Type:	Package
Version:	1.4.0
Title:	'DataSHIELD' Implementation on Local Datasets
Depends:	R (≥ 3.5.0), DSI (≥ 1.5), methods, R6, rly
Suggests:	resourcer, knitr, testthat, rmarkdown
Description:	'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This 'DataSHIELD Interface' implementation is for analyzing datasets living in the current R session. The purpose of this is primarily for lightweight 'DataSHIELD' analysis package development.
License:	LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2.1)]
URL:	https://github.com/datashield/DSLite/, https://datashield.github.io/DSLite/, https://www.datashield.org/, https://doi.org/10.1093/ije/dyu188
BugReports:	https://github.com/datashield/DSLite/issues/
RoxygenNote:	7.2.1
VignetteBuilder:	knitr
Encoding:	UTF-8
Collate:	'DSLiteDriver.R' 'DSLiteConnection.R' 'DSLiteResult.R' 'DSLiteServer.R' 'ast.R' 'data.cnsim.R' 'data.dasim.R' 'data.discordant.R' 'data.survival.R' 'data.testing.dataset.R' 'defaultDSConfiguration.R' 'getDSLiteData.R' 'lex-yacc.R' 'setupCNSIMTest.R' 'setupDASIMTest.R' 'setupDATASETTest.R' 'setupDISCORDANTTest.R' 'setupDSLiteServer.R' 'setupSURVIVALTest.R' 'testParse.R'
NeedsCompilation:	no
Packaged:	2022-10-07 08:28:49 UTC; yannick
Author:	Yannick Marcon [aut, cre]
Maintainer:	Yannick Marcon <yannick.marcon@obiba.org>
Repository:	CRAN
Date/Publication:	2022-10-07 09:00:02 UTC

Parse a key pairs string to a list

Description

Parse a key pairs string to a list

Usage

.strToList(str, pack = NULL)

Binary operation AST node

Description

AST node that represents a binary operation (such as '+', '-' etc.), and therefore having two child nodes.

Super class

DSLite::Node -> BinaryOpNode

Methods

Public methods

• BinaryOpNode$add_child()

• BinaryOpNode$to_string()

• BinaryOpNode$clone()

Method add_child()

Two children

Usage

BinaryOpNode$add_child(val)

Arguments

Method to_string()

Get the string representation of the BinaryOpNode

Usage

BinaryOpNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

BinaryOpNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: FormulaNode, FunctionNode, GroupNode, Node, NumericNode, ParameterNode, RangeNode, StringNode, SymbolNode, UnaryOpNode

Simulated dataset CNSIM 1

Description

Simulated dataset CNSIM 1, in a data.frame with 2163 observations of 11 harmonized variables. The CNSIM dataset contains synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of the obesity methodological development project. This dataset does contain some NA values.

Details

Simulated dataset CNSIM 2

Description

Simulated dataset CNSIM 1, in a data.frame with 3088 observations of 11 harmonized variables variables. The CNSIM dataset contains synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of the obesity methodological development project. This dataset does contain some NA values.

Details

Simulated dataset CNSIM 3

Description

Simulated dataset CNSIM 1, in a data.frame with 4128 observations of 11 harmonized variables variables. The CNSIM dataset contains synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of the obesity methodological development project. This dataset does contain some NA values.

Details

Simulated dataset DASIM 1

Description

Simulated dataset DASIM 1, in a data.frame with 10000 observations of 10 harmonized variables. The DASIM dataset contains synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of the obesity methodological development project. This dataset does not contain some NA values.

Details

Simulated dataset DASIM 2

Description

Simulated dataset DASIM 2, in a data.frame with 10000 observations of 10 harmonized variables. The DASIM dataset contains synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of the obesity methodological development project. This dataset does not contain some NA values.

Details

Simulated dataset DASIM 3

Description

Simulated dataset DASIM 3, in a data.frame with 10000 observations of 10 harmonized variables. The DASIM dataset contains synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of the obesity methodological development project. This dataset does not contain some NA values.

Details

Simulated dataset DISCORDANT 1

Description

Simulated dataset DISCORDANT 1, in a data.frame with 12 observations of 2 discordant variables.

