# Step 2. Obtain the sequence ratios

# Introduction

In this vignette we will explore the functionality and arguments of `summariseSequenceRatios()` function, which is used to generate the sequence ratios of the SSA. As this function uses the output of `generateSequenceCohortSet()` function (explained in detail in the vignette: Step 1. Generate a sequence cohort), we will pick up the explanation from where we left off in the previous vignette.

Recall that in the previous vignette: Step 1. Generate a sequence cohort, we’ve generated `cdm$aspirin` and `cdm$acetaminophen` before and using them we could generate `cdm$intersect` like so:

    # Generate a sequence cohort
    cdm <- generateSequenceCohortSet(
      cdm = cdm,
      indexTable = "aspirin",
      markerTable = "acetaminophen",
      name = "intersect",
      combinationWindow = c(0,Inf))

# Obtain sequence ratios

One can obtain the crude and adjusted sequence ratios (with its corresponding confidence intervals) using `summariseSequenceRatios()` function:

    summariseSequenceRatios(
      cohort = cdm$intersect
    ) %>%
      dplyr::glimpse()
    #> Rows: 10
    #> Columns: 13
    #> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
    #> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
    #> $ group_name       <chr> "index_cohort_name &&& marker_cohort_name", "index_co…
    #> $ group_level      <chr> "aspirin &&& acetaminophen", "aspirin &&& acetaminoph…
    #> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ variable_name    <chr> "crude", "adjusted", "crude", "crude", "adjusted", "a…
    #> $ variable_level   <chr> "sequence_ratio", "sequence_ratio", "sequence_ratio",…
    #> $ estimate_name    <chr> "point_estimate", "point_estimate", "lower_CI", "uppe…
    #> $ estimate_type    <chr> "numeric", "numeric", "numeric", "numeric", "numeric"…
    #> $ estimate_value   <chr> "1.8108504398827", "1.78715329996299", "1.64970963817…
    #> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

The obtained output has a summarised result format. In the later vignette (Step 3. Visualise results) we will explore how to visualise the results in a more intuitive way.

## Modify the cohort based on `cohort_definition_id`

This parameter is used to subset the cohort table inputted to the `summariseSequenceRatios()`. Imagine the user only wants to include `cohort_definition_id` \(= 1\) from `cdm$intersect` in the `summariseSequenceRatios()`, then one could do the following:

    summariseSequenceRatios(cohort = cdm$intersect,
                              cohortId = 1) %>%
      dplyr::glimpse()
    #> Rows: 10
    #> Columns: 13
    #> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
    #> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
    #> $ group_name       <chr> "index_cohort_name &&& marker_cohort_name", "index_co…
    #> $ group_level      <chr> "aspirin &&& acetaminophen", "aspirin &&& acetaminoph…
    #> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ variable_name    <chr> "crude", "adjusted", "crude", "crude", "adjusted", "a…
    #> $ variable_level   <chr> "sequence_ratio", "sequence_ratio", "sequence_ratio",…
    #> $ estimate_name    <chr> "point_estimate", "point_estimate", "lower_CI", "uppe…
    #> $ estimate_type    <chr> "numeric", "numeric", "numeric", "numeric", "numeric"…
    #> $ estimate_value   <chr> "1.8108504398827", "1.78715329996299", "1.64970963817…
    #> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

Of course in this case this does nothing because every entry in `cdm$intersect` has `cohort_definition_id` \(= 1\).

## Modify `confidenceInterval`

By default, the `summariseSequenceRatios()` function will use 95% (two-sided) confidence interval. If another confidence interval is desired, for example 99% confidence interval, one can use the `confidenceInterval` argument:

    summariseSequenceRatios(
      cohort = cdm$intersect,
      confidenceInterval = 99) %>%
      dplyr::glimpse()
    #> Rows: 10
    #> Columns: 13
    #> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
    #> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
    #> $ group_name       <chr> "index_cohort_name &&& marker_cohort_name", "index_co…
    #> $ group_level      <chr> "aspirin &&& acetaminophen", "aspirin &&& acetaminoph…
    #> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ variable_name    <chr> "crude", "adjusted", "crude", "crude", "adjusted", "a…
    #> $ variable_level   <chr> "sequence_ratio", "sequence_ratio", "sequence_ratio",…
    #> $ estimate_name    <chr> "point_estimate", "point_estimate", "lower_CI", "uppe…
    #> $ estimate_type    <chr> "numeric", "numeric", "numeric", "numeric", "numeric"…
    #> $ estimate_value   <chr> "1.8108504398827", "1.78715329996299", "1.60240541369…
    #> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

## Modify `movingAverageRestriction`

The idea of moving average restriction is necessary only for the null sequence ratio calculation, please refer to Lai et al. (2017) for more details on this parameter (parameter d when calculating P in page 578). Following Tsiropoulos et al. (2009), by default, the argument `movingAverageRestriction` is set to be \(548\) (\(18\) months). Should one wish to modify this, one could do something like:

    summariseSequenceRatios(
      cohort = cdm$intersect,
      movingAverageRestriction = 600) %>%
      dplyr::glimpse()
    #> Rows: 10
    #> Columns: 13
    #> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
    #> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
    #> $ group_name       <chr> "index_cohort_name &&& marker_cohort_name", "index_co…
    #> $ group_level      <chr> "aspirin &&& acetaminophen", "aspirin &&& acetaminoph…
    #> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ variable_name    <chr> "crude", "adjusted", "crude", "crude", "adjusted", "a…
    #> $ variable_level   <chr> "sequence_ratio", "sequence_ratio", "sequence_ratio",…
    #> $ estimate_name    <chr> "point_estimate", "point_estimate", "lower_CI", "uppe…
    #> $ estimate_type    <chr> "numeric", "numeric", "numeric", "numeric", "numeric"…
    #> $ estimate_value   <chr> "1.8108504398827", "1.78574458428809", "1.64970963817…
    #> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

## Modify `minCellCount`

By default, the minimum number of events to reported is 5, below which results will be obscured. If 0, all results will be reported and the user could do this via:

    summariseSequenceRatios(cohort = cdm$intersect,
                            minCellCount = 0) %>%
      dplyr::glimpse()
    #> Rows: 10
    #> Columns: 13
    #> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
    #> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
    #> $ group_name       <chr> "index_cohort_name &&& marker_cohort_name", "index_co…
    #> $ group_level      <chr> "aspirin &&& acetaminophen", "aspirin &&& acetaminoph…
    #> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ variable_name    <chr> "crude", "adjusted", "crude", "crude", "adjusted", "a…
    #> $ variable_level   <chr> "sequence_ratio", "sequence_ratio", "sequence_ratio",…
    #> $ estimate_name    <chr> "point_estimate", "point_estimate", "lower_CI", "uppe…
    #> $ estimate_type    <chr> "numeric", "numeric", "numeric", "numeric", "numeric"…
    #> $ estimate_value   <chr> "1.8108504398827", "1.78715329996299", "1.64970963817…
    #> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
    #> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…