OMOP CDM Helper

This class facilitates the creation of tables from a connection to an OMOP CDM database.

Public fields

OMOPCDMDatabase

An object representing the connection to the OMOP CDM database.

symbol

A symbol used to reference the retrieved data in the DataSHIELD environment.

Constructor for OMOP CDM Helper

Methods

Public methods

• OMOPCDMHelper$new()

• OMOPCDMHelper$append()

• OMOPCDMHelper$tables()

• OMOPCDMHelper$columns()

• OMOPCDMHelper$concepts()

• OMOPCDMHelper$auto()

• OMOPCDMHelper$get()

• OMOPCDMHelper$clone()

---

Method new()

Usage

OMOPCDMHelper$new(
  connections,
  resource,
  symbol,
  personColumns = NULL,
  personFilter = NULL,
  ...
)

Arguments

connections

Connection object to the DataSHIELD server.

resource

Either an identifier or a named list of identifiers for the specific resource(s) within the DataSHIELD server(s). If a named list, the name of each resource identifier should correspond to the server name in the connections.

symbol

A character string representing the symbol to which the resource will be assigned.

personColumns

Optional; a vector of column names to filter from the person table.

personFilter

Optional; a character string representing another object in the DataSHIELD environment whose person IDs will be used to filter the processed data (this speeds up the processing of the data if not all the person IDs are needed).

...

Additional parameters to be passed to the underlying get method.

Returns

An object of class OMOPCDMHelper.

---

Method append()

Usage

OMOPCDMHelper$append(
  table,
  columns = NULL,
  concepts = NULL,
  merge.x = NULL,
  merge.y = NULL,
  ...
)

---

Method tables()

Usage

OMOPCDMHelper$tables()

---

Method columns()

Usage

OMOPCDMHelper$columns(tables = NULL)

---

Method concepts()

Usage

OMOPCDMHelper$concepts(tables = NULL, max_length = 60)

---

Method auto()

Usage

OMOPCDMHelper$auto(
  tables = NULL,
  columns = NULL,
  concepts = NULL,
  silent = FALSE,
  ...
)

---

Method get()

Usage

OMOPCDMHelper$get(
  table,
  symbol = NULL,
  columnFilter = NULL,
  conceptFilter = NULL,
  personFilter = NULL,
  mergeColumn = NULL,
  dropNA = FALSE,
  ...
)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

OMOPCDMHelper$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.