Details

Simulated dataset DISCORDANT 2

Description

Simulated dataset DISCORDANT 2, in a data.frame with 12 observations of 2 discordant variables.

Details

Simulated dataset DISCORDANT 3

Description

Simulated dataset DISCORDANT 3, in a data.frame with 12 observations of 2 discordant variables.

Details

Create a DSLite driver

Description

Convenient function for creating a DSLiteDriver object.

Usage

DSLite()

Class DSLiteConnection.

Description

An DSLiteServer connection implementing the DataSHIELD Interface (DSI) DSConnection-class.

Class DSLiteDriver with constructor DSLite.

Description

An DSLite driver implementing the DataSHIELD Interface (DSI) DSDriver-class. This class should always be initialized with the DSLite function. It returns a singleton that allows you to connect to DSlite.

Class DSLiteResult.

Description

An DSLite result implementing the DataSHIELD Interface (DSI) DSResult-class.

Lightweight DataSHIELD server-side component

Description

DSLiteServer mimics a DataSHIELD server by holding datasets and exposing DataSHIELD-like functions: aggregate and assign. A DataSHIELD session is a R environment where the assignment and the operations happen.

Methods

Public methods

• DSLiteServer$new()

• DSLiteServer$config()

• DSLiteServer$profile()

• DSLiteServer$strict()

• DSLiteServer$home()

• DSLiteServer$workspaces()

• DSLiteServer$workspace_save()

• DSLiteServer$workspace_restore()

• DSLiteServer$workspace_rm()

• DSLiteServer$aggregateMethods()

• DSLiteServer$aggregateMethod()

• DSLiteServer$assignMethods()

• DSLiteServer$assignMethod()

• DSLiteServer$options()

• DSLiteServer$option()

• DSLiteServer$newSession()

• DSLiteServer$hasSession()

• DSLiteServer$getSession()

• DSLiteServer$getSessionIds()

• DSLiteServer$getSessionData()

• DSLiteServer$closeSession()

• DSLiteServer$tableNames()

• DSLiteServer$hasTable()

• DSLiteServer$resourceNames()

• DSLiteServer$hasResource()

• DSLiteServer$symbols()

• DSLiteServer$symbol_rm()

• DSLiteServer$assignTable()

• DSLiteServer$assignResource()

• DSLiteServer$assignExpr()

• DSLiteServer$aggregate()

• DSLiteServer$clone()

Method new()

Create new DSLiteServer instance. See defaultDSConfiguration function for including or excluding packages when discovering the DataSHIELD configuration from the DataSHIELD server-side packages (meta-data from the DESCRIPTION files).

Usage

DSLiteServer$new(
  tables = list(),
  resources = list(),
  config = DSLite::defaultDSConfiguration(),
  strict = TRUE,
  home = file.path(tempdir(), ".dslite"),
  profile = "default"
)

Arguments

Returns

A DSLiteServer object

Method config()

Get or set the DataSHIELD configuration.

Usage

DSLiteServer$config(value)

Arguments

Returns

The DataSHIELD configuration, if no parameter is provided.

Method profile()

Get or set the DataSHIELD profile name.

Usage

DSLiteServer$profile(value)

Arguments

Returns

The DataSHIELD profile, if no parameter is provided.

Method strict()

Get or set the level of strictness (stop when function call is not configured)

Usage

DSLiteServer$strict(value)

Arguments

Returns

The strict field if no parameter is provided.

Method home()

Get or set the home folder location where are located the session work directories and where to read and dump workspace images.

Usage

DSLiteServer$home(value)

Arguments

Returns

The home folder path if no parameter is provided.

Method workspaces()

List the saved workspaces in the home folder.

Usage

DSLiteServer$workspaces(prefix = NULL)

Arguments

Method workspace_save()

Save the session's workspace image identified by the sid identifier with the provided name in the home folder.

Usage

DSLiteServer$workspace_save(sid, name)

Arguments

Method workspace_restore()

Restore a saved session's workspace image into the session identified by the sid identifier with the provided name in the home folder.

Usage

DSLiteServer$workspace_restore(sid, name)

Arguments

Method workspace_rm()

Remove the workspace image with the provided name from the home folder.

