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Intersecting the index and marker cohorts prior to calculating Sequence Symmetry Ratios

Source: R/sequenceCohort.R
sequenceCohort.Rd

Join two tables in the CDM (one for index and the other for marker cohorts) into a new table in the cdm taking into account the maximum time interval between events. Index and marker cohorts should be instantiated in advance by the user.

Usage

sequenceCohort(
  cdm,
  indexCohortTable,
  markerCohortTable,
  name,
  indexCohortId = NULL,
  markerCohortId = NULL,
  cohortDateRange = as.Date(c(NA, NA)),
  sequencePriorObservation = 365,
  indexMarkerWashout = 365,
  indexMarkerGap = Inf,
  combinationWindow = c(0, 365)
)

Arguments

cdm

A CDM reference.

indexCohortTable

A table in the CDM that the index cohorts should come from.

markerCohortTable

A table in the CDM that the marker cohorts should come from.

name

The name within the cdm that the output is called. Default is joined_cohorts.

indexCohortId

Cohort definition IDs in indexCohortTable to be considered for the analysis. Change to NULL if all indices are wished to be included.

markerCohortId

Cohort definition IDs in markerCohortTable to be considered for the analysis. Change to NULL if all markers are wished to be included.

cohortDateRange

Two dates indicating study period and the sequences that the user wants to restrict to.

sequencePriorObservation

The minimum amount of prior observation required on the index marker sequence. Default is 365 days.

indexMarkerWashout

A washout window to be applied on both the index cohort and marker cohort. Default is 365 days.

indexMarkerGap

The maximum allowable gap between the end of the first episode and the start of the second episode in a sequence/combination. Default is Inf.

combinationWindow

A constrain to be placed on the gap between two initiations. Default c(0,365), meaning the gap should be larger than 0 but less than or equal to 365.

Value

A table within the cdm reference.

Examples

# \donttest{
library(CohortSymmetry)
cdm <- mockCohortSymmetry()
cdm$joined_cohorts <- sequenceCohort(
  cdm = cdm,
  name = "joined_cohorts",
  indexCohortTable = "cohort_1",
  markerCohortTable = "cohort_2"
)
 cdm$joined_cohorts
#> # A tibble: 11 × 6
#>    cohort_definition_id subject_id cohort_start_date cohort_end_date index_date
#>  *                <int>      <int> <date>            <date>          <date>    
#>  1                    1          3 2009-09-09        2010-01-01      2009-09-09
#>  2                    6          3 2010-01-01        2010-09-30      2010-01-01
#>  3                    3          1 2019-05-25        2020-04-01      2020-04-01
#>  4                    1          1 2020-04-01        2020-12-30      2020-04-01
#>  5                    2          1 2020-04-01        2021-01-01      2020-04-01
#>  6                    8          4 2021-01-01        2021-05-25      2021-01-01
#>  7                    7          1 2020-12-30        2021-01-01      2021-01-01
#>  8                    2          4 2021-05-25        2021-06-01      2021-06-01
#>  9                    3          4 2021-06-01        2022-05-25      2021-06-01
#> 10                    6          2 2022-05-22        2022-05-25      2022-05-22
#> 11                    5          2 2022-05-22        2022-05-31      2022-05-22
#> # ℹ 1 more variable: marker_date <date>
# }