Check.file.hash         Checks the consistency of the dependency
                        directory with the files within the file system
Check.file.hash.source
                        Checks the consistency of the dependency
                        directory with the files within the file system
                        Reports the source scripts that need to be
                        updated!
Check.file.mtime.source
                        Checks the consistency of the dependency
                        directory with the files within the file system
                        Reports the source scripts that need to be
                        updated!
Condense.file.info      Generate condensed information about files from
                        dependency object
Create.file.info        Creates a list containing information about a
                        file
Digest                  Digest files from (digest package)
Get.file.info           Retrieve the file info for the file by name OR
                        from the data subdirectory data
Graph                   Write object and capture file information
Harvest.trees           Collect trees from dependency directory
ID.sync                 Returns the source files needed to repair
                        synchrony
Load.branch             Loads a single R object from file
Make.dependency.graph.obj
                        Creates an graph object from a dependency
                        object
Make.summary.graph      Make.summary graph of projects based on files
                        in dependency directory
Read                    Read data and capture the file information
                        within dependency object
Read.cap                Read 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
Render_Rmd              Renders and Rmarkdown file
Sync.test               check the synchrony of source files and their
                        created objects
Sync.test.OLD           check the synchrony of source files and their
                        created objects
Sync.test.pi            Tests the synchrony of files in dependency tree
Sync.test_2nd           check the synchrony of source files and their
                        created objects
Write                   Write object and capture file information
Write.cap               Write data and capture 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
add_package             Add R package to a project
checkAdaprHashAlgo      Checks or changes the specified adapr hash
                        algorithm (adaprHashAlgo option)
checkRmdMode            Checks whether interactive R markdown session
                        is ON
commit.project          Git commit of project.
commit2char             git2r commit class to character converter
create_markdown         Renders and Rmarkdown file
create_program_graph    Make plot of project programs only Summarize
                        all programs. Sync status is assessed and
                        indicated.
create_program_graph_v2
                        Make plot of project programs only Summarize
                        all programs.
create_source_file_dir
                        Create source file directories
default.adapr.setup     Set up adapr 1st time
dependency-class        Dependency class
finalize_dependency     Writes dependency data to file in "Dependency"
                        directory
first.project           Create first project
get.fs.time             Retrun time of file system
get.project             Returns the adapr project in R option
                        "adaprProject"
get.project.info        Acquire all dependencies related to a project,
                        Generate graph of project dependencies, Get all
                        file information related to project
get.project.info.si     Given source_info object, retrieves project
                        information
get.project.path        Given Project name, Return project directory
get.project.publish.path
                        Given Project name, Return project publish
                        directory
get.project.swap.directory
                        Retrieve project swap directory
get.pubresults          Read result filepaths to publish
get_adapr_options       Returns the primary hub file with project
                        location and id information
get_orchard             Returns the primary hub file with project
                        location and id information
git.add                 git add to stage the file
git.commit              git commit. Requires git installation.
git.configure           Configure user.name and email for git. Requires
                        git installation.
git.configure.test      Checks git configuration. Requires git
                        installation
git.history.search      Performes git history search
git.info                Retrieves the information from git about a file
git.init                Initiate git
git_path                Find path for git executable
git_provenance          Identify git provenance of file within a
                        project
graph.project           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
guess.write.fcn         Return function for writing common file types
hashcopy                Given Project name, Return project publish
                        directory
id_new_libs             Captures libraries that are not loaded
                        automatically
init.project            initialize project
initialize_dependency_info
                        Initializes dependency object source_info
install_project_packages
                        Installs all packages
list.branches           Lists the branches available for loading in the
                        adapr project
list.datafiles          Lists the data files available for reading in
                        the adapr project
list.programs           Lists the R scripts in the adapr project
listBranches            Lists the branches available for loading in the
                        adapr project
listDatafiles           Lists the data files available for reading in
                        the adapr project
listScripts             Lists the R scripts in the adapr project
load.install.library.file
                        Loads librarys within the file
                        library.list.file
load.source.directory   Runs all source files within the directory
                        source.directory
make.hyperlink          Makes HTML hyper link
make.program            Generates the shell of a code that is project
                        specific
monitorParallelSync.project
                        Track parallelSync.project while in progress
open_orchard            Browses orchard in file system
parallelSync.project    Uses DOSNOW package for parallel
                        syncrhonization of project. Takes advantage of
                        directed acyclic graph structure to run R
                        script processes in parallel.
path.expand.2           Swap / for \ in path expand
plant.orchard           Create project hub files in root directory
plant.tree              initialize project
program.io.table        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
project_report_markdown
                        Make plot of network within html documents.
                        Summarize all programs.
project_report_send_rmd
                        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
pull_source_info        Create source_info from project.id
read.dependency         Read the dependcy data from file
read_library            Read library file
redirect.tree           Changes project directory/publish directory or
                        identifies imported project
relocate.project        Changes project directory/publish directory or
                        identifies imported project
remove.program          Remove an R script from a project. Removes
                        program, dependency, and results.
remove.project          Removes project from orchard, but doesn't
                        delete project from file system
remove_package          Remove R package to a project
report.project          Make plot of network within html documents.
                        Summarize all programs.
rework.project.path     Collects all trees in dependency.dir and
                        changes the project path
run.program             Run an R script within a project using
                        devtools::clean_source
scriptLoader            Initializes dependency object source_info
send.branch             Copy dependent programs to swap directory
send.branch.si          Copy dependent programs to swap directory
send.pubresults         Read in results to publish & Copies results to
                        the project's publication directory
set.project             Checks or changes the specified adapr project
                        in R option "adaprProject"
set_adapr_options       Returns Modifies the primary adapr option file
show.project            Opens project directory
show.pubresults         Browses publication table for editing
show.results            Opens results directory of project or R script
                        within a project
showProject             Opens project directory
showResults             Opens results directory
source.sync.si          Synchronize project by running necessary R
                        scripts
source_sync_si_load     Synchronize project by IDENTIFYING necessary R
                        scripts
sprout.program          Generates the shell of a code that is project
                        specific
swap.project.paths      Take list of dependency file data and changes
                        the project path
sync.project            Checks the synchronization project and runs
                        scripts needed for synchronization
sync.test.si            Tests the synchrony of files in dependency tree
synctest.project        Tests the synchrony of files in dependency tree
write.dependency        Write the dependcy object to file