Usage

DSLiteServer$workspace_rm(name)

Arguments

Method aggregateMethods()

Get or set the aggregate methods.

Usage

DSLiteServer$aggregateMethods(value)

Arguments

Returns

The aggregate methods when no parameter is provided.

Method aggregateMethod()

Get or set an aggregate method.

Usage

DSLiteServer$aggregateMethod(name, value)

Arguments

Returns

The aggregate method when no value parameter is provided.

Method assignMethods()

Get or set the assign methods.

Usage

DSLiteServer$assignMethods(value)

Arguments

Returns

The assign methods when no parameter is provided.

Method assignMethod()

Get or set an assign method.

Usage

DSLiteServer$assignMethod(name, value)

Arguments

Returns

The assign method when no value parameter is provided.

Method options()

Get or set the DataSHIELD R options that are applied when a new DataSHIELD session is started.

Usage

DSLiteServer$options(value)

Arguments

Returns

The R options when no parameter is provided.

Method option()

Get or set a R option.

Usage

DSLiteServer$option(key, value)

Arguments

Returns

The R option's value when only key parameter is provided.

Method newSession()

Create a new DataSHIELD session (contained execution environment), apply options that are defined in the DataSHIELD configuration and restore workspace image if restore workspace name argument is provided.

Usage

DSLiteServer$newSession(restore = NULL, profile = NULL)

Arguments

Method hasSession()

Check a DataSHIELD session is alive.

Usage

DSLiteServer$hasSession(sid)

Arguments

Method getSession()

Get the DataSHIELD session's environment.

Usage

DSLiteServer$getSession(sid)

Arguments

Method getSessionIds()

Get the DataSHIELD session IDs.

Usage

DSLiteServer$getSessionIds()

Method getSessionData()

Get the symbol value from the DataSHIELD session's environment.

Usage

DSLiteServer$getSessionData(sid, symbol)

Arguments

Method closeSession()

Destroy DataSHIELD session and save workspace image if save workspace name argument is provided.

Usage

DSLiteServer$closeSession(sid, save = NULL)

Arguments

Method tableNames()

List the names of the tables that can be assigned.

Usage

DSLiteServer$tableNames()

Method hasTable()

Check a table exists.

Usage

DSLiteServer$hasTable(name)

Arguments

Method resourceNames()

List the names of the resources (resourcer::Resource objects) that can be assigned.

Usage

DSLiteServer$resourceNames()

Method hasResource()

Check a resource (resourcer::Resource object) exists.

Usage

DSLiteServer$hasResource(name)

Arguments

Method symbols()

List the symbols living in a DataSHIELD session.

Usage

DSLiteServer$symbols(sid)

Arguments

Method symbol_rm()

Remove a symbol from a DataSHIELD session.

Usage

DSLiteServer$symbol_rm(sid, name)

Arguments

Method assignTable()

Assign a table to a symbol in a DataSHIELD session. Filter table columns with the variables names provided.

Usage

DSLiteServer$assignTable(sid, symbol, name, variables = NULL, id.name = NULL)

Arguments

Method assignResource()

Assign a resource as a resourcer::ResourceClient object to a symbol in a DataSHIELD session.

Usage

DSLiteServer$assignResource(sid, symbol, name)

Arguments

Method assignExpr()

Evaluate an assignment expression in a DataSHIELD session.

Usage

DSLiteServer$assignExpr(sid, symbol, expr)

Arguments

Method aggregate()

Evaluate an aggregate expression in a DataSHIELD session.

Usage

DSLiteServer$aggregate(sid, expr)

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

DSLiteServer$clone(deep = FALSE)

Arguments

See Also

Other server-side items: newDSLiteServer()

Formula AST node

Description

AST node that reprsents a formula (such as NAME ~ terms).

Super class

DSLite::Node -> FormulaNode

Methods

Public methods

• FormulaNode$add_child()

• FormulaNode$to_string()

• FormulaNode$clone()

Method add_child()

Two children

Usage

FormulaNode$add_child(val)

Arguments

Method to_string()

Get the string representation of the BinaryOpNode

Usage

FormulaNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

FormulaNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FunctionNode, GroupNode, Node, NumericNode, ParameterNode, RangeNode, StringNode, SymbolNode, UnaryOpNode

Function AST node

Description

AST node that represents a function with its arguments.

