AppLoadFlex             Loads a single R object from file for a R Shiny
                        app
Digest                  Digest files from (digest package)
Graph                   Write object and capture file information
Library                 Installs and loads library specific to a
                        project
Load.branch             Loads a single R object from file
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
ReadTrack               Tracks files that read by functions not in
                        adapr and captures the file information within
                        dependency object
Write                   Write object and capture file information
Write.cap               Lower level function that writes data and
                        captures the file information within dependency
                        object
WriteTrack              Tracks files written by functions not in adapr
                        and captures the file information within
                        dependency object
adapr-package           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
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
browsePubFiles          Browses publication table for editing
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
dataDir                 Returns project's data directory, allows
                        relative directories. Used within an R script.
defaultAdaprSetup       Set up adapr 1st time
dependency-class        Dependency class
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
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
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
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
initProject             initialize project
initialize_dependency_info
                        Initializes dependency object source_info
install                 Install package of specific version
installLibrary          Install package of specific version
installProjectPackages
                        Installs all packages
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
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
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
openProjectList         Browses orchard in file system
openScript              Opens script from a project with default R
                        program. Can open markdown files as well.
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
rapidPlot               Make project graph with sync status already
                        computed.
read.dependency         Lower level function that reads the script
                        dependcy data from file
readDependency          Collect trees from dependency directory
readLibrary             Read library file
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
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.
updateAdaprConfig       Updates the project list file to include
                        project specific libraries.
write.dependency        Lower level function that writes the dependency
                        object to file
