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> "-29", "40", "10", "20", "69", "-35", "89", "36", "10…
#> $ estimate_name <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value <chr> "6", "7", "6", "10", "5", "5", "5", "5", "3", "9", "9…
#> $ 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> "-212", "328", "45", "-60", "55", "-57", "558", "1", …
#> $ estimate_name <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value <chr> "1", "1", "13", "2", "5", "5", "1", "13", "10", "7", …
#> $ 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> "4412", "482", "-1139", "912", "1784", "253", "-11046…
#> $ estimate_name <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value <chr> "2", "5", "2", "3", "2", "1", "1", "1", "2", "2", "2"…
#> $ 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> "4", "-11", "31", "37", "-15", "-21", "34", "48", "39…
#> $ estimate_name <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value <chr> "71", "18", "5", "5", "8", "7", "5", "2", "2", "10", …
#> $ additional_name <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…