# Implementation of an Accountable Data Analysis Process

## Documentation for package ‘adapr’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D F G I L M O P R S U W misc

adapr-package | Implementation of an Accountable Data Analysis Process

## -- A --

adapr | Implementation of an Accountable Data Analysis Process
adaprApp | Launches Main app
adaprDependencies | Returns character string of adapr R package import dependencies
adaprHomeDir | Identify adapr Home directory. Location of options file and project listing.
adaprInstall | Install adapr in a library adaprInstall.R
adaprSheet | Browse adapr cheat sheet
adaprUpdate | Updates latest adapr from gitHub.
addPackage | Add R package to a project
AppLoadFlex | Loads a single R object from file for a R Shiny app
arcRead | Loads R object from archivist repository within the results directory of another adapr Script
arcWrite | Saves R object to archivist repository in results directory of adapr Script

## -- B --

browsePubFiles | Browses publication table for editing

## -- C --

checkAdaprHashAlgo | Checks or changes the specified adapr hash algorithm (adaprHashAlgo option)
checkFileHash | Checks the consistency of the dependency directory with the files within the file system
checkFileHashSource | Checks the consistency of the dependency directory with the files within the file system. Reports the source scripts that need to be updated.
checkFileMtimeSource | Checks the consistency of the dependency directory with the files within the file system Reports the source scripts that need to be updated!
checkRmdMode | Checks whether interactive R markdown session is ON
checkVersion | Check install of package of specific version
commit2char | git2r commit class to character converter
commitProject | Git commit of project.
condenseFileInfo | Generate condensed information about files from dependency object
createFileInfo | Creates a list containing information about a file
createMarkdown | Creates an Rmarkdown file in specified directory
createProgramGraph | Make plot of project programs only Summarize all programs. Sync status is assessed and indicated.
create_source_file_dir | Create source file directories

## -- D --

dataDir | Returns project's data directory, allows relative directories. Used within an R script.
defaultAdaprSetup | Set up adapr 1st time
dependency | Dependency class
dependency-class | Dependency class
Digest | Digest files from (digest package)

## -- F --

fileInfoProjects | List project file information disk space, modification timespan, days inactive
finalize_dependency | Writes dependency data to file in "Dependency" directory
firstProject | Create first project

## -- G --

getAdaprOptions | Returns the primary hub file with project location and id information
getDepSubgraph | Produces subgraph of dependencies of R script
getFileInfo | Retrieve the file info for the file by name OR from the data subdirectory data
getFileSysTime | Retrun time of file system
getLibrary | Get library for a project
getProject | Returns the adapr project in R option "adaprProject"
getProjectInfo | Acquire all dependencies related to a project, Generate graph of project dependencies, Get all file information related to project
getProjectInfoSI | Given source_info object, retrieves project information
getProjectLibrary | Given Project name, Return project library directory
getProjectPath | Given Project id, Return project directory
getProjectPublishPath | Given Project name, Return project publish directory
getProjectSwapPath | Retrieve project swap directory
getPubResults | Read result filepaths to publish
getSourceInfo | Returns the information related to the adapr script
getUpstream | Identifies dependencies in a DAG
get_orchard | Returns the primary hub file with project location and id information
gitAdd | git add to stage the file
gitCommit | git commit. Requires git installation.
gitConfigure | Configure user.name and email for git.
gitConfigureTest | Checks git configuration. Requires git installation
gitHistorySearch | Performes git history search
gitIgnoreLibrary | Git ignore the library file
gitInfo | Retrieves the information from git about a file
gitInit | Initiate git
gitProvenance | Identify git provenance of file within a project
git_path | Find path for git executable
Graph | Write object and capture file information
graphProject | Make plot of project programs only Summarize all programs. Sync status is assessed and indicated.
guess.read.fcn | Return function for reading common file types
guessWriteFcn | Return function for writing common file types

## -- I --

idPackages | Lower level function that captures packages that are explicitly loaded, not loaded automatically
idSync | Returns the source files needed to repair synchrony
importData | Import selected file into the project data directory
initialize_dependency_info | Initializes dependency object source_info
initProject | initialize project
install | Install package of specific version
installLibrary | Install package of specific version
installProjectPackages | Installs all packages