Super class

DSLite::Node -> FunctionNode

Methods

Public methods

• FunctionNode$to_string()

• FunctionNode$clone()

Method to_string()

Get the string representation of the FunctionNode

Usage

FunctionNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

FunctionNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, GroupNode, Node, NumericNode, ParameterNode, RangeNode, StringNode, SymbolNode, UnaryOpNode

Group AST node

Description

AST node that reprsents a group of tokens enclosed by parenthesis.

Super class

DSLite::Node -> GroupNode

Methods

Public methods

• GroupNode$to_string()

• GroupNode$clone()

Method to_string()

Get the string representation of the GroupNode

Usage

GroupNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

GroupNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, FunctionNode, Node, NumericNode, ParameterNode, RangeNode, StringNode, SymbolNode, UnaryOpNode

Simple AST node

Description

Abstract Syntaxic Tree (AST) node that will be created by the DSLite R parser.

Public fields

Methods

Public methods

• Node$new()

• Node$set_parent()

• Node$add_child()

• Node$to_string()

• Node$to_string_children()

• Node$accept()

• Node$clone()

Method new()

Simple node constructor

Usage

Node$new(name = NA, parent = NA)

Arguments

Returns

A Node object

Method set_parent()

Set parent Node

Usage

Node$set_parent(val)

Arguments

Method add_child()

Add a child Node

Usage

Node$add_child(val)

Arguments

Method to_string()

The string representation of the Node

Usage

Node$to_string()

Method to_string_children()

Get the string representation of the Node's children

Usage

Node$to_string_children()

Method accept()

Accept visitor

Usage

Node$accept(visitor)

Arguments

Method clone()

The objects of this class are cloneable with this method.

Usage

Node$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, FunctionNode, GroupNode, NumericNode, ParameterNode, RangeNode, StringNode, SymbolNode, UnaryOpNode

Numeric AST node

Description

AST node that reprsents a numeric (integer or float) value.

Super class

DSLite::Node -> NumericNode

Methods

Public methods

• NumericNode$add_child()

• NumericNode$to_string()

• NumericNode$clone()

Method add_child()

No children

Usage

NumericNode$add_child(val)

Arguments

Method to_string()

Get the string representation of the NumericNode

Usage

NumericNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

NumericNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, FunctionNode, GroupNode, Node, ParameterNode, RangeNode, StringNode, SymbolNode, UnaryOpNode

Parameter AST node

Description

AST node that represents a function's named parameter (such as NAME = expression).

Super class

DSLite::Node -> ParameterNode

Methods

Public methods

• ParameterNode$add_child()

• ParameterNode$to_string()

• ParameterNode$clone()

Method add_child()

Two children

Usage

ParameterNode$add_child(val)

Arguments

Method to_string()

Get the string representation of the BinaryOpNode

Usage

ParameterNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

ParameterNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, FunctionNode, GroupNode, Node, NumericNode, RangeNode, StringNode, SymbolNode, UnaryOpNode

Range AST node

Description

AST node that represents a range of values (such as min expression:max expression), therefore having two child nodes.

Super class

DSLite::Node -> RangeNode

Methods

Public methods

• RangeNode$add_child()

• RangeNode$to_string()

• RangeNode$clone()

Method add_child()

Two children

Usage

RangeNode$add_child(val)

Arguments

Method to_string()

Get the string representation of the BinaryOpNode

Usage

RangeNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

RangeNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, FunctionNode, GroupNode, Node, NumericNode, ParameterNode, StringNode, SymbolNode, UnaryOpNode

Simulated survival expand-with-missing dataset 1

Description

Simulated dataset SURVIVAL.EXPAND_WITH_MISSING 1, in a data.frame with 2060 observations of 12 harmonized variables. The dataset contains synthetic data based on a simulated survival model, including a censoring indicator.

Details

Simulated survival expand-with-missing dataset 2

Description

Simulated dataset SURVIVAL.EXPAND_WITH_MISSING 2, in a data.frame with 1640 observations of 12 harmonized variables. The dataset contains synthetic data based on a simulated survival model, including a censoring indicator.

