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:
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> "An OMOP CDM database", "An OMOP CDM database", "An O…
#> $ group_name <chr> "index_name &&& marker_name", "index_name &&& marker_…
#> $ 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> "temporal_symmetry", "temporal_symmetry", "temporal_s…
#> $ variable_level <chr> "456", "461", "-390", "-98", "-185", "205", "174", "1…
#> $ 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.
cohort_definition_idThis 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> "An OMOP CDM database", "An OMOP CDM database", "An O…
#> $ group_name <chr> "index_name &&& marker_name", "index_name &&& marker_…
#> $ 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> "temporal_symmetry", "temporal_symmetry", "temporal_s…
#> $ variable_level <chr> "-46", "230", "319", "201", "256", "278", "-119", "-7…
#> $ 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$intersect has cohort_definition_id =1.
timescaleRecall the default for the timescale is month, one could
also change this to either day or year.
summariseTemporalSymmetry(cohort = cdm$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> "An OMOP CDM database", "An OMOP CDM database", "An O…
#> $ group_name <chr> "index_name &&& marker_name", "index_name &&& marker_…
#> $ 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> "temporal_symmetry", "temporal_symmetry", "temporal_s…
#> $ variable_level <chr> "-12000", "-4565", "-8458", "661", "4371", "151", "75…
#> $ estimate_name <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value <chr> "-", "-", "-", "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> "An OMOP CDM database", "An OMOP CDM database", "An O…
#> $ group_name <chr> "index_name &&& marker_name", "index_name &&& marker_…
#> $ 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> "temporal_symmetry", "temporal_symmetry", "temporal_s…
#> $ variable_level <chr> "38", "25", "59", "41", "-14", "32", "9", "5", "27", …
#> $ estimate_name <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value <chr> "-", "11", "-", "-", "11", "8", "58", "62", "12", "-"…
#> $ additional_name <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…