## -- L --

Library | Installs and loads library specific to a project
listBranches | Lists the branches available for loading in the adapr project
listDatafiles | Lists the data files available for reading in the adapr project
listProjects | List projects
listScripts | Lists the R scripts in the adapr project
Load.branch | Loads a single R object from file
loadAdaprTest | Create adaprTest example project
loadFlex | Loads a single R object from file, more flexible than Load.branch or base::load
loadInstallLibraryFile | This function is no longer supported. Loads libraries within the file library.list.file

## -- M --

makeDependencyGraphObj | Creates an graph object from a dependency object
makeFunction | Generates the shell of a R function that is project specific in support_functions folder
makeHyperlink | Makes HTML hyper link
makeScript | Generates the shell of a code that is project specific
makeSummaryGraph | Make.summary graph of projects based on files in dependency directory
monitorParallelSync | Experimental (use with caution) track parallelSync while in progress

## -- O --

openProjectList | Browses orchard in file system
openScript | Opens script from a project with default R program. Can open markdown files as well.

## -- P --

parallelSync | Experimental (use with caution) parallel syncrhonization of project. Takes advantage of directed acyclic graph structure to run R script processes in parallel.
path.expand.2 | Location of options file and project listing. Swap / for \ in path expand.
plantOrchard | Create project hub files in root directory
plantTree | initialize project
programIOTable | Create program io table
project.directory.tree | Project directory tree structure contains the relative directory structure included analysis, data, texidr, dependency.dir, support functions, and library bank locations
projectReportMarkdown | Make plot of network within html documents. Summarize all programs.
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
publishResults | Read in results to publish & Copies results to the project's publication directory
pullSourceInfo | Create source_info from project.id

## -- R --

rapidPlot | Make project graph with sync status already computed.
Read | Read data and capture the file information within dependency object
Read.cap | Lower level function that reads data and capture the file information within dependency object
read.dependency | Lower level function that reads the script dependcy data from file
readDependency | Collect trees from dependency directory
readLibrary | Read library file
ReadTrack | Tracks files that read by functions not in adapr and captures the file information within dependency object
redirectTree | Lower level function that that changes project directory/publish directory or identifies imported project
relocateProject | changes project directory/publish directory/library locataion or identifies imported project
removePackage | Remove R package to a project
removeProject | Removes project from orchard, but doesn't delete project from file system
removeScript | Remove an R script from a project. Removes program, dependency, and results.
renderRmd | Renders and Rmarkdown file
reportProject | Make plot of network within html documents. Summarize all programs.
resultsDir | Returns project's results directory, allows relative directories. Only used within an R script, after create_source_file_dir.
reworkProjectPath | Lower level function that collects all trees in dependency.dir and changes the project path
runScript | Run an R script within a project using devtools::clean_source
runSourceDirectory | Runs all source files within the directory source.directory

## -- S --

scriptLoader | Initializes dependency object source_info
scriptSubgraph | Produces script only subgraph
searchScripts | Searches R scripts and R markdown files within a project.
sendBranch | Copy dependent programs to swap directory
sendBranchSI | Copy dependent programs to swap directory
setAdaprOptions | Returns Modifies the primary adapr option file
setProject | Checks or changes the specified adapr project in R option "adaprProject"
showProject | Opens project directory
showResults | Opens results directory of project or R script within a project
sourceSyncSI | Lower level function that synchronizes project by running necessary R scripts. Loads from source_info list.
sourceSyncSILoad | Synchronize project by IDENTIFYING necessary R scripts
sproutProgram | Lower level function that generates the shell of a code that is project specific
swapProjectPath | Lower level function that takes list of dependency file data and changes the project path
syncProject | Checks the synchronization project and runs scripts needed for synchronization
syncTest | Lower level function that checks the synchrony of source files and their created objects
syncTestPI | Lower level function that tests the synchrony of files in dependency tree given project information.
syncTestProject | Tests the synchrony of files in dependency tree
syncTestSI | Tests the synchrony of files in dependency tree
syncTrunk | Partial project synchronization of dependencies to an Rscript. Runs only scripts needed for synchronization.

## -- U --

updateAdaprConfig | Updates the project list file to include project specific libraries.

## -- W --

Write | Write object and capture file information
Write.cap | Lower level function that writes data and captures the file information within dependency object
write.dependency | Lower level function that writes the dependency object to file
WriteTrack | Tracks files written by functions not in adapr and captures the file information within dependency object

## -- misc --

{run.program} | Run an R script within a project using devtools::clean_source