Type: Package
Title: Create Pathways from Target to Event Cohorts
Version: 0.0.1
Date: 2025-03-18
Maintainer: Gowtham Rao <rao@ohdsi.org>
Description: Software tool designed to compute the temporal relationship defined as pathways between any two instantiated cohorts. The cohorts are input as Target and event cohorts.
Depends: DatabaseConnector (≥ 5.0.0), R (≥ 4.1.0)
Imports: checkmate, dplyr, lifecycle, rlang, SqlRender, tidyr
Suggests: remotes, testthat, withr
License: Apache License version 1.1 | Apache License version 2.0 [expanded from: Apache License]
RoxygenNote: 7.3.2
Encoding: UTF-8
Language: en-US
URL: https://github.com/OHDSI/CohortPathways
BugReports: https://github.com/OHDSI/CohortPathways/issues
NeedsCompilation: no
Packaged: 2025-03-18 15:18:14 UTC; gowth
Author: Gowtham Rao [aut, cre], Chris Knoll [aut], Observational Health Data Science and Informatics [cph]
Repository: CRAN
Date/Publication: 2025-03-19 13:30:02 UTC

CohortPathways: Create Pathways from Target to Event Cohorts

Description

Software tool designed to compute the temporal relationship defined as pathways between any two instantiated cohorts. The cohorts are input as Target and event cohorts.

Author(s)

Maintainer: Gowtham Rao rao@ohdsi.org

Authors:

Other contributors:

See Also

Useful links:

Execute cohort pathway analysis.

Description

Runs the cohort pathways on all instantiated combinations of target and event cohorts. Assumes the cohorts have already been instantiated.

Usage

executeCohortPathways(
  connectionDetails = NULL,
  connection = NULL,
  cohortDatabaseSchema,
  cohortTableName = "cohort",
  tempEmulationSchema = getOption("sqlRenderTempEmulationSchema"),
  targetCohortIds,
  eventCohortIds,
  minCellCount = 5,
  allowRepeats = FALSE,
  maxDepth = 5,
  collapseWindow = 30
)

Arguments

connectionDetails

An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package. Can be left NULL if connection is provided.

connection

An object of type connection as created using the connect function in the DatabaseConnector package. Can be left NULL if connectionDetails is provided, in which case a new connection will be opened at the start of the function, and closed when the function finishes.

cohortDatabaseSchema

Schema name where your cohort tables reside. Note that for SQL Server, this should include both the database and schema name, for example 'scratch.dbo'.

cohortTableName

The name of the cohort table.

tempEmulationSchema

Some database platforms like Oracle and Impala do not truly support temp tables. To emulate temp tables, provide a schema with write privileges where temp tables can be created.

targetCohortIds

A vector of one or more Cohort Ids corresponding to target cohort (s).

eventCohortIds

A vector of one or more Cohort Ids corresponding to event cohort (s).

minCellCount

(Default = 5) The minimum cell count for fields contains person counts or fractions.

allowRepeats

(Default = FALSE) Allow cohort events/combos to appear multiple times in the same pathway.

maxDepth

(Default = 5) Maximum number of steps in a given pathway to be included in the sunburst plot

collapseWindow

(Default = 30) Any dates found within the specified collapse days will be reassigned the earliest date. Collapsing dates reduces pathway variation, leading to a reduction in 'noise' in the result.

Value

                 An array of Data Frame objects.

Examples

## Not run: 

executeCohortPathways(
  connectionDetails = connectionDetails,
  cohorts = cohorts,
  cohortDatabaseSchema = "results"
)

## End(Not run)