Step 4: Obtain aggregated data on temporal symmetry

Introduction

In this vignette we will explore the functionality and arguments of summariseTemporalSymmetry() function. This function uses cdm$intersect introduced in the previous vignette Step 1. Generate a sequence cohort to produce aggregated statistics containing the frequency for different time gaps between the initiation of the marker and the initiation of the index (marker_date − index_date). The work of this function is best illustrated via an example.

Recall that in the previous vignette, we’ve used cdm$aspirin and cdm$acetaminophen to generate cdm$intersect like so:

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

Obtaining temporal symmetry

summariseTemporalSymmetry(cohort = cdm$intersect) |> 
  dplyr::glimpse()
#> Rows: 558
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
#> $ group_name       <chr> "index_name &&& marker_name", "index_name &&& marker_…
#> $ group_level      <chr> "1191_aspirin &&& 161_acetaminophen", "1191_aspirin &…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "temporal_symmetry", "temporal_symmetry", "temporal_s…
#> $ variable_level   <chr> "456", "461", "-83", "-313", "-374", "-183", "365", "…
#> $ estimate_name    <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type    <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value   <chr> "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"…
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

The default unit of the difference of two initiations is measured in months. In this example, the first row is showing there are 6 cases of index happening after marker with the gap being 29 months whereas the second row is showing there are 7 cases of index happening before marker with the gap being 40 months.

Modify the cohort based on cohort_definition_id

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

summariseTemporalSymmetry(cohort = cdm$intersect,
                          cohortId = 1) |> 
  dplyr::glimpse()
#> Rows: 558
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
#> $ group_name       <chr> "index_name &&& marker_name", "index_name &&& marker_…
#> $ group_level      <chr> "1191_aspirin &&& 161_acetaminophen", "1191_aspirin &…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "temporal_symmetry", "temporal_symmetry", "temporal_s…
#> $ variable_level   <chr> "-242", "474", "274", "419", "440", "-46", "230", "31…
#> $ estimate_name    <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type    <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value   <chr> "-", "-", "-", "-", "-", "-", "-", "-", "-", "-", "-"…
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

Of course and once again this does nothing because every entry in cdm$intersect has cohort_definition_id  = 1.

Modify timescale

Recall the default for the timescale is month, one could also change this to either day or year.

summariseTemporalSymmetry(cohort = cdm$intersect,
                          timescale = "day") |> 
  dplyr::glimpse()
#> Rows: 1,350
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
#> $ group_name       <chr> "index_name &&& marker_name", "index_name &&& marker_…
#> $ group_level      <chr> "1191_aspirin &&& 161_acetaminophen", "1191_aspirin &…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "temporal_symmetry", "temporal_symmetry", "temporal_s…
#> $ variable_level   <chr> "-12000", "8941", "-4565", "-8458", "11444", "-388", …
#> $ estimate_name    <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type    <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value   <chr> "-", "-", "-", "-", "-", "-", "5", "-", "5", "-", "-"…
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…
summariseTemporalSymmetry(cohort = cdm$intersect,
                          timescale = "year") |> 
  dplyr::glimpse()
#> Rows: 94
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name         <chr> "Synthea synthetic health database", "Synthea synthet…
#> $ group_name       <chr> "index_name &&& marker_name", "index_name &&& marker_…
#> $ group_level      <chr> "1191_aspirin &&& 161_acetaminophen", "1191_aspirin &…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "temporal_symmetry", "temporal_symmetry", "temporal_s…
#> $ variable_level   <chr> "-49", "57", "-17", "-42", "-25", "16", "30", "-6", "…
#> $ estimate_name    <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type    <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value   <chr> "-", "-", "5", "-", "-", "11", "11", "33", "41", "-",…
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…
CDMConnector::cdmDisconnect(cdm = cdm)