eras, eraCollapse (30)
    ##  Records: 8327
    ##  Subjects: 2142
    ## -- Iteration 1: minPostCombinationDuration (7), combinatinoWindow (7)
    ##  Records: 6799
    ##  Subjects: 2142
    ## -- Iteration 2: minPostCombinationDuration (7), combinatinoWindow (7)
    ##  Records: 6663
    ##  Subjects: 2142
    ## -- Iteration 3: minPostCombinationDuration (7), combinatinoWindow (7)
    ##  Records: 6662
    ##  Subjects: 2142
    ## -- After Combination
    ##  Records: 6662
    ##  Subjects: 2142
    ## -- filterTreatments (First)
    ##  Records: 6657
    ##  Subjects: 2142
    ## -- Max path length (5)
    ##  Records: 6653
    ##  Subjects: 2142
    ## -- treatment construction done
    ##  Records: 6653
    ##  Subjects: 2142

    results <- TreatmentPatterns::export(
      andromeda = outputEnv,
      minCellCount = 1,
      nonePaths = TRUE,
      outputPath = tempdir()
    )

    ## Wrote csv-files to: C:\Users\mvankessel\AppData\Local\Temp\RtmpyEHafT

## Saving results

Now that we ran our TreatmentPatterns analysis and have exported our results, we can evaluate the output. The `export()` function in TreatmentPatterns returns an R6 class of `TreatmentPatternsResults`. All results are query-able from this object. Additionally the files are written to the specified `outputPath`. If no `outputPath` is set, only the result object is returned, and no files are written.

If you would like to save the results to csv-, or zip-file after the fact you can still do this. Or upload it to a database:

    # Save to csv-, zip-file
    results$saveAsCsv(path = tempdir())

    ## Wrote csv-files to: C:\Users\mvankessel\AppData\Local\Temp\RtmpyEHafT

    results$saveAsZip(path = tempdir(), name = "tp-results.zip")

    ## Wrote zip-file to: C:\Users\mvankessel\AppData\Local\Temp\RtmpyEHafT

    # Upload to database
    connectionDetails <- DatabaseConnector::createConnectionDetails(
      dbms = "sqlite",
      server = file.path(tempdir(), "db.sqlite")
    )

    results$uploadResultsToDb(
      connectionDetails = connectionDetails,
      schema = "main",
      prefix = "tp_",
      overwrite = TRUE,
      purgeSiteDataBeforeUploading = FALSE
    )

    ## Warning: package 'R6' was built under R version 4.4.3

    ##
    ## Attaching package: 'DatabaseConnector'

    ## The following objects are masked from 'package:CDMConnector':
    ##
    ##     dbms, insertTable

    ## Connecting using SQLite driver
    ## Uploading file: attrition.csv to table: attrition

    ## Warning: The following named parsers don't match the column names: time

    ## - Preparing to upload rows 1 through 12

    ## Inserting data took 0.0163 secs
    ## Uploading file: counts_age.csv to table: counts_age

    ## - Preparing to upload rows 1 through 63

    ## Inserting data took 0.0329 secs
    ## Uploading file: counts_sex.csv to table: counts_sex

    ## - Preparing to upload rows 1 through 2

    ## Inserting data took 0.0119 secs
    ## Uploading file: counts_year.csv to table: counts_year

    ## Warning: The following named parsers don't match the column names: year

    ## - Preparing to upload rows 1 through 52

    ## Inserting data took 0.0204 secs
    ## Uploading file: metadata.csv to table: metadata

    ## - Preparing to upload rows 1 through 1

    ## Inserting data took 0.00926 secs
    ## Uploading file: summary_event_duration.csv to table: summary_event_duration

    ## Warning: The following named parsers don't match the column names: min, q1,
    ## median, q2, max, average, sd, count

    ## - Preparing to upload rows 1 through 88

    ## Inserting data took 0.0199 secs
    ## Uploading file: treatment_pathways.csv to table: treatment_pathways

    ## Warning: The following named parsers don't match the column names: path

    ## - Preparing to upload rows 1 through 372

    ## Inserting data took 0.0228 secs
    ## Uploading file: cdm_source_info.csv to table: cdm_source_info

    ## - Preparing to upload rows 1 through 1

    ## Inserting data took 0.0167 secs
    ## Uploading file: analyses.csv to table: analyses

    ## - Preparing to upload rows 1 through 1

    ## Inserting data took 0.0187 secs
    ## Uploading file: arguments.csv to table: arguments

    ## - Preparing to upload rows 1 through 1

    ## Inserting data took 0.0204 secs

    ## Uploading data took 5.77 secs

## Evaluating Results

### treatmentPathways

The treatmentPathways file contains all the pathways found, with a frequency, pairwise stratified by age group, sex and index year.

    head(results$treatment_pathways)

We can see the pathways contain the treatment names we provided in our event cohorts. Besides that we also see the paths are annoted with a `+` or `-`. The `+` indicates two treatments are a combination therapy, i.e. `amoxicillin+clavulanate` is a combination of amoxicillin and clavulanate. The `-` indicates a switch between treatments, i.e. `acetaminophen-penicillinv` is a switch from acetaminophen to penicillin v. Note that these combinations and switches can occur in the same pathway, i.e. `acetaminophen-amoxicillin+clavulanate`. The first treatment is acetaminophen that switches to a combination of amoxicillin and clavulanate.

### countsAge, countsSex, and countsYear

The countsAge, countsSex, and countsYear contain counts per age, sex, and index year.

    head(results$counts_age)

    head(results$counts_sex)

    head(results$counts_year)

### summaryStatsTherapyDuration

The summaryEventDuration contains summary statistics from different events, across all found “lines”. A “line” is equal to the level in the Sunburst or Sankey diagrams. The summary statistics allow for plotting of boxplots with the `plotEventDuration()` function.

    results$plotEventDuration()

Not that besides our events there are two extra rows: mono-event, and combination-event. These are both types of events on average.

We see that most events last between 0 and 100 days. We can see that for combination-events and amoxicillin+clavulanate there is a tendency for events to last longer than that. amoxicillin+clavulanate most likely skews the duration in the combination-events group.

We can alter the x-axis to get a clearer view of the durations of the events:

    results$plotEventDuration() +
      ggplot2::xlim(0, 100)

Now we can more clearly investigate particular treatments. We can see that penicilin v tends to last quite short across all treatment lines, while aspirin and acetaminophen seem to skew to a longer duration.

Additionally we can also set a `minCellCount` for the individual events.

    results$plotEventDuration(minCellCount = 10) +
      ggplot2::xlim(0, 100)

### metadata

The metadata file is a file that contains information about the circumstances the analysis was performed in, and information about R, and the CDM.

    results$metadata

### Sunburst Plot & Sankey Diagram

From the filtered treatmentPathways file we are able to create a sunburst plot.

The inner most layer is the first event that occurs, going outwards. This aligns with the event duration plot we looked at earlier.

    results$plotSunburst()

We can also create a Sankey Diagram, which in theory displays the same data. Additionally you see the Stopped node in the Sankey diagram. This indicates the end of the pathway. It is mostly a practical addition so that single layer Sankey diagrams can still be plotted.

    results$plotSankey()