Details

Simulated survival expand-with-missing dataset 3

Description

Simulated dataset SURVIVAL.EXPAND_WITH_MISSING 3, in a data.frame with 2688 observations of 12 harmonized variables. The dataset contains synthetic data based on a simulated survival model, including a censoring indicator.

Details

String AST node

Description

AST node that represent a string value, either single or double quoted.

Super class

DSLite::Node -> StringNode

Methods

Public methods

• StringNode$add_child()

• StringNode$to_string()

• StringNode$clone()

Method add_child()

No children

Usage

StringNode$add_child(val)

Arguments

Method to_string()

Get the string representation of the StringNode

Usage

StringNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

StringNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, FunctionNode, GroupNode, Node, NumericNode, ParameterNode, RangeNode, SymbolNode, UnaryOpNode

Symbol AST node

Description

AST node that represents a R symbol (variable name, function name etc.).

Super class

DSLite::Node -> SymbolNode

Methods

Public methods

• SymbolNode$add_child()

• SymbolNode$to_string()

• SymbolNode$clone()

Method add_child()

No children

Usage

SymbolNode$add_child(val)

Arguments

Method to_string()

Get the string representation of the SymbolNode

Usage

SymbolNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

SymbolNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, FunctionNode, GroupNode, Node, NumericNode, ParameterNode, RangeNode, StringNode, UnaryOpNode

Simulated dataset TESTING.DATASET 1

Description

Simulated dataset TESTING.DATASET 1, in a data.frame with 71 observations of 17 harmonized variables.

Details

Simulated dataset TESTING.DATASET 2

Description

Simulated dataset TESTING.DATASET 2, in a data.frame with 71 observations of 17 harmonized variables.

Details

Simulated dataset TESTING.DATASET 3

Description

Simulated dataset TESTING.DATASET 3, in a data.frame with 71 observations of 17 harmonized variables.

Details

Unary operator AST node

Description

AST node that represents a unary operator (such as '-'), therefore having a single child node.

Super class

DSLite::Node -> UnaryOpNode

Methods

Public methods

• UnaryOpNode$add_child()

• UnaryOpNode$to_string()

• UnaryOpNode$clone()

Method add_child()

One children

Usage

UnaryOpNode$add_child(val)

Arguments

Method to_string()

Get the string representation of the UnaryOpNode

Usage

UnaryOpNode$to_string()

Method clone()

The objects of this class are cloneable with this method.

Usage

UnaryOpNode$clone(deep = FALSE)

Arguments

See Also

Other parser items: BinaryOpNode, FormulaNode, FunctionNode, GroupNode, Node, NumericNode, ParameterNode, RangeNode, StringNode, SymbolNode

Default DataSHIELD configuration

Description

Find the R packages that have DataSHIELD server configuration information in them and extract this information in a data frame of aggregation/assignment methods and a named list of R options. The DataSHIELD packages can be filtered by specifying explicitly the package names to be included or excluded. The package exclusion prevails over the inclusion.

Usage

defaultDSConfiguration(include = NULL, exclude = NULL)

Arguments

Examples

## Not run: 
# detect DS packages
defaultDSConfiguration()
# exclude a DS package
defaultDSConfiguration(exclude="dsBase")
# include explicitely some DS packages
defaultDSConfiguration(include=c("dsBase", "dsOmics"))

## End(Not run)

Aggregate data

Description

Aggregate some data from the DataSHIELD R session using a valid R expression. The aggregation expression must satisfy the data repository's DataSHIELD configuration.

Usage

## S4 method for signature 'DSLiteConnection'
dsAggregate(conn, expr, async = TRUE)

Arguments

Assign the result of an expression

Description

Assign a result of the execution of an expression in the DataSHIELD R session.

Usage

## S4 method for signature 'DSLiteConnection'
dsAssignExpr(conn, symbol, expr, async = TRUE)

Arguments

Value

A DSLiteResult-class object.

Assign a resource

Description

Assign a DSLite resource in the DataSHIELD R session.

