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adapr (version 2.0.0)

Implementation of an Accountable Data Analysis Process

Description

Tracks reading and writing within R scripts that are organized into a directed acyclic graph. Contains an interactive shiny application adaprApp(). Uses git2r package, Git and file hashes to track version histories of input and output. See package vignette for how to get started. V1.02 adds parallel execution of project scripts and function map in vignette. Makes project specification argument last in order. V2.0 adds project specific libraries, packrat option, and adaprSheet().

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Version

Install

install.packages('adapr')

Monthly Downloads

14

Version

2.0.0

License

LGPL-2

Maintainer

Jonathan Gelfond

Last Published

November 30th, 2017

Functions in adapr (2.0.0)

Lower level function that writes data and captures the file information within dependency object

Write object and capture file information

Read data and capture the file information within dependency object

Loads a single R object from file for a R Shiny app

Tracks files that read by functions not in adapr and captures the file information within dependency object

Digest files from (digest package)

Write object and capture file information

Installs and loads library specific to a project

Lower level function that reads data and capture the file information within dependency object

Add R package to a project

Loads R object from archivist repository within the results directory of another adapr Script

Loads a single R object from file

checkAdaprHashAlgo

Checks or changes the specified adapr hash algorithm (adaprHashAlgo option)

Browse adapr cheat sheet

Checks the consistency of the dependency directory with the files within the file system

dependency-class

Dependency class

Updates latest adapr from gitHub.

Create first project

Saves R object to archivist repository in results directory of adapr Script

getAdaprOptions

Returns the primary hub file with project location and id information

Browses publication table for editing

Tracks files written by functions not in adapr and captures the file information within dependency object

Launches Main app

git2r commit class to character converter

adaprDependencies

Returns character string of adapr R package import dependencies

Git commit of project.

fileInfoProjects

List project file information disk space, modification timespan, days inactive

Checks whether interactive R markdown session is ON

finalize_dependency

Writes dependency data to file in "Dependency" directory

Check install of package of specific version

Returns the adapr project in R option "adaprProject"

defaultAdaprSetup

Set up adapr 1st time

getProjectSwapPath

Retrieve project swap directory

Identify adapr Home directory. Location of options file and project listing.

condenseFileInfo

Generate condensed information about files from dependency object

Install adapr in a library adaprInstall.R

Creates a list containing information about a file

checkFileHashSource

Checks the consistency of the dependency directory with the files within the file system. Reports the source scripts that need to be updated.

create_source_file_dir

Create source file directories

Produces subgraph of dependencies of R script

Returns project's data directory, allows relative directories. Used within an R script.

Retrieve the file info for the file by name OR from the data subdirectory data

getProjectInfoSI

Given source_info object, retrieves project information

Acquire all dependencies related to a project, Generate graph of project dependencies, Get all file information related to project

git commit. Requires git installation.

Configure user.name and email for git.

checkFileMtimeSource

Checks the consistency of the dependency directory with the files within the file system Reports the source scripts that need to be updated!

Identify git provenance of file within a project

Creates an Rmarkdown file in specified directory

Import selected file into the project data directory

createProgramGraph

Make plot of project programs only Summarize all programs. Sync status is assessed and indicated.

Read result filepaths to publish

gitIgnoreLibrary

Git ignore the library file

Retrun time of file system

Retrieves the information from git about a file

Get library for a project

initialize_dependency_info

Initializes dependency object source_info

Install package of specific version

Given Project id, Return project directory

loadInstallLibraryFile

This function is no longer supported. Loads libraries within the file library.list.file

getProjectPublishPath

Given Project name, Return project publish directory

makeDependencyGraphObj

Creates an graph object from a dependency object

Returns the primary hub file with project location and id information

Find path for git executable

git add to stage the file

Make plot of project programs only Summarize all programs. Sync status is assessed and indicated.

Return function for reading common file types

getProjectLibrary

Given Project name, Return project library directory

Return function for writing common file types

initialize project

Returns the information related to the adapr script

Create adaprTest example project

Identifies dependencies in a DAG

Loads a single R object from file, more flexible than Load.branch or base::load

Install package of specific version

gitConfigureTest

Checks git configuration. Requires git installation

installProjectPackages

Installs all packages

gitHistorySearch

Performes git history search

Generates the shell of a code that is project specific

Lists the branches available for loading in the adapr project

makeSummaryGraph

Make.summary graph of projects based on files in dependency directory

monitorParallelSync

Experimental (use with caution) track parallelSync while in progress

Lists the data files available for reading in the adapr project

openProjectList

Browses orchard in file system

Generates the shell of a R function that is project specific in support_functions folder

Read library file

Lower level function that captures packages that are explicitly loaded, not loaded automatically

Returns the source files needed to repair synchrony

Makes HTML hyper link

Opens script from a project with default R program. Can open markdown files as well.

Experimental (use with caution) parallel syncrhonization of project. Takes advantage of directed acyclic graph structure to run R script processes in parallel.

Lists the R scripts in the adapr project

projectReportSend

Make plot of network within html documents. Summarize all programs. Make a readme file at top project directory copy to target.directory Uses pander and pandoc unlike project_report

initialize project

Create program io table

relocateProject

changes project directory/publish directory/library locataion or identifies imported project

Initializes dependency object source_info

Remove R package to a project

project.directory.tree

Project directory tree structure contains the relative directory structure included analysis, data, texidr, dependency.dir, support functions, and library bank locations

Produces script only subgraph

projectReportMarkdown

Make plot of network within html documents. Summarize all programs.

Create source_info from project.id

sourceSyncSILoad

Synchronize project by IDENTIFYING necessary R scripts

updateAdaprConfig

Updates the project list file to include project specific libraries.

Lower level function that generates the shell of a code that is project specific

Location of options file and project listing. Swap / for \ in path expand.

Create project hub files in root directory

Partial project synchronization of dependencies to an Rscript. Runs only scripts needed for synchronization.

read.dependency

Lower level function that reads the script dependcy data from file

Read in results to publish & Copies results to the project's publication directory

Collect trees from dependency directory

Renders and Rmarkdown file

Run an R script within a project using devtools::clean_source

Make plot of network within html documents. Summarize all programs.

runSourceDirectory

Runs all source files within the directory source.directory

Searches R scripts and R markdown files within a project.

Copy dependent programs to swap directory

Opens results directory of project or R script within a project

write.dependency

Lower level function that writes the dependency object to file

Lower level function that synchronizes project by running necessary R scripts. Loads from source_info list.

Lower level function that that changes project directory/publish directory or identifies imported project

Returns project's results directory, allows relative directories. Only used within an R script, after create_source_file_dir.

syncTestProject

Tests the synchrony of files in dependency tree

reworkProjectPath

Lower level function that collects all trees in dependency.dir and changes the project path

Tests the synchrony of files in dependency tree

setAdaprOptions

Returns Modifies the primary adapr option file

swapProjectPath

Lower level function that takes list of dependency file data and changes the project path

Make project graph with sync status already computed.

Checks the synchronization project and runs scripts needed for synchronization

Removes project from orchard, but doesn't delete project from file system

Lower level function that tests the synchrony of files in dependency tree given project information.

Remove an R script from a project. Removes program, dependency, and results.

Copy dependent programs to swap directory

Checks or changes the specified adapr project in R option "adaprProject"

Opens project directory

Lower level function that checks the synchrony of source files and their created objects