Package 'RDO'

Title: Reproducible Data Objects
Description: A Reproducible Data Object (RDO) encapsulates both data and R code needed to reproduce those data. Each RDO can have other RDOs as dependencies. RDOs can be composed into complex tree hierarchies. Interacting with an RDO tree is similar to interacting with a single RDO. You can (re)run the code and refresh the cache, check status, validate if the code still gives the same cached data, clear data cache, access code and data cache of any of the dependencies. RDOs can be cloned and code of cloned dependencies can be modified.
Authors: Kamil Wais [aut, cre]
Maintainer: Kamil Wais <[email protected]>
License: MIT + file LICENSE
Version: 0.1.0
Built: 2024-12-12 04:11:22 UTC
Source: https://github.com/openpharma/RDO

Help Index

RDO (Reproducible Data Object)

Description

Create and interact with Reproducible Data Objects.

Methods

Public methods

Method print()

Default print method of current RDO status

Usage
RDO$print(...)
Arguments
...

Other params for print function.

Method new()

Creating a new RDO object,

Usage
RDO$new(name, dependencies = list())
Arguments
name

Unique name of the object.

dependencies

An RDO object or a list of RDO objects.

Returns

A new 'RDO' object.

Method get_status()

Getting current status.

Usage
RDO$get_status()
Returns

A list.

Method get_name()

Getting object name.

Usage
RDO$get_name()
Returns

A character with object name.

Method has_dependencies()

Checking if object has dependencies.

Usage
RDO$has_dependencies()
Returns

TRUE if has or FALSE if not.

Method add_dependencies()

Adding new or update existing RDO dependencies.

Usage
RDO$add_dependencies(dependencies = list())
Arguments
dependencies

An RDO object or a list of RDO objects.

Returns

The RDO object (self) returned invisibly.

Method get_dependencies()

Getting dependencies of the object.

Usage
RDO$get_dependencies(deep = FALSE)
Arguments
deep

A logical. Should the function return only direct dependencies (FALSE) or also deep indirect dependencies (dependencies of dependencies). Default is FALSE.

Returns

A named list of RDO dependencies with unique names.

Method get_dependency_register()

Getting dependency register showing which RDO is a direct parent for other RDO dependencies.

Usage
RDO$get_dependency_register()
Returns

A data.frame.

Method plot_dependencies()

Plotting the tree of RDO dependencies. Needs visNetwork package for plotting.

Usage
RDO$plot_dependencies()

Method get_code()

Getting reproducible R code.

Usage
RDO$get_code(deep = FALSE)
Arguments
deep

A logical. Should the function return only code for this particular RDO (FALSE) or also from all dependencies. Default is FALSE.

Returns

An R named expression.

Method print_code()

Printing reproducible R code.

Usage
RDO$print_code(deep = FALSE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function return only code for this particular RDO (FALSE) or also from all dependencies. Default is FALSE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

A character. Reproducible R code returned invisibly.

Method run()

Running reproducible R code.

Usage
RDO$run(deep = FALSE, cache = TRUE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function run only code for this particular RDO (FALSE) or should it run also dependencies' code if they are not validated. The function is lazy and it checks if all deep dependencies are validated first. If so, there is no need to rerun their code again. Default is FALSE.

cache

A logical. Should the result of code evaluation be cached inside an RDO object. Default is TRUE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

The RDO object (self) returned invisibly.

Method is_validated()

Checking if RDO is validated. A RDO is validated when the result of running reproducible R code saved inside the RDO is the same as data cached inside the RDO.

Usage
RDO$is_validated(deep = FALSE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function validate only this particular RDO (FALSE) or should it validate also all deep dependencies (TRUE). Default is FALSE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

A logical. TRUE if RDO is validated, FALSE if not.

Method invalidate()

Invalidating the RDO explicitly by setting the 'is_validated' status to 'FALSE'.

Usage
RDO$invalidate(deep = FALSE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function invalidate only this particular RDO (FALSE) or should it invalidate also all deep dependencies (TRUE). Default is FALSE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

The RDO object (self) returned invisibly.

Method validate()

Validating the RDO explicitly by running deep reproducible R code and checking if the result is the same as cached data inside the RDO.

Usage
RDO$validate(deep = FALSE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function validate only this particular RDO (FALSE) or should it validate also all deep dependencies (TRUE). Default is FALSE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

The RDO object (self) returned invisibly.

Method lock()

Locking the RDO object. When RDO object is locked you cannot change the R code and data cache saved inside the object.

Usage
RDO$lock(deep = FALSE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function lock only this particular RDO (FALSE) or should it lock also all deep dependencies (TRUE). Default is FALSE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

The RDO object (self) returned invisibly.

Method unlock()

Unlocking previously locked RDO object.

Usage
RDO$unlock(deep = FALSE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function unlock only this particular RDO (FALSE) or should it unlock also all deep dependencies (TRUE). Default is FALSE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

The RDO object (self) returned invisibly.

Method is_locked()

Checking if an RDO object is locked.

Usage
RDO$is_locked(deep = FALSE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function check only this particular RDO (FALSE) or should it check also all deep dependencies (TRUE). Default is FALSE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

A logical. TRUE if RDO is locked, FALSE if not.

Method prune_cache()

Pruning (clearing) RDO data cache by setting cache to NULL. It can save memory when we no longer need to keep cache in dependencies.

Usage
RDO$prune_cache(deep = FALSE, verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
deep

A logical. Should the function prune cache of only this particular RDO (FALSE) or should it prune cache also of deep dependencies (TRUE). If an RDO is locked the cache in this particular RDO is not pruned. Default is FALSE.

verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

The RDO object (self) returned invisibly.

Method prune_dependencies()

Pruning RDO dependencies by ensuring that RDO objects in deep dependencies with the same name point to the same RDO objects. This type of pruning may be useful after deep clonning of complex RDO tree with duplicated dependencies.

Usage
RDO$prune_dependencies(verbose = Sys.getenv("RDO_VERBOSE"))
Arguments
verbose

A logical. Should the messages be sent to console. If the param is not set, it is read from an environmental variable RDO_VERBOSE. If the variable is not set, than the default is TRUE.

Returns

The RDO object (self) returned invisibly.

Method clone()

The objects of this class are cloneable with this method.

Usage
RDO$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.