Usage

## S4 method for signature 'DSLiteConnection'
dsAssignResource(conn, symbol, resource, async = TRUE)

Arguments

Value

A DSLiteResult-class object.

Assign a table

Description

Assign a DSLite dataset in the DataSHIELD R session.

Usage

## S4 method for signature 'DSLiteConnection'
dsAssignTable(
  conn,
  symbol,
  table,
  variables = NULL,
  missings = FALSE,
  identifiers = NULL,
  id.name = NULL,
  async = TRUE
)

Arguments

Value

A DSLiteResult-class object.

Connect to a DSLite server

Description

Connect to a DSLite server, with provided datasets symbol names.

Usage

## S4 method for signature 'DSLiteDriver'
dsConnect(drv, name, url, restore = NULL, profile = NULL, ...)

Arguments

Value

A DSLiteConnection-class object.

Disconnect from a DSLite server

Description

Save the session in a local file if requested.

Usage

## S4 method for signature 'DSLiteConnection'
dsDisconnect(conn, save = NULL)

Arguments

Fetch the result

Description

Fetch the DataSHIELD operation result.

Usage

## S4 method for signature 'DSLiteResult'
dsFetch(res)

Arguments

Value

TRUE if table exists.

Get result info

Description

Get the information about a command (if still available).

Usage

## S4 method for signature 'DSLiteResult'
dsGetInfo(dsObj, ...)

Arguments

Value

The result information, including its status.

Verify DSLite server resource

Description

Verify resource exists and can be accessible for performing DataSHIELD operations.

Usage

## S4 method for signature 'DSLiteConnection'
dsHasResource(conn, resource)

Arguments

Value

TRUE if dataset exists.

Verify DSLite server dataset

Description

Verify dataset exists and can be accessible for performing DataSHIELD operations.

Usage

## S4 method for signature 'DSLiteConnection'
dsHasTable(conn, table)

Arguments

Value

TRUE if dataset exists.

DSLite asynchronous support

Description

No asynchronicity on any DataSHIELD operations.

Usage

## S4 method for signature 'DSLiteConnection'
dsIsAsync(conn)

Arguments

Value

The named list of logicals detailing the asynchronicity support.

Get whether the operation is completed

Description

Always TRUE because of synchronous operations.

Usage

## S4 method for signature 'DSLiteResult'
dsIsCompleted(res)

Arguments

Value

Always TRUE.

Keep connection with a DSLite server alive

Description

No operation due to the DSLiteServer nature.

Usage

## S4 method for signature 'DSLiteConnection'
dsKeepAlive(conn)

Arguments

List methods

Description

List methods defined in the DataSHIELD configuration.

Usage

## S4 method for signature 'DSLiteConnection'
dsListMethods(conn, type = "aggregate")

Arguments

Value

A data frame.

List packages

Description

List packages defined in the DataSHIELD configuration.

Usage

## S4 method for signature 'DSLiteConnection'
dsListPackages(conn)

Arguments

Value

A data frame.

List profiles

Description

List profiles defined in the DataSHIELD configuration.

Usage

## S4 method for signature 'DSLiteConnection'
dsListProfiles(conn)

Arguments

Value

A list containing the "available" character vector of profile names and the "current" profile (in case a default one was assigned).

List DSLite server resources

Description

List resource names living in the DSLite server for performing DataSHIELD operations.

Usage

## S4 method for signature 'DSLiteConnection'
dsListResources(conn)

Arguments

Value

The fully qualified names of the resources.

List R symbols

Description

List symbols living in the DataSHIELD R session.

Usage

## S4 method for signature 'DSLiteConnection'
dsListSymbols(conn)

Arguments

Value

A character vector.

List DSLite server datasets

Description

List dataset names living in the DSLite server for performing DataSHIELD operations.

Usage

## S4 method for signature 'DSLiteConnection'
dsListTables(conn)

Arguments

Value

The fully qualified names of the tables.

List workspaces

Description

List workspaces saved in the data repository.

Usage

## S4 method for signature 'DSLiteConnection'
dsListWorkspaces(conn)

Arguments

Value

A data frame.

Restore workspace

Description

Restore workspace from the data repository.

