| 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:
Chris Knoll cknoll@ohdsi.org
Other contributors:
Observational Health Data Science and Informatics [copyright holder]
See Also
Useful links:
Report bugs at https://github.com/OHDSI/CohortPathways/issues
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
|
connection |
An object of type |
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)