### Index breakdown

```{r}
#| label: characterization_index_target
#| echo: false
#| results: 'asis'

# check ROhdsiWebApi installed and skip otherwise
if(system.file(package = "ROhdsiWebApi") != ""){

# TARGET
  
targetIds <- cohortDefinitions %>%
  dplyr::filter(.data$subsetParent == params$targetId) %>%
  dplyr::arrange(.data$order, .data$cohortDefinitionId) %>%
  dplyr::select("cohortDefinitionId") 
targetIds <- targetIds$cohortDefinitionId

for(i in 1:length(params$outcomeIds)){
  jsonList <- ParallelLogger::convertJsonToSettings(json = cohortDefinitions$json[cohortDefinitions$cohortDefinitionId == params$outcomeIds[i]])
  
  if(!is.null(params$authMethod)){
  ROhdsiWebApi::authorizeWebApi(
    baseUrl = params$webAPI, 
    authMethod = params$authMethod, 
    webApiUsername = params$webApiUsername, 
    webApiPassword = params$webApiPassword
  )
  }
  
  conceptsInOutcome <- c()
  if(length(jsonList$ConceptSets)>0){
    for(jListInd in 1:length(jsonList$ConceptSets)){
      conceptsInOutcome <- unique(c(conceptsInOutcome, ROhdsiWebApi::resolveConceptSet(
        conceptSetDefinition = jsonList$ConceptSets[[jListInd]], 
        baseUrl = params$webAPI
      )))
    }
  }

  for(j in 1:length(targetIds)){
    
    res <- OhdsiReportGenerator::getBinaryCaseSeries(
      connectionHandler = connectionHandler, 
      schema = params$schema, 
      targetId = targetIds[j], 
      outcomeId = params$outcomeIds[i],
      conceptIds = unique(conceptsInOutcome),
      minVal = 0.01
    )

        if(nrow(res)>0){
    
    res <- OhdsiReportGenerator::addTarColumn(res) 
    
    # make the covariateName nicer
    res <- OhdsiReportGenerator::formatBinaryCovariateName(res)
    
    counts <- OhdsiReportGenerator::getCaseCounts(
      connectionHandler = connectionHandler, 
      schema = params$schema, 
      targetIds = targetIds[j], 
      outcomeIds = params$outcomeIds[i] 
    ) 
    counts <- OhdsiReportGenerator::addTarColumn(counts) %>%
      dplyr::select("databaseName", "personCount", "tar")
    
    index <- res %>% 
      dplyr::filter(.data$type == 'During') %>%
      dplyr::select("databaseName", "targetCohortId", "outcomeCohortId",
                    "covariateName", 
                    "averageValue", "tar") %>% 
      dplyr::inner_join(counts, by = c("databaseName", "tar"))
    
    aggreggateIndex <- index %>% 
      dplyr::group_by(.data$targetCohortId, .data$outcomeCohortId, .data$covariateName, .data$tar) %>%
      dplyr::summarise(
        averageValue = mean(.data$averageValue, na.rm = T),
        personCount = 0
      ) %>%
      dplyr::mutate(
        databaseName = 'all'
      )
    
    # add the combined that will be used to order table
    index <- dplyr::bind_rows(index, aggreggateIndex)
    
  tempCd <- cohortDefinitions[,c("friendlyName","subsetText","cohortDefinitionId")]
colnames(tempCd) <- paste0(colnames(tempCd), 'Target')
index <- merge(index, tempCd, by.x = 'targetCohortId', by.y = 'cohortDefinitionIdTarget')
tempCd <- cohortDefinitions[,c("friendlyName","subsetText","cohortDefinitionId")]
colnames(tempCd) <- paste0(colnames(tempCd), 'Outcome')
index <- merge(index, tempCd, by.x = 'outcomeCohortId', by.y = 'cohortDefinitionIdOutcome')

ibOutcome <- unique(index$friendlyNameOutcome)

# now we add the N to the databaseName we need to loop over TAR
for(ibTar in unique(index$tar)){

indexTar <- tidyr::pivot_wider(
  data = index %>%
    dplyr::filter(.data$tar == !!ibTar) %>% 
    dplyr::select(-"tar") %>%
    dplyr::mutate(
      databaseName = paste0(.data$databaseName, ' (N = ', 
                            ifelse(.data$personCount >= 0 ,
                                   .data$personCount,
                                   paste0('<',abs(.data$personCount))
                                   ),')')
      ) 
    , 
  names_from = "databaseName", 
  #values_from = c("sumValue","averageValue"), 
  values_from = c("averageValue"), 
  id_cols = c("covariateName","friendlyNameTarget","subsetTextTarget")
) %>%
    dplyr::arrange(-1*.data$`all (N = 0)`) %>%
  dplyr::select(-"all (N = 0)") %>%
  dplyr::group_by(
    .data$friendlyNameTarget,.data$subsetTextTarget
  )

# display

boxName <- paste0('Frequency of ',ibOutcome,' concept codes when the patient exposed to ', indexTar$friendlyNameTarget[1], ' ', indexTar$subsetTextTarget[1],' has the outcome during ', ibTar)

  cat('\n\n::: {.callout-note collapse="true"}')
  cat(paste0("\n# ",boxName, '\n\n'))
      
print(htmltools::tagList(
  indexTar  %>%  
    gt::gt() %>%
    gt::fmt_percent(
      columns = colnames(indexTar)[! colnames(indexTar) %in% c("covariateName","friendlyNameTarget","subsetTextTarget", "friendlyNameOutcome", "tar")],
      decimals = 2
    ) %>%
    gt::cols_label(
      covariateName = "Covariate"
    ) %>%
    gt::tab_options(
      heading.align = "left",
      data_row.padding = gt::px(7),
      column_labels.font.size = gt::px(12),
      column_labels.background.color = "#EB1800",
      column_labels.font.weight = "bold",
      row_group.background.color = "#D3D3D3",
      row_group.font.weight = "bold"
    ) %>%
    gt::tab_style(
      style = gt::cell_text(
        color = "darkgrey",
        font = gt::google_font("Source Sans Pro"),
        transform = "uppercase"
      ),
      locations = gt::cells_column_labels(gt::everything())
    ) %>%
    gt::tab_header(
      title = paste0('Frequency of ',ibOutcome,' concept codes when the patient in the target cohort has the outcome during ', ibTar)
    )
))

cat('\n\n:::\n\n')

} # end tar loop
  
    } # if res has results
  
  }


}

}

```