Usage

## S4 method for signature 'DSLiteConnection'
dsRestoreWorkspace(conn, name)

Arguments

Remove a R symbol

Description

Remoe a symbol living in the DataSHIELD R session.

Usage

## S4 method for signature 'DSLiteConnection'
dsRmSymbol(conn, symbol)

Arguments

Remove a workspace

Description

Remove a workspace on the data repository.

Usage

## S4 method for signature 'DSLiteConnection'
dsRmWorkspace(conn, name)

Arguments

Save workspace

Description

Save workspace on the data repository.

Usage

## S4 method for signature 'DSLiteConnection'
dsSaveWorkspace(conn, name)

Arguments

Get data value from DSLite connection(s)

Description

Get the data value corresponding to the variable with the symbol name from the DSLiteServer associated to the DSConnection-class object(s). Can be useful when developping a DataSHIELD package.

Usage

getDSLiteData(conns, symbol)

Arguments

Value

The data value or a list of values depending on the connections parameter. The value is NA when the connection object is not of class DSLiteConnection-class.

Examples

## Not run: 
# DataSHIELD login
logindata <- setupCNSIMTest()
conns <- datashield.login(logindata, assign=TRUE)
# retrieve symbol D value from each DataSHIELD connections
getDSLiteData(conns, "D")
# retrieve symbol D value from a specific DataSHIELD connection
getDSLiteData(conns$sim1, "D")

## End(Not run)

DataSHIELD login data for the CNSIM simulated datasets

Description

DataSHIELD login data.frame for connecting with CNSIM datasets. The CNSIM datasets contain synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of the obesity methodological development project. These datasets do contain some NA values.

Details

DataSHIELD login data for the DASIM simulated datasets

Description

DataSHIELD login data.frame for connecting with DASIM datasets. The DASIM datasets contain synthetic data based on a model derived from the participants of the 1958 Birth Cohort, as part of the obesity methodological development project. These datasets do not contain some NA values.

Details

DataSHIELD login data for the DISCORDANT simulated datasets

Description

DataSHIELD login data.frame for connecting with DISCORDANT datasets which purpose is to test datasets that are NOT harmonized.

Details

DataSHIELD login data for the simulated survival expand-with-missing datasets

Description

DataSHIELD login data.frame for connecting with SURVIVAL datasets which purpose is to perform survival tests. The datasets contain synthetic data based on a simulated survival model, including a censoring indicator.

Details

DataSHIELD login data for the TESTING.DATASET simulated datasets

Description

DataSHIELD login data.frame for connecting with TESTING.DATASET datasets which purpose is to evaluate each base data types.

Details

Create a new DSLite server

Description

Shortcut function to create a new DSLiteServer instance.

Usage

newDSLiteServer(
  tables = list(),
  resources = list(),
  config = DSLite::defaultDSConfiguration(),
  strict = TRUE,
  home = file.path(tempdir(), ".dslite")
)

Arguments

See Also

Other server-side items: DSLiteServer

Setup a test environment based on the CNSIM simulated datasets

Description

Load the CNSIM datasets, the corresponding login data object, instanciate a new DSLiteServer hosting these datasets and verify that the required DataSHIELD server-side packages are installed.

Usage

setupCNSIMTest(packages = c(), env = parent.frame())

Arguments

Value

The login data for the datashield.login function.

See Also

Other setup functions: setupDASIMTest(), setupDATASETTest(), setupDISCORDANTTest(), setupDSLiteServer(), setupSURVIVALTest()

Examples

## Not run: 
logindata <- setupCNSIMTest()
conns <- datashield.login(logindata, assign=TRUE)
# do DataSHIELD analysis
datashield.logout(conns)

## End(Not run)

Setup a test environment based on the DASIM simulated datasets

Description

Load the DASIM datasets, the corresponding login data object, instanciate a new DSLiteServer hosting these datasets and verify that the required DataSHIELD server-side packages are installed.

Usage

setupDASIMTest(packages = c(), env = parent.frame())

Arguments

Value

The login data for the datashield.login function.

See Also

Other setup functions: setupCNSIMTest(), setupDATASETTest(), setupDISCORDANTTest(), setupDSLiteServer(), setupSURVIVALTest()

Examples

## Not run: 
logindata <- setupDASIMTest()
conns <- datashield.login(logindata, assign=TRUE)
# do DataSHIELD analysis
datashield.logout(conns)

## End(Not run)

Setup a test environment based on the TESTING.DATASET simulated datasets

Description

Load the TESTING.DATASET datasets, the corresponding login data object, instanciate a new DSLiteServer hosting these datasets and verify that the required DataSHIELD server-side packages are installed.

Usage

setupDATASETTest(packages = c(), env = parent.frame())

Arguments

Value

The login data for the datashield.login function.

See Also

Other setup functions: setupCNSIMTest(), setupDASIMTest(), setupDISCORDANTTest(), setupDSLiteServer(), setupSURVIVALTest()

Examples

## Not run: 
logindata <- setupDATASETTest()
conns <- datashield.login(logindata, assign=TRUE)
# do DataSHIELD analysis
datashield.logout(conns)

## End(Not run)

Setup a test environment based on the DISCORDANT simulated datasets

Description

Load the DISCORDANT datasets, the corresponding login data object, instanciate a new DSLiteServer hosting these datasets and verify that the required DataSHIELD server-side packages are installed.

Usage

setupDISCORDANTTest(packages = c(), env = parent.frame())

Arguments

Value

The login data for the datashield.login function.

See Also

Other setup functions: setupCNSIMTest(), setupDASIMTest(), setupDATASETTest(), setupDSLiteServer(), setupSURVIVALTest()

Examples

## Not run: 
logindata <- setupDISCORDANTTest()
conns <- datashield.login(logindata, assign=TRUE)
# do DataSHIELD analysis
datashield.logout(conns)

## End(Not run)

Setup an environment based on named datasets and logindata

Description

Load the provided datasets and the corresponding logindata object, instanciate a new DSLiteServer hosting these datasets, verifies that the required DataSHIELD server-side packages are installed. All the data structures are loaded by data which supports various formats (see data() documentation).

Usage

setupDSLiteServer(
  packages = c(),
  datasets,
  logindata,
  pkgs = NULL,
  dslite.server = NULL,
  env = parent.frame()
)

Arguments

Value

The login data for the datashield.login function.

See Also

Other setup functions: setupCNSIMTest(), setupDASIMTest(), setupDATASETTest(), setupDISCORDANTTest(), setupSURVIVALTest()

Examples

## Not run: 
logindata <- setupDSLiteServer(
                 datasets = c("CNSIM1", "CNSIM2", "CNSIM3"),
                 logindata = "logindata.dslite.cnsim", pkgs = "DSLite",
                 dslite.server = "dslite.server")
conns <- datashield.login(logindata, assign=TRUE)
# do DataSHIELD analysis
datashield.logout(conns)

## End(Not run)

Setup a test environment based on the SURVIVAL (EXPAND_WITH_MISSING) simulated datasets

Description

Load the SURVIVAL (EXPAND_WITH_MISSING) datasets, the corresponding login data object, instanciate a new DSLiteServer hosting these datasets and verify that the required DataSHIELD server-side packages are installed.

Usage

setupSURVIVALTest(packages = c(), env = parent.frame())

Arguments

Value

The login data for the datashield.login function.

See Also

Other setup functions: setupCNSIMTest(), setupDASIMTest(), setupDATASETTest(), setupDISCORDANTTest(), setupDSLiteServer()

Examples

## Not run: 
logindata <- setupSURVIVALTest()
conns <- datashield.login(logindata, assign=TRUE)
# do DataSHIELD analysis
datashield.logout(conns)

## End(Not run)

Parse an expression according to DataSHIELD syntax rules and returns an Abstract Syntaxic Tree (AST) node.

Description

Parse an expression according to DataSHIELD syntax rules and returns an Abstract Syntaxic Tree (AST) node.

Usage

testParse(expr, debug = FALSE)

Arguments

Value

An Abstract Syntaxic Tree node

Examples

## Not run: 
# a function call with a valid formula
ast <- testParse("someregression(D$height ~ D$diameter + D$length)")
# a function call with an invalid formula including a function call
testParse("someregression(D$height ~ D$diameter + poly(D$length,3,raw=TRUE))")

## End(Not run)